Publications

2021

1.  Koga, N.; Koga, R.; Liu, G.; Castellanos, J.; Montelione, GT.; Baker, D.; Nature Communication. 2021. Role of backbone strain in de novo design of complex alpha/beta protein structures. (in review).

2. Li, Y.; Zhang, R.; Forouhar, F.; Wang, C.; Montelione, GT.; Szperski, T.; Xu, Y.; Hunt, JF. Proc Natl Acad Sci USA. 2021. Conserved oligomeric interactions maintain active-site structure in a non-cooperative enzyme superfamily. (in review).

2020

1.  Bafna., K.; White K.; Harish, B; Acton, T.; Rosales, T.R.; Kehrer, T.; Miorin, L.; Moreno, E.; Ramelot, T.A.; Royer, C.; García-Sastre, A.; Krug, R.M.; Montelione, G.T. bioRxiv 2020. Hepatitis C virus drugs simeprevir and grazoprevir synergize with remdesivir to suppress SARS-CoV-2 replication.

Image comparing HCV protease and SARS CoC2 Mpro protease structures
Comparison of the structures of (A) SARS CoV2 Mpro and (B) HCV protease structures

2. Maisuradze, GG.; Montelione, GT.; Rackovsky, S.; Skolnick, J. J Phys. Chem. B. 2020. Tribute to Howard A. Scheraga

3. Bafna, K.; Krug, RM.; Montelione, GT. ChemRxiv. 2020. Structural similarity of SARS-CoV2 Mpro and HCV NS3/4A proteases suggests new approaches for identifying existing drugs useful as COVID-19 therapeutics. PMC7263768

Fold topology diagrams demonstrate similar fold architectures but different topologies

4. Wang, X.; Jing, X.; Deng, Y.; Nie, Y.; Xu, F.; Xu, Y.; Zhao, YL.; Montelione, GT.; Hunt, J.F. FEBS Letters. 2020, 594 (5): 799-812. Evolutionary coupling saturation mutagenesis: coevolution‐guided identification of distant sites influencing Bacillus naganoensis pullulanase activity. PMC7263768

The spatial location in the homology model of BnPUL of the
three residue pairs (K631/Q597, V328/I565, D541/D473) identified as mutational hotspots based on EC analysis resulting in mutant enzymes with improved catalytic activity.

5. Chen, G.; Ma, L.C.; Wang, S.; Woltz, R.L.; Grasso, E.M.; Montelione, G.T.; Krug, R.M. Nucleic Acids Research. 2020, 48 (1): 304-315. A double-stranded RNA platform is required for the interaction between a host restriction factor and the NS1 protein of influenza A virus. PMC6943125

Structure of the RBD showing the amino acid residues
(R37/R37, R38/R38, K41/K41, K70/K70) that were replaced with alanines

6. Aiyer, S.; Swapna, G.V.T.; Liu, G.; Ma, L.C.; Hao, J.; Chalmers, G.; Jacobs, B.; Montelione, G.T; Roth, M. bioRxiv. 2020. Structure (Cell Press) 2021 (in press) . A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

Conformational plasticity in molecular recognition of BRD3 ET

7. Cole, C.A.; Daigham, N.S.; Liu, G.; Montelione, G.T.; Valafar, H. bioRxiv. 2020. PLOS Computational Biology 2021 (in press). REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins without NOEs

2019

1. Rosario-Cruz, Z.; Eletsky, A.; Daigham, N.; Al-Tameemi, H.; Swapna, G.V.T.; Kahn, P.C.; Szyperski, T.; Montelione, G.T.; Boyd, J.M. J Biol Chem. 2019, 294: 4027 – 4044. The copBL operon protects Staphylococcus aureus from copper toxicity: CopL is an extracellular membrane-associated copper-binding protein. suppl. material.

Space-filling representation of the same conformer showing the degree of residue conservation calculated with ConSurf. Conservation scores are arranged into nine groups with the corresponding colors ranging from cyan (most variable) to burgundy (most conserved). The numbering shown here is that
of the UniProt entry BSU05790

2. Ranaivoson, F.M.; Turk, L.S.; Ozgul, S.; Kakehi, S.; von Daake, S.; Lopez, N.; Trobiani, L.; De Jaco, A.; Denissova, N.; Demeler, B.; Ozkan, E.; Montelione, G.T.; Comoletti, D. Structure (Cell Press) 2019, 27: 893 – 906. A proteomic screen of neuronal cell surface molecules reveals IgLONs as structurally conserved interaction modules at the synapse. 

(A) Overall superimposition of all the IgLON dimeric crystal structures in cartoon representation.(B) Ca traces of superimposed Ig1-Ig1 dimeric assemblies as observed in the
different crystals. (C) Superimposition of Ig1 domains of all the monomers, illustrating an overall flexibility of the IgLONs, to highlight their structural and architectural
similarities.

3. Koepnick, B.; Flatten, J.; Husain, T.; Ford, A.; Silva, D.-A.; Bick, M.J.; Bauer, A.; Liu, G.; Ishida, Y.; Boykov, A.; Estep, R.D.; Kleinfelter, S.; Wei, L.; Foldit Players, Montelione, G.T.; Popovic, Z.; Khatib, F.; Cooper, S.; Baker, D. Nature 2019, 570: 390 – 394. De novo protein design by citizen scientists. 

The Foldit1 design (fold V in Fig. 3: three β-strands with sheet order
1–2–3) model backbone (rainbow) aligns to the crystal structure (grey) with Cα r.m.s.d. of 1.1 Å

4. Grime, G.W.; Zeldin, O.B.; Snell, M.E.; Lowe, E.D.; Montelione, G.T. J Amer Chem Soc 2019, 142 (1): 185-197. High-throughput PIXE as an essential quantitative assay for accurate metalloprotein structural analysis: development and application

Metalloproteins

5. Berman, H.M.; Adams, P.D.; Bonvin, A.A.; Burley, S.K.; Carragher, B.; Chiu, W. et al. Structure (Cell Press). 2019, 27 (12): 1745-1759. Federating structural models and data: outcomes from a workshop on archiving integrative structures. PMC7108332

Illustration of Federating Structural Models and Experimental Data

6. Sala, D.; Huang, Y.J.; Cole, C.A.; Snyder, D.A.; Liu, G.; Ishida, Y.; Swapna, G.V.T.; Brock, K.P.; Sander, C.; Fidelis, K.; Kryshtafovych, A.; Inouye, M.; Tejero, R.; Valafar, H.; Rosato, A.; Montelione, G.T. Proteins; Structure, Function, and Bioinformatics. 2019, 87 (12): 1315-1332. Protein structure prediction assisted with sparse NMR data in CASP13. suppl. material. PMC7213643

Best Regular Venclovas GDT_TS

7. Zhang, M.; Yu, X.W.; Xu, Y.; Guo, R.T.; Swapna, G.V.T.; Szyperski, T.; Hunt, J.F.; Montelione, G.T. Biochemistry. 2019, 58 (38): 3943-3954. Structural basis by which the N-terminal polypeptide segment of Rhizopus chinensis lipase regulates its substrate binding affinity. supp. material. PMC7195698

Biphasic interfacial activation of Rhizopus chinensis lipase

8. Acton, T.B.; Anderson, S.; Huang, Y.J.; Montelione, G. US Patent 10,385,350. Transcript optimized expression enhancement for high-level production of proteins and protein domains

9. Lee, J.; Huang, Y.J.; Montelione, G.T.; Im, W. Biophysical Journal. 2019, 116 (3): 289a. Charmm-Gui NMR Structure Calculator: A web-Based tool for calculating biomolecular NMR structures

10. Ozgul, S.; von Daake, S.; Kakehi, S.; Sereni, D.; Denissova, N.; Hanlon, C. ; Huang, J.Y.; Everett, J.K.; Yin, C.; Montelione, G.T.; Comoletti, D. Methods in Enzymology. 2019, 615: 453-475. An ELISA-based screening platform for ligand–receptor discovery

Schematic representation of the two plasmids used in this protocol and the ELISA orientation.

11. Huang, Y.J.; Brock, K.P.; Ishida, Y.; Swapna, G.V.T.; Inouye, M.; Marks, D.S.; Sander, C.; Montelione, G.T. Methods in Enzymology. 2019, 614: 363-392. Combining evolutionary covariance and NMR data for protein structure determination. PMC6640129

Performance vs. Reference Experimental Structure.

2018

1. Zhang, M.; Yu, X.-W.; Swapna, G.V.T.; Liu, G.; Xiao, R.; Xu, Y.; Montelione, G.T. Biomol NMR Assign 2018, 12: 63 – 68. Backbone and Ile-δ 1, Leu, Val methyl 1H, 15N, and 13C, chemical shift assignments for Rhizopus chinensis lipase. 

Binding modes

3. Venkataraman, A.; Yang, K.; Irizarry, J.; Mackiewicz, M.; Mita, P.; Kuang, Z.; Xue, L.; Ghosh, D.; Liu, S.; Ramos, P.; Hu, S.; Bayron, D.; Keegan, S.; Saul, R.; Colantonio, S.; Zhang, H.; Behn, F.P.; Song, G.; Albino, E.; Asencio, L.; Ramos, L.; Lugo, L.; Morell, G.; Rivera, J.; Ruiz, K.; Almodovar, R.; Nazario, L.; Murphy, K.; Vargas, I.; Rivera-Pacheco, Z.A.; Rosa, C.; Vargas, M.; McDade, J.; Clark, B.S.; Yoo, S.; Khambadkone, S.G.; de Melo, J.; Stevanovic, M.; Jiang, L.; Li, Y.; Yap, W.Y.; Jones, B.; Tandon, A.; Campbell, E.; Montelione, G.T.; Anderson, S.; Myers, R.M.; Boeke, J.D.; Fenyö, D.; Whiteley, G.; Bader, J.S.; Pino, I.; EichingerD.J.; Zhu, H.; Blackshaw, S. Nature Methods 2018, 15: 303 – 338. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. suppl. material. suppl. material2. suppl. material3. suppl. material4. suppl. material5. suppl. material6. suppl. material7. suppl. material8. suppl. material9. suppl. material10. suppl. material11. suppl. material12. suppl. material13. suppl. material14. suppl. material15. suppl. material16. suppl. material17. suppl. material18. suppl. material19. suppl. material20. suppl. material21. suppl. material22  PMC60603793

The attrition funnel through which immunogens entering the
PCRP pipeline ultimately generate high-quality mAbs.

4. Kim, J.D.; Pike, D.H.; Tyryshkin, A.M.; Swapna, G.V.T.; Raanan, H.; Montelione, G.T.; Nanda, V.; Falkowski, P.G. J Amer Chem Soc. 2018, 140: 11210 – 11213. Minimal heterochiral de novo designed 4Fe–4S binding peptide capable of robust electron transfer. suppl. material.

 (d) Sequences and computationally determined structural models of ambidoxin peptides. (e) Portion of ambidoxin model and natural ferredoxin structures are superimposable.

5. Nie, Y.; Wang, S.; Xu, Y.; Luo, S.; Zhao, Y-L.; Xiao, R.; Montelione, G.; Hunt, J.; Szyperski, T. ACS Catalysis 2018, 8: 5145 – 5152. Enzyme engineering based on X-ray structures and kinetic profiling of substrate libraries: alcohol dehydrogenases for stereospecific synthesis of a broad range of chiral alcohols. suppl. material.

ratio of kcat

6. Song, F.; Li, M.; Liu, G.; Swapna, G.V.T.; Daigham, N.S.; Xia, B.; Montelione, G.T.; Bunting, S.F. Biochemistry 2018, 57: 6568 – 6591. Antiparallel coiled-coil interactions mediate homodimerization of the DNA damage repair protein, PALB2. suppl. material. PMC6652205.

Formation of monomeric PALB2cc to PALB2cc homodimer and PALB2cc- BRCA1cc heterodimer

7. Huang, Y. J.; Brock, K.; Sander, C.; Marks, D.S.; Montelione, G.T. in H. Nakamura, G. Kleywegt, S. Burley and J. Markley, Eds. 2018, Adv Exp Med Biol., v.1105 Integrative Structural Biology with Hybrid Methods, pp. 153 – 169.A hybrid approach for protein structure determination combining sparse NMR with evolutionary coupling sequence data. PMC6630173.

EC-NMR structures determined using only HN-HN NOESY data superimposed on
reference conventional NMR structures.
2017

1. Marcos, E.; Basanta, B.; Chidyausiku, T.M.; Tang, Y.; Oberdorfer, G.; Liu, G.; Swapna, G.V.T.; Guan, R.; Silva, D.-A.; Dou, J.; Pereira, J.H.; Xiao, R.; Banumathi Sankaran, B.; Zwart, P.H.; Montelione, G.T.; Baker, D. Science 2017, 355: 201 – 206. Principles for designing proteins with cavities formed by curved β-sheets.  suppl. material  PMC5588894

Bulges and register shifts enhance beta-sheet curvature

2. Harish, B.; Swapna, G.V.T.; Kornhaber, G.J.; Montelione, G.T.; Carey, J. PROTEINS: Struct. Funct. Bioinformatics 2017, 85: 731 – 740. Multiple helical conformations of the helix-turn-helix region revealed by NOE-restrained MD simulations of tryptophan aporepressor, TrpR.  suppl. material  journal cover image  PMC5757375

(A) The WT holoTrpR dimer crystal structure (PDB ID: 2OZ9), showing the arrangement of helices (light subunit: A–F; dark
subunit: a–f) and L-tryptophan ligands (black skeletal models and dotted surfaces). Leu 75 (stick model at black arrowheads) lies within the DNA-binding helix-turn-helix region. (B) Overlay of HtH regions from each subunit in the crystal structure of the mutant L75F apoTrpR dimer
(PDB ID: 3SSX), showing two conformations of helices D and E. Orange, WT-like conformation; green, distorted conformation.

3. Pederson, K.; Chalmers, G.R.; Gao, Q.; Elnatan, D.; Ramelot T.A.; Ma, L-C.; Montelione, G.T.; Kennedy, M.A.; Agard, D.A.; Prestegard, J.H.; J. Biomol. NMR 2017, 68: 225 – 236. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine.  suppl. material  PMC5546222

Superimposed ribbon structures of the N-terminal (a) and middle plus C-terminal (b) domains of apo (green) and AMPPNP
(blue) forms of HtpG. 13C–1 H-labeled alanines with resonances that differ in chemical shift are shown in red

4. Zhang, M.; Yu, X-W.; Xu, Y.; Jouhten, P.; Swapna, G.V.T.; Glaser, R.W.; Hunt, J.F.; Montelione, G.T.; Maaheimo, H.; Szyperski, T. FEBS Letts 2017, 18: 3100 – 3111. 13 C metabolic flux profiling of Pichia pastoris grown in aerobic batch cultures on glucose revealed high relative anabolic use of TCA cycle and limited incorporation of provided precursors of branched-chain amino acidssuppl. material.

Biochemical reaction and metabolite transporter network of Pichia pastoris.

5. Alasadi, A.; Chen, M.; Swapna, G.V.T.; Tao, H.; Guo, J.; Collantes, J.; Fadhil, N.; Montelione, G.; Jin, S.V. Cell Death and Disease 2017, 9: 215. Effect of mitochondrial uncouplers niclosamide ethanolamine (NEN) and oxyclozanide on hepatic metastasis of colon cancer.  contents suppl. material. Table S1. Figure S1 Figure S2. Figure S3. Figure S4. Figure S5. Figure S6. Figure S7. PMC5833462

A Schematic representation showing mitochondrial uncoupling process
2016

1. Boël, G.; Letso, R.; Neely, H.; Price, W.N.; Wong, K.H.; Su, M.; Luff, J.; Valecha, M.; Everett, J.; Acton, T.B.; Xiao, R.; Montelione, G.T.; Aalberts, D.P.; Hunt, J.F. Nature 2016, 529: 358 – 363. Codon influence on protein expression in E. coli correlates to mRNA levels. suppl. material. Logistic Regressions. Optimized Genes. Protein Data Set. Figure 1. PMC5054687

Variation in codon influence as a function of position in the coding sequence

2. Boël, G.; Montelione, G.T.; Aalberts, D.P.; Hunt, J.F. Cell Systems 2016, 2: 60 – 64. Principles of Systems Biology, No. 2. 

3. Basanta, B.; Kui, B.; Chan, K.; Barth, P.; King, T.; Hinshaw, J.R.; Sosnick, T.R.; Liu, G.; Everett, J.; Xiao, R.; Montelione, G.T.; Baker, D. Protein Science 2016, 25: 1299 – 1307. Introduction of a polar core into the de novo designed protein Top7.  suppl. material.  PMC4918430

Top7_PC and Top7 models. Close up view comparing the core region of Top7 before (B) and after (A) hydrogenbond network incorporation. (C) Hydrogen-bond network in the context of the whole structure of one of the initial “inverted”
Top7 models. (D) Model of the disulfide-bonded variant of Top7. (E) Model of disulfide-bonded Top7 with core hydrogen-bond network.

4. Adams, P.D.; Aertgeerts, K.; Bauer, C.; Bell, J.A.; Berman, H.M.; Bhat, T.N.; Blaney, J.; Bolton, E.; Bricogne, G.; Brown, D.; Burley, S.K.; Case, D.A.; Clark, K.L.; Darden, T.; Emsley, P.; Feher, V.; Feng, Z.; Groom, C.R.; Harris, S.F.; Hendle, J.; Holder, T.; Joachimiak, A.; Kleywegt, G.; Krojer, T.; Marcotrigiano, J.; Mark, A.E.; Markley, J.L.; Miller, M.; Minor, W.; Montelione, G.T.; Murshudov, G.; Nakagawa, A.; Nakamura, H.; Nichols, A.; Nicklaus, M.; Nolte, R.; Padyana, A.K.; Peishoff, C.E.; Pieniazek, S.; Read, R.J.; Shao, C.; Steven Sheriff, S.; Smart, O.; Soisson, S.; Spurlino, J.; Stouch, T.; Svobodova, R.; Tempel, W.; Terwilliger, T.; Tronrud, D.; Velankar, S.; Ward, S.; Warren, G.; Westbrook, J.D.; Williams, P.; Yang, H.; Young, J. Structure (Cell Press) 2016, 24: 502 – 508. Outcome of the first wwPDB/CCDC/D3R ligand validation workshop. suppl. material.  PMC5070601

Electron density around 468 A 501.

5. MacCallum, J.L.; Tang, Y.; Huang, J.; Montelione, G.T. Biophysical Journal 2016, 110: 153a. Automatic protein structure determination from sparse NMR spectroscopy data. 

6. Zhang, M.; Yu, X.W.; Swapna, G.V.T.S.; Xiao, R.; Zheng, H.; Sha, C.; Xu, Y.; Montelione, G.T. Microb Cell Factories 2016, 15: 123. Efficient production of 2H, 13C, 15N-enriched proteins with native disulfide bonds: Application to the enzyme Rhizopus chinensis lipase.  PMC494443

2 Expression and purification of r27RCL by P. pastoris and E. coli. 1
soluble protein, 2 r27RCL(His)6 after HisTrap column, 3 soluble protein, 4 MBP-proRCL after one-step HisTrap-size-exclusion chromatography, 5 after Kex2 cleavage, 6 r27RCL after HisTrap column

7. Ma, L-C.; Guan, R.; Hamilton, K.; Aramini, J.; Mao, L.; Wang, S.; Krug, R.M.; Montelione, G.T. Structure (Cell Press) 2016, 24: 1562 – 1572. A second RNA-binding site in the NS1 protein of influenza B virus.  suppl. material 1  suppl. material 2  PMC5014651

Influenza B virus

8. Sachleben, J.R.; Adhikari, A.N.; Gawlak, G.; Hoey, R.J.; Liu, G.; Joachimiak, A.; Montelione, G.T.; Sosnick, T.R.; Koide, S. Protein Science 2016, 26: 208 – 217. Aromatic Claw: A new fold with high aromatic content that evades structural prediction.  suppl. material  PMC5275723

 Superposition of the backbone of 18 the lowest energy structures
as determined from NMR constraints. The a1, a2, and a3 helices of the aromatic claw are colored red, yellow, and blue, respectively, while the pseudo-sheet is cyan.

9. Cai, K.; Liu, G.; Frederick, R.O.; Xiao, R.; Montelione, G.T.; Markley, J.L. Structure (Cell Press) 2016, 24: 2080 – 2091. Structural/functional properties of human NFU1, an intermediate [4Fe-4S] carrier in human mitochondrial iron-sulfur cluster biogenesis.  suppl. material 1  suppl. material 2  PMC5166578

(A–D) Superimposed conformers representing the solution structures of the (A) N-terminal domain (NTD) and (C) C-terminal domain (CTD). Ribbon diagrams representing the (B) NTD and (D) CTD. The residues in each domain are colored from blue at the N terminus to red at the C terminus.

2015

1. Parmeggiani, F.; Huang, P-S.; Vorobiev, S.; Xiao, R.; Park, K.; Caprari, S.; Su, M.; Jayaraman, S.; Mao, L.; Janjua, H.; Montelione, G.T.; Hunt, J.F.; Baker, D. J Mol Biol 2015, 427: 563 – 575. Beyond consensus: a general computational approach for repeat protein design.  suppl. material 1  suppl. material 2 (zip) PMC4303030

Superposition of models and crystal structures for ank3 (a) (RMSD of 0.9 Å), arm8 (b) (RMSD of 0.9 Å) and
LRR_1440 (c) (RMSD of 1.1 Å). Models are in green and crystal structures are in blue. In most cases, the core residues assume the conformation predicted in the models, as shown in (a), (b) and (c) insets for some of the side chains. Parts of the structures have been removed to display the core residues. RMSD was calculated using backbone heavy atoms. For LRR, the N-terminal capping repeat was not included in the RMSD calculation; when it is considered, the RMSD increases to 1.6 Å. Pictures were realized with PyMOL (Schroedinger).

2. Rossi, P.; Shi, L.; Liu, G.; Barbieri, C.M.; Lee, H.-W.; Grant, T.D.; Luft, J.R.; Xiao, R.; Acton, T.B.; Snell, E.H.; Montelione, G.T.; Baker, D.; Lange, O.F.; Sgourakis, N.G. PROTEINS: Struc. Funct. Bioinformatics 2015, 83: 309 – 317. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.  suppl. material  PMC5061451

Examples of variability in the bet-V1 clan dimer interfaces. Aggregation screening was conducted prior to structure determination by NESG and the proteins were found to be dimeric under the crystallization conditions: A) SSP2350 (PDB ID 3Q6A). B) MM0500 (PDB ID 1XUV). C, D) Two plausible crystallographic dimer interfaces observed for MLL2253 (PDB ID 3Q63).

3. Luft, J.R.; Wolfley, J.R.; Franks, E.C.; Lauricella, A.M.; Gualtieri, E.J.; Snell, E.H.; Xiao, R.; Everett, J.K.; Montelione, G.T. Structural Dynamics 2015, 2: 041710. The detection and subsequent volume optimization of biological nanocrystals.  PMC4711624

 Correlating DVR outcomes with a phase diagram

4. Aiyer, S.; Rossi, P.; Malani, N.; Schneider, W.M.; Chanda, A.; Bushman, F.D.; Montelione, G.T.; Roth, M.J. Nucleic Acids Research 2015, 43: 5647 – 5663. Structural and sequencing analysis of local target DNA recognition by MLV integrase.  PMC4477651

The C! backbone trace of IN 329–408

5. Sali, A.; Berman, H.M.; Schwede, T.; Trewhella, J.; Kleywegt, G.; Burley, S.K.; Markley, J.; Nakamura, H.; Adams, P.; Bonvin, A.M.J.J.; Chiu, W.; Dal Peraro, M.; Di Maio, F.; Ferrin, T.E.; Grünewald, K.; Gutmanas, A.; Henderson, R.; Hummer, G.; Iwasaki, K.; Johnson, G.; Lawson, K.L.; Meiler, J.; Marti-Renom, M.A.; Montelione, G.T.; Nilges, M.; Nussinov, R.; Patwardhan, A.; Rappsilber, J.; Read, R.J.; Saibil, H.; Schröder, G.F.; Schwieters, C.; Seidel, C.A.M.; Svergun, D.; Topf, M.; Ulrich, E.L.; Velankar, S.; Westbrook, J.D. Structure (Cell Press) 2015, 23: 1156 – 1167. Outcome of the first wwPDB hybrid / integrative methods task force workshop.  PMC4933300

Genome architecture

6. Gutmanas, A.; Adams, P.D.; Bardiaux, B.; Berman, H.M.; Case, D.A.; Fogh, R.H.; Güntert, P.; Hendrickx, P.M.S.; Herrmann, T.; Kleywegt, G.J.; Kobayashi, N.; Lange, O.F.; Markley, J.L.; Montelione, G.T.; Nilges, M.; Ragan, T.J.; Schwieters, C.D.; Tejero, R.; Ulrich, E.; Velankar, S.; Vranken, W.F.; Wedell, J.R.; Westbrook, J.; Wishart, D.S.; Vuister, G.W. Nature Struct Mol Biol 2015, 22: 433 – 434. NMR Exchange Format: a unified and open standard for representation of NMR restraint data.  PMC4546829

Growth in the number of NMR entries in the PDB archive

7. Ragan, T.J.; Fogh, R.H.; Tejero, R.; Vranken, W.; Montelione, G.T.; Rosato, A.; Vuister, G.W. J Biomol NMR 2015, 62: 527 – 540. Analysis of the structural quality of the CASD-NMR 2013 entries. suppl. material 1  suppl. material 2  PMC4569653

6 Correlation between entry pairwise RMSD and NOE restraint
overlap.

8. Huang, Y.P.; Mao, B.; Xu, F.; Montelione, G.T. J Biomol NMR 2015, 62: 439 – 451. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score. PMC4943320

Superimposed ribbon diagrams using different regions for three HR8254A ensembles: 2M2E, ASDP structures before Rosetta refinement, and ASDP structures after Rosetta refinement

9. Rosato, A.; Vranken, W.; Fogh, R.H.; Ragan, T.J.; Tejero, R.; Pederson, K.; Lee, H.-W.; Prestegard, J.; Yee, A.; Wu, B.; Lemak, A.; Houliston, S.; Arrowsmith, C.; Kennedy, M.; Acton, T.B.; Liu, G.; Xiao, R.; Montelione, G.T.; Vuister, G.W. J Biomol NMR 2015, 62: 413 – 424. The second round of critical assessment of automated structure determination of proteins by NMR: CASD-NMR-2013.  suppl. materialPMC4569658

Side by side superimposed backbone ribbon traces and cartoon representations for the ten manually-determined CASD-NMR-2013 reference structures, labeled with PDB codes and coloured blue to red from N- to C-terminus

10. Tang, Y.; Huang, Y.P.; Hopf, T.A.; Sanders, C.; Marks, D.S.; Montelione, G.T. Nature Methods 2015, 12: 751 – 754. Protein structure determination by combining sparse NMR spectroscopy data with evolutionary couplings.  suppl. material  PMC4521990

The EC-NMR approach

11. Aramini, J.M.; Vorobiev, S.M.; Tuberty, L.M.; Janjua, H.; Campbell, E.T.; Seethraman, J.; Su, M.; Huang, Y.P.; Acton, T.B.; Xiao, R.; Tong, L.; Montelione, G.T. Structure (Cell Press) 2015, 23: 1 – 12. The RAS- binding domain of human BRAF protein serine/threonine kinase exhibits allosteric conformational changes upon binding HRAS.  suppl. material 1 suppl. material 2  PMC4963008

Solution NMR and X-ray crystal structures of BRAF RASbinding domain

12. Choi, H.W.; Tian, M.; Song, F.; Venereau, E.; Preti, A.; Park, S.-W.; Hamilton, K.; Swapna, G.V.T.; Manohar, M.; Moreau, M.; Agresti, A.; Gorzanelli, A.; De Marchis, F.; Wang, H.; Antonyak, M.; Micikas, R.J.; Gentile, D.R.; Cerione, R.A.; Schroeder, F.C.; Montelione, G.T.; Bianchi, M.E.;Klessig, D.F. Molecular Medicine 2015, 21: 526 – 535. Aspirin’s active metabolite salicylic acid targets High Mobility 1 Group Box 1 (HMGB1) to modulate inflammatory responses.  PMC4607614

Arg24 and Lys28 are required for binding SA

13. Everett, J.K.; Tejero, R.; Murthy, S.B.K.; Acton, T.B.; Aramini, J.M.;Baran, M.C.; Benach, J.; Cort, J.R.; Eletsky, A.; Forouhar, F.; Guan, R.; Kuzin, A.P.; Lee, H.-W.; Liu, G.; Mani, R.; Mao, B.; Mills, J.L.; Montelione, A.F.; Pederson, K.; Powers, R.; Ramelot, T.; Rossi, P.; Seetharaman, J.; Snyder, D.; Swapna, G.V.T.; Vorobiev, S.M.; Wu, Y.; Xiao, R.; Yang, Y.; Arrowsmith, C.H.; Hunt, J.F.; Kennedy, M.A.; Prestegard, J.H.; Szyperski, T.; Tong, L.; Montelione, G.T. Protein Science 2015, 25: 30 – 45. A community resource of experimental data for NMR – X-ray crystal structure pairs.  suppl. material  PMC4815321

. Examples of NESG NMR / X-ray pairs with low C 5 RMSXtal/RMSens. Nine NMR / X-ray pairs, from the NESG or NESG/R3 sets, with lowest values of C.

14. Lin, Y-R.; Koga, N.; Tatsumi-Koga, R.; Liu, G.; Clouser, A.F.; Montelione, G.T.; Baker, D. Proc Natl Acad Sci USA 2015, 112: e5478 – 5485. Control over overall shape and size in de novo design proteins.  suppl. material  PMC4603489

Discrete state model of protein local geometry.

15. Wolf, C.; Siegel, J.B.; Tinberg, C.; Camarca, A.; Gianfrani, C.; Paski, S.; Guan, R.; Montelione, G.T.; Baker, D.; Pultz, I.S. J Amer Chem Soc 2015, 137: 13106 – 13113. Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions.  suppl. material  PMC4958374

Immunogenic gluten epitopes

16. King, I.C.; Gleixner, J.; Doyle, L.; Kuzin, A.; Hunt, J.F.; Xiao, R.; Montelione, G.T.; Stoddard, B.L.; DiMaio, F.; Baker, D. eLIFE 2015, 4: e11012. Precise assembly of complex beta sheet topologies from de novo design building blocks.  suppl. material  PMC4737653

Comparison of the crystal structure of the ferredoxin-ferredoxin fusion to the design model.
2014

1. Mao, B.; Tejero, R,; Baker, D.; Montelione, G.T. J Amer Chem Soc 2014, 136: 1893 – 1906. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures.  suppl material  PMC4129517

Rosetta refinement with NMR restraints

2. Vorobiev, S.; Gensler, Y.; Vahedian-Movahed, H.; Seetharaman, J.; Su, M.; Huang, Y-P.; Xiao, R.; Kornhaber, G.; Montelione, G.T.; Tong, L.; Ebright, R.H.; Nickels, B.E. Structure (Cell Press) 2014, 22: 488 – 495. Structure of the DNA-binding and RNA polymerase-binding region of transcription antitermination factor λQ.  suppl. material  PMC3951671

lQ Regulates Gene Expression from lPR

3. Srinivisan, B.; Forouhar, F.; Shukla, A.; Sampangi, C.; Kulkarni, S.; Abashidze, M.; Seetharaman, J.; Lew, S.; Mao, L.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.T.; Tong, L.; Balaram, H. FEBS Lett. 2014, 281: 1613 – 1628. Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila  suppl. material 1  suppl. material 2  PMC3982195

. PO4-complexed tetrameric LpcN-II structures

4. Stark, J.L.; Mehla, K.; Chaika, N.; Acton, T.B.; Xiao, R.; Singh, P.K.; Montelione, G.T.; Powers, R. Biochemistry 2014, 53: 1360 – 1372. The structure and function of DnaJ homolog subfamily A member 1 (DNAJA1) and its relationship to pancreatic cancer.  PMC3985919

The human protein DnaJ homologue subfamily A member 1 (DNAJA1) was previously shown to be downregulated 5-fold in pancreatic cancer cells and has been targeted as a biomarker for pancreatic cancer, but little is known about the specific biological function for DNAJA1 or the other members of the DnaJ family encoded in the human genome.

5. Aramini, J.M.; Hamilton, K.; Ma, L-C.; Swapna, G.V.T.;Leonard, P.G.; Ladbury, J.E.; Krug, R.M.; Montelione, G.T. Structure (Cell Press) 2014, 22: 515 – 525. 19F NMR reveals multiple conformations at the dimer interface of the NS1 effector domain from influenza A virus.  suppl. material  PMC4110948

. Locations of 5-F-Trp Residues in the Dimer Structures of Ud NS1A Domains
and Assignment of 19F Resonances in 5-FTrp-labeled Ud NS1A ED

6. Aiyer, S.; Swapna, G.V.T.; Malani, N.; Aramini, J.M.; Schneider, W.M.; Plumb, M.R.; Ghanem, M.; Larue, R.C.; Sharma, A.; Studamire, B.; Kvaratskhelia, M.; Bushman, F.D.; Montelione, G.T.; Roth, M.J. Nucleic Acids Research 2014, 42: 5917 – 5928. Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction  suppl. material  PMC4027182

C� backbone trace, along with key structural features, of an ensemble of 20 conformers of MLV IN CTD from amino acids 329–408 (PDB ID 2M9U) is shown in this panel with the same color codes as described in panel A

7. Pulavarti, S.; Eletsky, A.; Huang, Y.J.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Szyperski, T. Biomol NMR Assign 2014, 9: 135 – 138. Polypeptide backbone, Cb and methyl group resonance assignments of the 24 kDa plectin repeat domain 6 from human protein plectin  PMC4194182

8. Xu, X.; Pulavarti, S.V.; Eletsky, A.; Huang, Y.J.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2014, 15: 201 – 207. Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network.  suppl. material  PMC4239167

a Overlay of the ribbon representations of ALX4 (209–280) (green), ZHX1
(462–532) (red), and CASP8AP2 (1916–1982) (blue)

9. Sathyamoorthy, B,; Parish, D.M.; Montelione, G.T.; Xiao, R.; Szyperski, T. Chem Physchem. 2014, 15: 1872 – 1879. Spatially selective heteronuclear multiple-quantum coherence spectroscopy for biomolecular NMR studies.  suppl. material  PMC4121990

SS HMQC RF-pulse schemes implemented for n=4 slices

10. Bruno, E.B.; Ruby, A.M.; Luft, J.R.; Grant, T.D.; Seetharaman, J.; Montelione, G.T.; Hunt, J.F.; Snell, E.H. PLoS One 2014, 9: e100782. Comparing chemistry to outcome: The development of a chemical distance metric coupled with clustering and hierarchal visualization applied to macromolecular crystallography.  suppl. material  PMC4074061

. Pairwise distance matrix for the 1,536 cocktails in the
generation 8 crystallization screen.

11. Pulavarti, S.V.; Huang, Y.J.; Pederson, K.; Acton, T.B.; Xiao, R.; Everett, J.K.; Prestegard, J.H.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2014, 15: 209 – 214. Solution NMR structures of immunoglobulin-like domains 7 and 12 from obscurin-like protein 1 contribute to the structural coverage of the human cancer protein interaction network.  suppl. material  PMC4945113

e Surface and space filling representations of the lowest-energy conformer of OBSL1(805–892) colored according to scores from PredUs prediction of regions potentially involved in protein–protein interactions; the default PredUs color scheme for residues with scores larger than zero are shown from
light red to red with increasing score.f

12. Eletsky, A.; Michalska, K.; Houliston, S.; Zhang, Q.; Daily, M.D.; Xu, X.; Cui, H.; Yee, A.; Lemak, A.; Wu, B.; Garcia, M.; Burnet, M.C.; Meyer, K.M.; Aryal, U.K.; Sanchez, O.; Ansong, C.; Xiao, R.; Acton, T.B.; Adkins, J.N.; Montelione, G.T.; Joachimiak, A.; Arrowsmith, C.H.; Savchenko, A.; Szyperski, T.; Cort, J.R. PLoS One 2014, 9: e101787. Structural and functional characterization of DUF1471 domains of salmonella.  suppl. material  PMC4092069

Proteins structurally similar to DUF1471 proteins

13. Elshahawi, S.; Ramelot, T.; Seetharaman, J.; Chen, J.; Singh, S.; Yang, Y.; Pederson, K.; Kharel, M.; Xiao, R.; Yennamalli, R.; Wang, J.; Tong, L.; Montelione, G.; Kennedy, M.; Bingman, C.; Phillips, G.; Thorson, J. ACS Chemical Biology 2014, 9: 2347 – 2358. Structure-guided functional characterization of enediyne self-sacrifice resistance proteins CalU16 and CalU19.  suppl. material  PMC4201346

Structure of CalU16

14. Yang, Y.; Ramelot, T.A.; Lee, H-W.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Prestegard, J.H.; Kennedy, M. J Biomol NMR 2014, 60: 189 – 195. Solution structure of the free Zα domain of human DLM-1 (ZBP1/DAI), a Z-DNA binding domain.  PMC4527548

Stereoview of the
superimpositions of the 20 lowest energy structures of
human ZaDLM-1

15. Yang, Y.; Ramelot, T.A.; Lee, H-W.; Xiao, R.;Everett, J.K.; Montelione, G.T.; Prestegard, J.H.; Kennedy, M. J Biomol NMR 2014, 60: 197 – 202. Solution structure of a C-terminal fragment (175-257) of CV_0373 protein from Chromobacterium violaceum adopts a winged helix-turn-helix (wHTH) fold.  PMC4928572

Stereoview of the superimpositions of the 20 lowest energy structures of CV_0373 CTD.

16. Bruno, A.; Ruby, A.; Luft, J.; Grant, T.; Seetharman, J.; Hunt, J.; Montelione, G.; Snell, E. Acta Cryst. 2014, A70: C1145. Chemical clustering and visualization applied to macromolecular crystallography. suppl. material.  PMC4074061

Chemical clustering and visualization applied to macromolecular crystallography
2013

1. Rossi, P.; Barbieri, C.M.; Aramini, J.M.; Bini, E.; Xiao,R.; Acton, T.B.; Montelione, G.T. Nucleic Acids Research 2013, 41: 2756 – 2768. Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the role of protein family DUF2128 and expand the single-stranded DNA binding domain proteome.  suppl. material  PMC3575825

2. Mills, J.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2013, 14: 19 – 24. Solution NMR structure of the helicase associated domain BVU_0683(627-691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA.  suppl. material  PMC3637686

1 NMR Structures of BVU_0683(627–691) (only residues 631–689 are shown for clarity)

3. Bjelic, S.; Nivón, L.G.; Celebi-Ölçüm, N.; Kiss, G.; Rosewall, C.F.; Lovick, H.M.; Ingalls, E.L.; Gallaher, J.L.; Seetharaman, J.; Lew, S.; Montelione, G.T.; Hunt, J.F.; Michael, F.E.; Houk, K.N.; Baker, D. ACS Chem. Biol. 2013, 8: 749 – 757. Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction.  suppl. material  PMC3647451

 Morita−Baylis−Hillman reaction

4. Forouhar.; Arragain, S.; Atta, M.; Gambarelli, S.; Mouesca, J.M.; Hussain, M.; Xiao, R.; Kieffer-Jaquinod, S.; Seetharaman, J.; Acton, T.B.; Montelione, G.T.; Mulliez, E.; Hunt, J.F.; Fontecave, M. Nature Chemical Biology 2013, 9: 333 – 338. Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases.  suppl. material  PMC4118475

) Ribbon diagram
showing the UPF0004, radical-SAM and TRAM domains in cyan, yellow and magenta, respectively.

5. Froese, D.S.; Forouhar, F.; Tran, T.H.; Vollmar, M.; Kim, Y.; Lew, S.; Neely, H.; Seetharaman, J.; Shen, Y.; Xiao, R.; Acton, T.B.; Everett, J.K.; Cannone, G.; Puranik, S.; Savitsky, P.; Krojer, T.; Pilka, E.S.; Kiyani, W.; Lee, W.H.; Marsden, B.D.; von Delft, F.; Allerston, C.K.; Spagnolo, L.; Gileadi, O.; Montelione, G.T.; Oppermann, U.; Yue, W.W.; Tong, L. Structure (Cell Press) 2013, 21: 1182 – 1192. Crystal structures of malonyl-CoA decarboxylase provide insights into its catalytic mechanism and disease-causing mutations.  suppl. material  PMC3701320

Schematic drawing of the structures of HsMCD (A), RpMCD (B), AvMCD (C), and CmMCD (D).

6. Procko, E.; Hedman, R.; Hamilton, K.; Seetharaman, J.; Fleishman, S.; Su, M.; Aramini, J.; Kornhaber, G.; Hunt, J.; Tong, L.; Montelione, G.; Baker, D. J Mol Biol 2013, 425: 3563 – 3575. Computational design of a protein-based enzyme inhibitor.  suppl. material  PMC3818146

 Cell wall hydrolysis of an M. lysodeikticus suspension by 500 nM HEL is inhibited by HtsptLB12 variants.

7. Tejero, R.; Snyder, D.; Mao, B.; Aramini, J.M.; Montelione, G.T.; J Biomol NMR 2013, 56: 337 – 351. PDBStat: A universal restraint converter and restraint analysis software package for protein NMR.  suppl. material  PMC3932191

FindCore provides atom-specific designations for well-defined and not-well-defined regions of NESG protein SgR42 (PDB id 2jz2)

8. Rosato, A.; Tejero, R.; Montelione, G.T. Current Opinions in Structural Biology 2013, 23: 715 – 724. Quality assessment of protein NMR structures.  PMC4110634

Comparison of DOAP and variance distance matrix results for identifying well-defined atom sets.

9. Montelione, G.T.; Nilges, M.; Bax, A.; Güntert, P.; Herrmann, T.; Richardso J.S.; Schwieters, C.; Vranken, W.F.; Vuister, G.W.; Wishart, D.S.; Berman, H. Kleywegt, G.J.; Markley, J.L. Structure (Cell Press) 2013, 21: 1563 – 1570. Recommendations of the wwPDB NMR validation task force.  PMC3884077

10. Neklesa, T.K.; Noblin, D.J.; Kuzin, A.P.; Lew, S.; Seetharaman, J.; Acton, T.B.; Kornhaber, G.; Xiao, R.; Montelione, G.T.; Tong, L.; Crews, C.M. ACS Chem Biol 2013, 8: 2293 – 2300. A bidirectional system for the dynamic small molecule control of intracellular fusion proteins.  suppl. material  PMC4113957

Characterization of HALTS1 activity in cells.

11. Pulavarti, S.; Eletsky, A.; Lee, H-W.; Acton, T.B.; Xiao, R.; Everett, J.K.; Prestegard, J.H.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2013, 14: 155 – 160. Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct αhelical architecture and provides first structural representative of protein domain family PF14203.  suppl. material  PMC3844015

Solution NMR structure of CD1104B from Clostridium difficile (PDB ID, 2L7K).

12. Ramelot, T.A.: Yang, Y.; Sahu, I.D.; Lee, H.W.; Xiao, R.; Lorigan, G.A.; Montelione, G.T.; Kennedey, M. FEBS Lett 2013, 587: 3522 – 3528. NMR structure and MD simulations of the AAA protease intermembrane space domain indicates peripheral membrane localization within the hexaoligomer.  suppl. material  PMC4043124

(E and F) ConSurf [17] image showing the conserved surface residues. Residue coloring reflects the degree of residue conservation for selected eukaryotic homologs from Pfam06480 (42 sequences).

13. Xu, S.Y.; Kuzin, A.P.; Seetharaman, J.; Gutjahr, A.; Chan, S.H.; Chen, Y.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L. PLoS One 2013, 8:e72114. Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15.  suppl. material  PMC3765158

Structure of Hpy99I dimer in complex with duplex DNA [18]. The catalytic domains are colored in cyan and green, and the N-terminal segment in yellow

14. Meng, L.; Forouhar, F.; Thieker, D.; Gao, Z.; Ramiah, A.; Moniz, H.; Seetharaman, J.; Milaninia, S.; Su, M.; Bridger, R.; Veillon, L.; Azadi, P.; Kornhaber, G.; Wells, L.; Montelione, G.; Woods, R.J.; Tong, L.; Moremen, K.W. J Biol Chem 2013, 288: 34680 – 34698. Enzymatic basis for N-glycan sialylation: structure of ST6GAL1 reveals conserved and unique features for glycan sialylation.  suppl. material  PMC3843080

Schematic representation of the activities of the mammalian sialyltransferase subfamily members.

15. Pulavarti, S.; He, Y.; Feldmann, E.A.; Eletsky, A.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Kennedy, M.A.; Szyperski, T. J Struct Funct Genomics 2013, 14: 119 – 126. Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and complementary structural coverage of dark operative protochlorophyllide oxidoreductase complexes.  suppl. material  PMC3982801

The (BchN-BchB)2 from R. capsulatus (PDB ID: 3AEK) was superimposed on the (BchN-BchB)2 unit of P. marinus DPOR complex (PDB ID: 2YNM) and is shown as a space filling representation colored according to scores from PredUs prediction for regions potentially involved in protein–protein interaction (residues with scores larger than zero are shown from light red to red with increasing score

16. Kronfel, C.M.; Kuzin, A.P.; Forouhar, F.; Biswas, A.; Su, M.; Lew, S.; Seetharaman, J.; Xiao, R.; Everett, J.K.; Ma, L-C.; Acton, T.B.; Montelione, G.T.; Hunt, J.F.; Paul, C.E.C.; Dragomani, T.M.; M. Nazim Boutaghou, M.N.; Cole, R.B.; Riml, C.; Alvey, R.M.; Bryant, D.A.; Schluchter, W.M. Biochemistry 2013, 52: 8663 – 8676. Structural and biochemical characterization of the bilin lyase CpcS from Thermosynechococcus elongates.  suppl. material  PMC3932240

Cyanobacterial phycobiliproteins have evolved to capture light energy
over most of the visible spectrum due to their bilin chromophores, which are linear tetrapyrroles that have been covalently attached by enzymes called bilin lyases

17. Huang, Y.J.; Acton, T.B.; Montelione, G.T. Methods in Mol Biol 2013, 1091: 3 – 16. DisMeta – a meta server for construct design and optimization.  PMC4115584

Disorder prediction

18. Huang, Y.P.; Mao, B.; Aramini, J.; Montelione, G.T. PROTEINS: Struct Funct Genomics 2014, 82: Suppl 2: 43 – 56. Assessment of template based protein structure predictions in CASP10.  suppl. material 1  suppl. material 2  suppl. material 3  suppl. material 4  PMC3932189

Comparison of models using distance networks

19. Taylor, T.; Tai, C-H.; Huang, J.; Block, J.; Bai, H.; Kryshtafovych, A.; Montelione, G.T.; Lee, B. PROTEINS: Struc Funct Genomics 2014, 82: Suppl 2: 14 – 25 Definition and classification of evaluation units for CASP10.  PMC4133092

T0719: an example of the case where each domain is an evaluation
unit. The colors indicate different domains. The N-terminus is in the dark blue domain, the C-terminus in the red domain

20. Snyder, D.A.; Grullon, J.; Huang, Y.J.; Tejero, R.; Montelione, G.T. PROTEINS: Struc Funct Genomics 2014, 82: Suppl 2: 219 – 230. The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.  suppl. material  PMC3932188

CASP Target T0657 (PH domain of tyrosine protein kinase TEC, PDB ID 2LUL) and (B) CASP Target T0754 (human MLL5 PHD domain)

21. Uemura, Y.; Nakagawa, N.; Wakamatsu, T.; Kim, K.; Montelione, G.T.; Hunt, J.F.; Kuramitsu, S.; Masui, R. FEBS Lett 2013, 587: 2669 – 2674. Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins.  suppl. material  PMC4113422

2012

1. Thompson, J.; Sgourakis, N.G.; Liu, G.; Rossi, P.; Tang, Y.; Mills, J.; Szyperski, T.; Montelione, G.; Baker, D. Proc Natl Acad Sci USA 2012, 109: 9875 – 9880. Accurate protein structure modeling using sparse NMR data and homologous structure information.  suppl. material  PMC3382498

Structural comparison of high-resolution CS-HM-Rosetta structures
with conventionally determined NMR (A, B, and D) and X-ray (C) structures.

2. Rosato, A.; Aramini, J.M.; Arrowsmith, C.; Bagaria, A.; Baker, D.; Cavalli, A.; Doreleijers, J.F.;Eletsky, A.; Giachetti, A.; Guerry, P.; Gutmanas, A.; Güntert, P.; He, Y.; Herrmann, T.; Huang, Y.J.; Jaravine, V.; Jonker, H.R.A.; Kennedy, M.A.; Lange, O.F.; Liu G.; Malliavan, T.E.; Mani, R.; Mao, B.; Montelione, G.T.; Nilges, M.; Possi, P.; van der Schot, G.; Schwalbe, H.; Szyperski, T.A.; Vendruscolo, M.; Vernon, R.; Vranken, W.F.; de Vries, S.; Vuister, G.W.; Wu, B.; Yang, Y.; Bonvin, A.M.J.J. Structure (Cell Press) 2012, 20: 227 – 236. Blind testing of routine, fully automated determination of protein structures from NMR data.  suppl. material 1  suppl. material 2  PMC3609704

Structural Similarity between Reference and CASDNMR2010 Structures

3. Ramelot, T.A.; Yang, Y.; Xiao, R.; Acton, T.B.; Everett, J.K.; Montelione, G.T.; Kennedy, M.A. PROTEINS: Struct Funct Bioinformatics 2012, 2: 667 – 670. Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron.  suppl. material  PMC3766420

(A) Cartoon view of the lowest energy conformer from the solution NMR structure of BT_0084 (PDB ID, 2L3B, residues 11 to 115).

4. Bagaria, A.; Jaravine, V.; Huang, Y.P.; Montelione, G.T.; Güntert, P. Protein Science 2012, 21: 229 – 238. Protein structure validation by generalized linear model root-mean-square deviation prediction.  suppl. material  PMC3324767

Examples of structural quality prediction for the CASD-NMR target AtT13. Three models of decreasing accuracy are shown in ribbon style from left to right. The values of the normalized validation scores, the predicted GLM-RMSDs, and the actual RMSDs to the reference structure are indicated.

5. Kobayashi, H.; Swapna, G.V.T.; Wu, K-P; Afinogenova, Y.; Conover, K.; Mao, B.; Montelione, G.T.; Inouye, M. J Biomol NMR 2012, 52: 303 – 313. Segmental isotope labeling of proteins for NMR structural study using a protein S tag for higher expression and solubility.  suppl. material 1  suppl. material 2  PMC4117381

Efficiency of expression and solubility of PrS2IN and PrS2IC

6. Eletsky, A.; Petrey, D.; Zhang, Q.C.; Lee, H.-W.; Acton, T.; Xiao, R.; Everett, J.; Prestegard, J.; Honig, B.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2012, 13: 1 – Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771.  suppl. material  PMC3654790

 a Multiple sequence alignment of a representative subset of
members of PF10771, including Bvu3908, Bt2368 along with
homologues from Bacteroides ovatus, Bacteroides caccae, Bacteroides fragilis and Bacteroides thetaiotaomicron.

7. Eletsky, A.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2012, 13: 9 –  Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536.  suppl. material  PMC360422

1 a Stereoview of the 20 conformers representing the solution
structure of CG2496(41–180) obtained after superposition of the Ca atoms of the regular secondary structure elements for minimal RMSD.

8. Wu, Y.; Punta, M.; Xiao, R.; Acton, T.; Sathyamoorthy, B.; Dey, F.; Fischer, M.; Skerra, A.; Rost, B.; Montelione, G.T.; Szyperski, T. PLOS One 2012, 7: e37404. NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli.  PMC3367933

 NMR structure of the soluble domain of lipoprotein YxeF.

9. Ertekin, A.; Aramini, J.M.; Rossi, P.; Leonard, P.G.; Janjua, H.; Xiao, R.; Maglaqui, M.; Lee, H.-W.; Prestegard, J.H.; Montelione, G.T. J Biol Chem 2012, 287: 16541 – 16549. Human cyclin dependent kinase 2 associated protein 1 is dimeric in its disulfide-reduced state, with natively disordered n-terminal region.  suppl. material  PMC3351331

Solution NMR structure of CDK2AP1(61–115).

10. Huang, Y.; Rosato, A.; Singh, G.; Montelione, G.T. Nucleic Acids Research 2012, 40: W542 – 546. RPF – A quality assessment tool for protein NMR structures.  PMC3394279

Correlation between accuracy measures (backbone RMSD to the reference structure and GDT_TS score) and the DP-score.

11. Snyder, D.; Aramini, J.M.; Yu, B.; Huang, Y.; Xiao, R.; Cort, J.; Shastry, R.; Ma, L.-M.; Liu, J.; Rost, B.; Action, T.; Kennedy, M.; Montelione, G.T. PROTEINS: Struct Funct Genomics 2012, 80: 1901 – 1906. Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus.  suppl. material  PMC3639469

Solution NMR structure of RP-L35Ae from Pyrococcus furiosus.

12. Montelione, G.T. Faculty 1000 Commentary 2012, 4: 7. The Protein Structure Initiative: achievements and visions for the future.  PMC3318194

13. Lange, O.F.; Rossi, P.; Sgourakis, N.; Song, Y.; Lee, H.-W.; Aramini, J.M.; Ertekin, A.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Baker, D. Proc Natl Acad Sci U.S.A. 2012, 109: 10873 – 10878. The determination of solution structures of proteins up to 40 kDa using CS- Rosetta with sparse NMR data from deuterated samples.  PMC3390869

RASREC Rosetta results for maltose-binding protein.

14. Feldmann, E.A.; Seetharaman, J.; Ramelot, T.A.; Lew, S.; Zhao, L.; Hamilton, K.; Ciccosanti, C.; Xiao, R.; Acton, T.B.; Everett, J.K.; Tong, L.; Montelione, G.T.; Kennedy, M.A. J Struct Funct Genomics2012, 13: 155 – 162. Solution NMR and X-ray crystal structure of Pspto_3016 from Pseudomonas syringae, a member of protein domain family PF04237 (DUF419) that adopts a “double wing” DNA binding motif.  suppl. material  PMC3697073

Three-dimensional structure of the Pspto_3016 protein from P. syringae (PDB IDs 2KFP and 3H9X). a

15. Vorobiev, S.M.; Neely, H.; Yu, B.; Seetharaman, J.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Hunt, J.F. J Struct Funct Genomics 2012, 13: 177 – 183. Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product.  suppl. material  PMC3683829

a Sequence alignment of the DGC domains of A1U3W3, PleD from C. crescentus, and WspR from P. aeruginosa by ClustalW

16. Swapna, G.V.T.; Rossi, P.; Montelione, A.F.; Benach, J.; Yu, B.; Abashidze, M.; Seetharaman, J.; Xiao, R.; Acton, T.B.; Tong, L.; Montelione, G.T. J Struct Funct Genomics 2012, 13: 163 – 170. Three structural representatives of the PF06855 protein domain family from Staphyloccocus aureus and Bacillus subtilis have SAM domain- like folds and different functions.  PMC4075964

. i Least-squares superposition of yozE

17. Aramini, J.M.; Petrey, D.; Lee, D.Y.; Janjua, H.; Xiao, R.; Acton, T.B.; Everett, J.K.; Montelione G.T. J Struct Funct Genomics 2012, 13: 171 – 176. Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267.  suppl. material  PMC3897273

image showing the conserved residues in Alr2454 (residues 3–101). Residue coloring, reflecting the degree of residue conservation over the entire PF11267 protein domain family (Pfam 25.0 [1]; 80 sequences), ranges from magenta (highly conserved) to cyan (variable).

18. Aramini, J.M.; Hamilton, K.; Rossi, P.; Ertekin, A.; Lee, H.-W.; Lemak, A.; Wang, H.; Xiao, R.; Acton, T.B.; Everett, J.K.; Montelione, G.T. Biochemistry 2012, 51: 3705 – 3707. Solution NMR structure, backbone dynamics, and heme-binding properties of a novel cytochrome c maturation protein CcmE from Desulfovibrio vulgaris.  suppl. material  PMC3366507

) Structure-based sequence alignment of the soluble C-terminal domains of D. vulgaris CcmE (dvCcmE′, residues 44−137), E. coli CcmE (ecCcmE′, residues 51−159), and S. putrefaciens CcmE (spCcmE′, residues 51−161).

19. Aziz, A.; Hess, J.F.; Budamagunta, M.S.; Voss, J.C.; Kuzin, A.P.; Huang, Y.J.; Xiao, R.; Montelione, G.T.; Fitzgerald, P.G.; Hunt, J.F. J Biol Chem 2012, 287: 28349 – 283461. The structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and x-ray crystallography.  PMC3436525

Schematic depiction of the central rod domain of vimentin with rod and linker domains indicated.

20. Cho, E.J.; Xia, S.; Ma, L.-C.; Robertus, J.; Krug, R.M.; Anslyn, E.V.; Montelione, G.T.; Ellington, A.D. J Biomol Screen 2012, 17: 448 – 459. Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay. 

 Schematic representation of the fluorescence polarization (FP)–based assay monitoring biological interaction.

21. Ramelot, T.A.; Rossi, P.; Forouhar, F,; Lee, H.-W.; Yang, Y.; Ni, S.; Unser, S.; Lew, S.; Seetharaman, J.; Xiao, R.; Acton, T.B.; Everett, J.K.; Prestegard, J.H.; Hunt, J.F.; Montelione, G.T.; Kennedy, M.A. Biochemistry 2012, 51: 7239 – 7249. Structure of a specialized acyl carrier protein essential for lipid A biosynthesis with very long chain fatty acids in open and closed conformations.  suppl. material  PMC4104962

The solution nuclear magnetic resonance (NMR) structures and backbone 15N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4′-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation.

22. Koga, N.; Tatsumi-Koga, R.; Liu, G.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Baker, D. Nature 2012, 491: 222 – 227. Principles for designing ideal protein structures.  supplmaterialPMC3705962

Derivation of secondary structure lengths from the rules for five
protein topologies.

23. Montelione, G.T. Faculty 1000 Commentary 2012, 4: 7. The Protein Structure Initiative: achievements and visions for the future.  PMC3318194

24. Lange, O.F.; Rossi, P.; Sgourakis, N.; Song, Y.; Lee, H.-W.; Aramini, J.M.; Ertekin, A.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Baker, D. Proc Natl Acad Sci USA 2012, 109: 10873 – 10878. The determination of solution structures of proteins up to 40 kDa using CS- Rosetta with sparse NMR data from deuterated samples. suppl. material.  PMC3390869

RASREC Rosetta results for maltose-binding protein.

25. Vorobiev, S.M.; Neely, H.; Yu, B.; Seetharaman, J.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Hunt, J.F. J Struct Funct Genomics 2012, 13: 177 – 183. Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product.  suppl. material  PMC3683829

Crystal structure of the diguanylate cyclase (DGC) domain
from M. aquaeolei protein A1U3W3. a Sequence alignment of the DGC domains of A1U3W3, PleD from C. crescentus, and WspR from P. aeruginosa by ClustalW

26. Aziz, A.; Hess, J.F.; Budamagunta, M.S.; Voss, J.C.; Kuzin, A.P.; Huang, Y.J.; Xiao, R.; Montelione, G.T.; Fitzgerald, P.G.; Hunt, J.F. J Biol Chem 2012, 287: 28349 – 283461. The structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and x-ray crystallography.  PMC3436525

Schematic depiction of the central rod domain of vimentin with rod and linker domains indicated.

27. Cho, E.J.; Xia, S.; Ma, L.-C.; Robertus, J.; Krug, R.M.; Anslyn, E.V.; Montelione, G.T.; Ellington, A.D. J Biomol Screen 2012, 17: 448 – 459. Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay.  PMC in process

Fluorescence characteristics of the fluorescence polarization (FP)–based binding assay

28. Koga, N.; Tatsumi-Koga, R.; Liu, G.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Baker, D. Nature 2012, 491: 222 – 227. Principles for designing ideal protein structures.  suppl. materialPMC3705962

 Comparison of computational models with experimentally determined structures.

29. Kim, D.; Zheng; H.; Huang, Y.J.; Montelione, G.T.; Hunt, J.F. J Amer Chem Soc 2012, 135: 2999 – 3010. ATPase active-site electrostatic interactions control the global conformation of the 100 kDa SecA translocase.  suppl. material  PMC4134686

SecA is an intensively studied mechanoenzyme that uses ATP hydrolysis to drive processive extrusion of secreted proteins through a protein-conducting channel in the cytoplasmic
membrane of eubacteria.

30. Richter, F.; Blomberg, R.; Khare, S.D.; Kiss, G.; Kuzin, A.P.; Smith, A.J.; Gallaher, J.L.; Pianowski, Z.; Helgeson, R.C.; Grjasnow, A.; Xiao, R.; Seetharaman, J.; Su, M.; Vorobiev, S.; Lew, S.; Forouhar, F.; Kornhaber, G.J.; Hunt, J.F.; Montelione, G.T.; Tong, L.; Houk, K.N.; Hilvert, D.; Baker, D. J Amer Chem Soc 2012, 135: 16197 – 16206. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.  suppl. material  PMC4104585

Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis

31. Eletsky, A.; Jeong, M-Y.; Kim, H.; Lee, H-W.; Xiao, R.; Pagliarini, D.J.; Prestegard, J.H.; Winge, D.R.; Montelione, G.T.; Szyperski, T. Biochemistry 2012, 51: 8475 – 8477. Solution NMR structure of yeast succinate dehydrogenase flavinylation factor Sdh5 reveals a putative Sdh1 binding site.  suppl. material  PMC3667956

 Sdh5 conformers after superposition of the Cα atoms of the helices. Residues 43-58 and 151-152 of the disordered N- and Cterminal polypeptide segments were omitted, and the termini are
labeled as “N” and “C”

2011

1. Vaiphei, S.T.; Tang, Y.; Montelione, G.T.; Inouye, M. Molecular Biotechnology 2011, 47: 205 – 210. The use of the condensed single protein production (cSPP) system for isotope- labeled outer membrane proteins, OmpA and OmpX in E. coli.  PMC4190416

Schematic diagram of pCold IV expression vector used for OMP expression.

2. You, L.; Cho, E.J.; Leavitt, J.; Ma, L.-C.; Montelione, G.T.; Anslyn, E.V.; Krug, R.M.; Ellington, A.; Robertus, J.D. Bioorg Med Chem Lett 2011, 21: 3007 – 3011. Synthesis and evaluation of quinoxaline derivatives as potential NS1A protein inhibitors.  suppl. material  PMC3114437

3. Schauder, C.; Ma, L.-C.; Krug, R.M.; Montelione, G.T.; Guan, R. Acta Cryst F. 2010, F66: 1567 – 1571. Structure of iSH2 domain of human phosphatidylinositol 3-kinase p85β subunit reveals conformational plasticity in the interhelical turn region.  PMC2998356

Overall structure of p85 iSH2 domain and comparison with other iSH2 domain
structures

4. Vorobiev, S.M.; Huang, Y.J.; Seetharaman, J.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L. Protein Peptide Letts 2011, 19: 194 – 197. Human retinoblastoma binding protein 9, a serine hydrolase implicated in pancreatic cancers.  PMC3677193

RBBP9 interacts with the Rb family members, including Rb, RBL1 (p107 in the text), and RBL2 (p130 in the text).

5. Acton, T.B.; Xiao, R.; Anderson, S.; Aramini, J.M.; Buchwald, W.; Ciccosanti, C.; Conover, K.; Everett, J.K.; Hamilton, K.; Huang, Y.J.; Janjua, H.; Kornhaber, G.J.; Lau, J.; Lee, D.Y.; Liu, G.; Maglaqui, M.; Ma, L.-C.; Mao, L.; Patel, D.; Rossi, P.; Sahdev, S.; Sharma, S.; Shastry, R.; Swapna, G.V.T.; Tang, Y.; Tong, S.N.; Wang, D.; Wang, H.; Zhao, L.; Montelione, G.T. Methods in Enzymology 2011, 493: 21 – 60. Preparation of protein samples for NMR structure, function, and small molecule screening studies.  PMC4110644

The NESG Disorder Prediction Server (DisMeta)

6. Mao, L.; Inoue, K.; Tao, Y.; Montelione, G.T.; McDermott, A.E.; Inouye, M. J Biomol NMR 2011, 49: 131 – 137. Suppression of phospholipid biosynthesis by cerulenin in the condensed Single-Protein- Production (cSPP) system.  PMC3164850

Cell growth blocked by cerulenin.

7. Ramelot, T.A.; Smola, M.J.; Lee, H.-W.; Ciccosanti, C.; Hamilton, K.; Acton, T.B.; Xiao, R.; Everett, J.K.; Prestegard, J.H.; Montelione, G.T.; Kennedy, M.A. Biochemistry 2011, 50: 1442 – 1453. Solution NMR structure of 4’-phosphopantetheine – GmACP3 from Geobacter metallireducens : a specialized acyl carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis.  suppl. material  PMC3063093

) ConSurf (54) images, front view (same orientation as A) and back view. Magenta is highly conserved and cyan is variable. All
structure figures in this paper were created with PyMol.

8. Yin, C.; Aramini, J.M.; Ma,L-C; Cort, J.R.; Swapna, G.V.T.; Krug, R.M.; Montelione, G.T. J Biomol NMR Assignments 2011, 5: 215 – 219. Backbone and Ile-δ1, Leu, Val methy 1H, 13C and 15N NMR chemical shift assignments for human interferon-stimulated gene 15 protein.  PMC3167004

Two dimensional 1
H-15N HSQC spectrum of 0.7 mM human [U2H,13C,15N]-ISG15 at 18C, pH 6.5 in 95% H2O/5% 2 H2O containing 50 mM ammonium citrate, 10 mM DTT, 5 mM CaCl2.

9. Karanicolas, J.; Corn, J.E.; Chen, I; Joachimiak, L.A.; Dym, O.; Peck, S.H.; Albeck, S.; Unger, T.; Hu, W.; Liu, G.; Delbecq, S.; Montelione, G.T.; Spiegel, C.P.; Liu, D.R.; Baker, D. Molecular Cell 2011, 42: 250 – 260. A de novo protein binding pair by computational design and directed evolution.  suppl. material  PMC3102007

 The Ankyrin Repeat protein (redesigned to become Pdar) is colored gray and its partner protein (redesigned from PH1109 to become Prb) is colored yellow. In (A), the surfaces of each protein are first matched by general shape complementarity and local docking. Promising rigid-body orientations are used in an
attempt to place a central hydrogen-bonding tyrosine or tryptophan motif, followed by local design to enforce hydrophobic packing around the motif.

10. Grant, T.; Luft, J.R.; Wolfley, J.R.; Tsuruta, H.; Martel, A.; Montelione, G.T.; Snell, E. Biopolymers 2011, 95: 517 – 530. Small angle x-ray scattering as a complementary tool for high-throughput structural studies.  PMC3124082

Structures of oligomers based on analysis of the SAXS data and known monomer structure. The ab initio SAXS-derived envelopes are shown assuming a monodisperse solution.

11. Sgourakis, N.G.; Lange, O.F.; DiMaio, F.; André, I.; Fitzkee, N.C.; Rossi, P.; Montelione, G.T.; Bax, A.; Baker, D. J Amer Chem Soc 2011, 133: 6288 – 6298. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.  suppl. material  PMC3080108

Symmetric protein dimers, trimers, and higher order cyclic oligomers play key roles in many biological processes

12. Barb, A.W.; Cort, J.R.; Seetharaman, J.; Lew, S.; Lee, H.W.; Acton, T.; Xiao, R.; Kennedy, M.A.; Tong, L.; Montelione, G.T.; Prestegard, J.H. Protein Science 2011, 20: 396 – 405. Structures of domains I and IV from YbbR are representative of a widely distributed protein family.  PMC3048424

Structures of Domain I and IV from the Ybbr family protein of Desulfitobacterium hafniense.

13. Chu, C.; Das, K.; Tyminski, J.R.; Bauman, J.D.; Guan, R.; Qiu, W.; Montelione, G.T.; Arnold, E.; Shatkin, A.J. Proc Natl Acad Sci USA 2011, 108: 10104 – 10108. Structure of the guanylyltransferase domain of human mRNA capping enzyme.  suppl. material  PMC3121809

Structure of the hGTase domain of hCE. hGTase has an ATP-grasp fold domain with two subdomains (green and blue) and an OB-fold domain
(orange).

14. Mao, B.; Guan, R.; Montelione, G.T. Structure (Cell Press) 2011, 19: 757 – 766. Improved technologies now routinely provide protein NMR structures useful for molecular replacement.  suppl. material  PMC3612016

15. Aramini, J. M.; Ma, L.-C.; Zhou, L.; Schauder, C. M.; Hamilton, K.; Amer, B.R.; Mack, T. R.; Lee, H.-W.; Ciccosanti, C. T.; Zhao, L.; Xiao, R.; Krug, R. M.; Montelione, G. T. J Biol Chem 2011, 286: 26050 – 26060. The dimer interface of the effector domain of non-structural protein 1 from influenza A virus: an interface with multiple functions.  suppl. material  PMC3138300

Solution NMR studies of [W187R]Ud and wild type Ud NS1A(85–215)

16. Aramini, J.M.; Rossi, P.; Fischer, M.; Xiao, R.; Acton, T.B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2011, 79: 2988 – 2991. Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic-acid binding function.  suppl. material  PMC3172673

 Superposition of the final ensemble of 20 conformers from the solution NMR structure of VF0530 (PDB ID, 2JVW).

17. Guan, R.; Ma, L.-C.; Leonard, P.G.; Amer, B.R.; Sridharan, H.; Zhao, C.; Krug, R.M.; Montelione, G.T. Proc Natl Acad Sci USA. 2011, 108: 13468 – 13473. Structural basis for the sequence-specific recognition of human ISG15 by the NS1 protein of influenza B virus.  suppl. material  PMC3158222

Each NS1B-NTR homodimer binds two ISG15 molecules. (A) Overview of
the ISG15: NS1B-NTR complex. The complex structure is a hetero-tetramer composed of two NS1B-NTR molecules (NS1B-NTR-A, green; NS1B-NTR-B, brown), which form an interwoven dimer, and two ISG15 molecules (ISG15-C, magenta;
ISG15-D, cyan).

18. Eletsky, A.; Ruyechan, W.T.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2011, 12: 159 – 166. Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25.  suppl. material  PMC3609412

a Ribbon diagrams of MED25(391–543) in blue and the SPOC domain of SHARP (1OW1) in orange after superposition of Ca atoms identified by DALI.

19. Forouhar, F.; Saadat, N.; Hussain, M.; Seetharaman, J.; Lee, I.; Janjua, H.; Xiao, R.; Shastry, R.; Acton, T.; Montelione, G.T.; Tong, L. Acta Cryst. F 2011, 67: 1323 – 1327. A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding.  PMC3212444

Crystal structure of the P. furiosus PF0828 homodimer

20. Lowery, J.; Szul, T.; Seetharaman, J.; Xiaoying, J.; Su, M.; Forouhar, F.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Lin, H.; Wright, J.W.; Lee, E.; Holloway, Z.G.; Randazzo, P.A.; Tong, L.; Sztul, E. J Biol Chem 2011, 286: 36898 – 36906. A novel C-terminal motif within the Sec7 domain of guanine nucleotide exchange factors regulates ARF binding and activation.  suppl. material.  PMC3196086

a schematic drawing of the Sec7 domain of human BIG2. The 10 α-helices are labeled A through J. D, overlay of the BIG 2 Sec7 domain (in green) and the complex of Gea1 Sec7 domain (in yellow) and ARF1 (in cyan).

21. Yang, Y.; Ramelot, T.A.; Cort, J.R.; Wang, D.; Ciccosanti, C.; Jiang, M.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Kennedy, M. J Struct Funct Genomics 2011, 12: 175 – 179. Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: First structure representative of the YapB domain family of proteins involved in spore coat assembly.  suppl. material  PMC3697068

Stereoview of the lowest energy conformer of the final NMR ensemble of the Dsy0195 homodimer (PDB ID: 2KYI). The C2
symmetry axis of Dsy0195 homodimer is indicated by as red dashed line and labeled C2.

22. Kryshtafovych, A.; Bartual, S.G.; Bazan, J.F.; Berman, H.; Casteel, D.E.; Christodoulou, E.; Everett, J.K.; Hausmann, J.; Heidebrecht, T.; Hills, T.; Hui, R.; Hunt, J.F.; Tong, L.; Seetharaman, J.; Joachimiak, A.; Kennedy, M.; Kim, C.; Lingel, A.; Michalska,K.; Montelione, G.T.; Otero, J.M.; Perrakis, A.; Pizarro, M.J.; van Raaij, M.J.; Ramelot, T.A.; Rousseau, F.; Weraimont, A.K.; Young, J.; Schwede, T. PROTEINS: Struct Funct Bioinformatics 2011, 79: S10: 6 – 20. Target highlights in CASP9: experimental target structures for the critical assessment of techniques from protein structure prediction.  PMC369200

A surface representation of the PKGIβ D/D domain is shown and colored according to its electrostatic potential (blue = electropositive, red = electronegative).

23. Feldmann, E.A.; Ramelot, T.A.; Yang, Y.; Xiao, R.; Acton, T.B.; Everett, J.K.; Montelione, G.T.; Kennedy, M.A. PROTEINS: Struct Funct Bioinformatics 2011, 80: 671 – 675. Solution NMR structure of Asl3597 from Nostoc sp. PCC7120, the first structure from protein domain family PF12095, adopts a novel fold. suppl. material PMC3315617

 Superposition of the final ensemble of 20 conformers from the solution NMR structure of Asl3597 (PDB ID, 2KRX).
2010

1. Singarapu, K.K.; Mills, J.; Xiao, R.; Acton, T.; Punta, M.; Fischer, M.; Honig, B.; Rost, B.; Montelione, G.T.; Szyperski, T. PROTEINS: Struct Funct Bioinformatics 2010, 78: 779 – 784. Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage from protein domain family PFAM 04175.  suppl. material  PMC2860719

NMR structures of proteins VPA0419 (residues 13–82; on the left) and
yiiS (residues 28–101; on the right).

2. Mao, L.; Vaiphei. S.T.; Shimazu, T.; Schneider, W.M.; Tang, Y.; Mani, R.; Roth, M.J.; Montelione, G.T.; Inouye, M. J Struct Funct Genomics 2010, 11: 81-84. The E. coli single protein production (cSPP) system for production and structural analysis of membrane proteins.  PMC4190415

A schematic model for the SPP system in E. coli. In the left panel, the regulatory mechanism for the MazE-MazF toxin-antitoxin (TA) system is shown.

3. Rossi, P.; Swapna, G.V.T.; Huang, Y.J.; Aramini, J.M.; Anklin, C.; Conover, K.; Hamilton, K.; Xiao, R.; Acton, T.B.; Ertekin, A.; Everett, J.K.; Montelione, G.T. J Biomol NMR 2010, 46: 11 – 22. A microscale protein NMR sample screening pipeline.  suppl. material  PMC2797623

1D 1H NMR spectra with H2O presaturation of representative NESG targets obtained with a 1.7-mm micro NMR cryoprobe

4. Raman, S.; Huang, Y.J.; Mao, B.; Rossi, P.; Aramini, J.M.; Liu, G.; Montelione, G.T.; Baker, D. J Amer Chem Soc 2010, 132: 202 – 207. Accurate automated protein NMR structure determination using unassigned NOESY data.  suppl. material  PMC2841443

Model generation from raw and refined peak lists with CYANA/AutoStructure and Rosetta for protein SR213.

5. Raman, S.; Lange, O.F.; Rossi, P.; Tyka, M.; Wang, X.; Aramini, J.; Liu, G.; Ramelot, T.; Eletsky, A.; Szyperski, T.; Kennedy, M.; Prestegard, J.; Montelione, G.T.; Baker, D. Science 2010, 327: 1014 – 1018. NMR structure determination for larger proteins using backbone-only data.  suppl. material  PMC2909653

 Ensemble of 10 lowest-energy Rosetta structures [below line in (A)].
Regions with more than 3 Å RMSF are depicted in gray.

6. Liu, G.; Huang, Y.J.; Xiao, R.; Wang, D.; Acton, T.B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2010, 78: 1326 – 1330. NMR structure F-actin binding domain of Arg/Ab12 from Homo sapiens.  suppl. material  PMC2821974

 Comparison of Arg FABD (green) and some other structures available in PDB:
1zvz (vinculin tail, magenta); 1dow (alpha-catenin, yellow), 1ktm (focal adhesion targeting domain of focal adhesion kinase, pink), 2b0h (talin-1, gray). All figures were prepared with the programs MOLMOL35 or PYMOL

7. Montelione, G.T.; Szyperski, T.; Curr Opin Drug Discovery 2010, 13: 335 – 349. Advances in protein NMR impacting drug discovery provided by the NIGMS Protein Structure Initiative.  PMC4002360

Cumulative PDB depositions of NESG NMR and X-ray crystal structures in each month of the PSI Program.

8. Arragain, S.; Garcia-Serres, R.; Blondin, G.; Douki, T.; Clemancey, M.; Latour, J-M.; Forouhar, F.; Neely, H.; Montelione, G.T.; Hunt, J.F.; Mulliez, E.; Fontecave, M.; Atta, M. J Biol Chem 2010, 285: 5792 – 5801. Post- translational modification of ribosomal proteins: Structural and functional characterization of RimO from Thermotoga maritima, a radical S- adenosylmethionine methylthiotransferase.  suppl. material  PMC282080

Mass spectrometric sequencing (MS2) unambiguously established that the methylthio group of compound 1 is located exclusively at the aspartate residue of the peptide

9. Aramini, J.M.; Tubbs, J.L.; Kanugula, S.; Rossi, P.; Ertekin, A.; Maglaqui, M.; Hamilton, K.; Ciccosanti, C.T.; Jiang, M.; Xiao, R.; Soong, T.- T.; Rost, B.; Acton, T.B.; Everett, J.K.; Pegg, A.E.; Tainer, J.A.; Montelione, G.T. J Biol Chem 2010, 285: 13736 – 13741. Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein.  suppl. material  PMC2859536

ConSurf
(28) image showing the conserved residues in the alkyl-binding site of vpAtl (same view as in B). Residue
coloring ranges from magenta (highly conserved) to cyan (variable) and reflects the degree of residue conservation across ATL sequences extracted from the entire O6
-alkylguanine-DNA methyltransferase protein domain family (PF01035, Pfam 23.0).

10. Arbing, M.A.; Handelman, S.K.; Kuzin, A.P.; Verdon, G.; Wang, C.; Su, M.; Rothenbacher, F.P.; Abashidze, M.; Liu, M.; Hurley, J.M.; Xiao, R.; Acton, T.; Inouye, M.; Montelione, G.T.; Woychik, N.A.; Hunt, J.F. Structure (Cell Press) 2010, 18: 996 – 1010. Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems.  suppl. material  Open access journal

Homologous Phd/YefM/NE2111 Antitoxins Neutralize Toxins with Disparate Folds

11. Price, W.N. 2nd; Handelman, S.K.; Everett, J.; Tong, S.N.; Bracic, A.; Luff, J.D.; Naumov, V.; Acton, T.; Manor, P.; Xiao, R.; Rost, B.; Montelione, G.T.; Hunt, J.F. Microbial Informatics and Experimentation 2011, 1: 6 – 26. Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. Coli.  suppl. material  PMC3372292

Distribution of proteins by expression level and solubility score

12. Nie, Y.; Xiao, R.; Xu, Y.; Montelione, G.T. Org Biomol Chem 2011, 9: 4070 – 4078. Novel anti-Prelog stereospecific carbonyl reductases from Candida parapsilosis for asymmetric reduction of prochiral ketones.  suppl. material  PMC4104987

Analysis of the overexpression of SCR1, SCR2, and SCR3. The proteins were separated on a 12% SDS-polyacrylamide gel and stained with Coomassie Brilliant Blue G-250.

13. Schneider, W.M.; Tang, Y.; Vaiphei, S.T.; Mao, L.; Maglaqui, M.; Inouye, M.; Roth, M.J.; Montelione, G.T. J Struct Funct Genomics 2010, 11: 143 – 154. Efficient condensed-phase production of perdeuterated soluble and membrane proteins.  suppl. material  PMC4119428

7 NMR spectra of E. coli membrane proteins YaiZ and OmpX

14. Liu, G.; Huang, Y.J.; Xiao, R.; Wang, D.; Acton, T.B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2010, 78: 2170 – 2175. Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: A human cancer protein interaction network target.  suppl. material  PMC2869213

Comparison of the ARID domain of human ARID3A (red) with drosophila ‘‘dead ringer’’ Dri in the presence of dsDNA (blue, PDB code 1kqq) and in the absence of dsDNA (green, PDB code 1c20) after superposition of backbone N, Ca, and C’ atoms of regular secondary structure elements for minimal RMSD.

15. Zhao, L.; Zhao, K.; Hurst, R.; Slater, M.; Acton, T.B., Swapna, G.V.T.; Shastry, R.; Kornhaber, G.J.; Montelione, G.T. J Struct Funct Genomics 2010, 11: 210 – 209. Engineering of a wheat germ expression system to provide compatibility with a high throughput pET-based cloning platform.  suppl. material  PMC2921493

Vector engineering schema illustrating the creation of the
plasmid pWGHisAmp from pTSHQn (Promega), and the NESG
modified pET15 vector. PCR and In-FushionTM ligation independent cloning methods were used to replace the ORF and HQ metal affinity tag in pTSHQn with the pET15 linker region and 6xHis metal affinity tag to generate pWGHisKan.

16. Lee, H-W.; Wylie, G.; Bansal, S.; Wang, X.; Barb, A.W.; Macnaughtan, M.A.; Ertekin, A.; Montelione, G.T.; Prestegard, J.H. Protein Science 2010, 19: 1673 – 1685. Three-dimensional structures of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping.  PMC2975131

The ensemble of 10 structures with the least distance violations showing the monomeric form of SeR13 calculated using XPLOR-NIH.

17. Stark, J.L.; Mercier, K.A.; Mueller, G.A.; Acton, T.B.; Xiao, R.; Montelione, G.T.; Powers, R. PROTEINS: Struct Funct Bioinformatics 2010, 78: 3328 – 3340. Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis.  PMC2976784

The NMR solution structure of B. subtilis protein YndB

18. Tang, Y.; Xiao, R.; Ciccosanti, C.; Janjua, H.; Lee, Y.L.; Everett, J.; Swapna, G.V.T.; Acton, T.B.; Rost, B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2010, 78: 2563 – 2568. Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG.  suppl. material  PMC2931792

. (H) the conserved basic cavities of the domain II of protein NusG from A. aeolicus (residue 50 - 133) and (I) Lin0431 protein from L. innocua (residue 39 to 127). Cavities generated by ProFunc36 are shown in red and ribbons are shown in gray

19. Xiao, R.; Anderson, S.; Aramini, J.M.; Belote, R.; Buchwald, W.; Ciccosanti, C.; Conover, K.; Everett, J.K.; Hamilton, K.; Huang, Y.J.; Janjua, H.; Jiang, M.; Kornhaber, G.J.; Lee, D.Y.; Locke, J.Y.; Ma, L.-C.; Maglaqui, M.; Mao, L.; Mitra, S.; Patel, D.; Rossi, P.; Sahdev, S.; Sharma, S.; Shastry, R.; Swapna, G.V.T.; Tong, S.N.; Wang, D.; Wang, H.; Zhao, L.; Montelione, G.T.; Acton, T.B. J Struct Biol 2010, 172: 21 – 33. The high- throughput protein sample production platform of the Northeast Structural Genomics Consortium.  PMC4110633

Protein Sample Production Platform currently used at the NESG.

20. Tang, Y.; Schneider, W.M.; Shen, Y.; Raman, S.; Inouye, M.; Baker, D.; Roth, M.J.; Montelione, G.T. J Struct Funct Genomics 2010, 11: 223 – 232. Fully automated high quality NMR structure determination of small 2H- enriched proteins.  PMC2970817

Stereoview of the superimposition of AutoStructure-CNS structure for [1H-13C]-I(d1)LV, 13C, 15N, 2 H-enriched CspA determined by conventional automated analysis methods (blue) with 1mjc
(red).

21. Yang, Y.; Ramelot, T.A.; Cort, J.R.; Wang, D.; Ciccosanti, C.; Hamilton, K.; Nair, R.; Rost, B.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Kennedy, M. PROTEINS: Struct Funct Bioinformatics 2011, 79: 340 – 344. Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. strain PCC 6803.  suppl. material 1  suppl. material 2  suppl. material 3  PMC3248274

A: Rainbow-colored superposition of Ca trace of 20 lowest energy
conformers of Psb28 (1–105).

22. Yang, Y.; Ramelot, T.A.; McCarrick, R.; Ni, S.; Feldmann, E.; Cort, J.R.; Wang, D.; Ciccosanti, C.; Jiang, M.; Janjua, H.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.; Kennedy, M. J Amer Chem Soc 2010, 132: 11910 – 11913. Combining NMR and EPR methods for homo-dimer protein structure determination. suppl. material. suppl. materialPMC3057626

Ribbon drawings of (A) average structure of Dsy0195 determined by combined NMR, PRE, and DEER constraints and (B) crystal structure

23. Love, J.; Mancia, F.; Shapiro, L.; Punta, M.; Rost, B.; Girvin, M.; Wang, D.-N.; Zhou, M.; Hunt, J.F.; Szyperski, T.; Gouaux, E.; MacKinnon, R.; McDermott, A.; Honig, B.; Inouye, M.; Montelione, G.T.; Hendrickson, W.A. J Struct Funct Genomics 2010, 11: 191 – 199. The New York Consortium on Membrane Structure (NYCOMPS): A high-throughput platform for structural genomics of integral membrane proteins.  PMC3099345

Coommassie blue stained SDS-PAGE showing expression and purification results of 22 different membrane proteins

24. Mani, R.; Vorobiev, S.; Swapna, G.V.T.; Neely, H.; Janjua, H.; Ciccosanti, C.; Xiao, R.; Acton, T.B.; Everett, J.K.; Hunt, J.F.; Montelione, G.T. J Struct Funct Genomics 2011, 12: 27 – 32. Solution NMR and X-ray crystal structures of membrane-associated lipoprotein-17 domain reveal a novel fold.  suppl. material  PMC3636556

Surface representation of the lipoprotein-17 domain of Q9PRA0_UREPA

25. Zhang, H.; Constantine, R.; Vorobiev, S.; Chen, Y. ;Seetharaman, J.; Huang, Y.J.; Xiao, R.; Montelione, G.T.; Gerstner, C.D.; Davis, M.W.; Inana, G.; Whitby, F.G.; Jorgensen, E.M.; Hill, C.P.; Tong, L.; Baehr, W. Nature Neuroscience2011, 14: 874 – 880. UNC119 is required for G protein trafficking in sensory neurons.  suppl. material  PMC3178889

26. Aramini, J.M.; Rossi, P.; Cort, J.; Ma, L.-C.; Xiao, R.; Acton, T.B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2011, 79: 335 – 339. Solution NMR structure of the plasmid-encoded fimbriae regulatory protein PefI from Salmonella enterica serovar Typhimurium.  suppl. material  PMC2995844

. (D) APBS9 electrostatic surface potential of stPefI showing negative (red), neutral (white), and positive (blue) charges. Selected basic residues are indicated. (E) ConSurf10 image showing the conserved residues in the wHTH motif of stPefI. Residue coloring, reflecting the degree of residue conservation over the entire FaeA-like protein domain family (PF04703, Pfam 24.0), ranges from magenta (highly conserved) to cyan (variable). (F) Overlay of the solution NMR structures of stPefI (red) and ecPapI (PDB ID, 2HTJ11; green).

27. Forouhar, F.; Lew, S.; Seetharaman, J.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L. Acta Cryst F 2010, F66: 1562 – 1566. Crystal structures of bacterial biosynthetic arginine decarboxylases.  PMC2998355

Protein domains

28. Montelione, G.T.; Szyperski, T. Advances in BioNMR Spectroscopy 2010, IOS Press, Editors A.J. Dingley and S.M. Pascal. Advances in NMR-based structural genomics spectroscopy.

2009

1. Vorobiev, S.M.; Su, M.; Seetharaman, J.; Huang, Y.J.; Chen, X.C.; Cunningham, K.; Maglaqui, M.; Owens, L.; Proudfoot, M.; Yakunin, A.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L. PROTEINS: Struct Funct Bioinformatics 2009, 74: 526 – 529. Crystal structure of human retinoblastoma binding protein 9 (RBBP9).  PMC2684859

Structure of RBBP9. A: Ribbon representation of the RBBP9 structure. The secondary structure is depicted as red (a-helixes), yellow (b-strands), and green (loops). The LxCxE residues are shown in magenta. B: The putative hydrolase active site of RBBP9. Molecular surface of RBBP9 is shown in green, and the catalytic triad Ser-His-Asp is shown as stick models.

2. Cort, J.R.; Ramelot, T.A.; Murray, D.; Acton, T.B.; Ma, L-C.; Xiao, R.; Montelione, G.T.; Kennedy, M.A. PROTEINS: Struct Funct Bioinformatics 2008, 9: 7 – 20. Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5- related N -acetyltransferase-like proteins. 

) Map of acetyl-CoA ligand-induced amide 1 H and 15N chemical shift perturbations

3. Ramelot, T.A.; Raman, S.; Kuzin, A.P.; Xiao, R.; Ma, L.-C.; Acton, T.B.; Hunt, J.F.; Montelione, G.T.; Baker, D.; Kennedy, M.A. PROTEINS: Struct Funct Bioinformatics 2008, 75: 147 – 167. Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study.  suppl. material  PMC2878636

 side chains for residues WYF. In all cases, the structures are superimposed on the X-ray structure shown with thick lines.

4. Rossi, P.; Aramini, J.M.; Xiao, R.; Chen, C.X.; Nwosu, C.; Owens, L.A.; Maglaqui, M.; Nair, R.; Fischer, M.; Acton, T.B.; Honig, B.; Rost, B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2009, 74: 515 – 519. Structural elucidation of the Cys-His-Glu-Asn proteoytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus.  suppl. material  PMC2735724

. (B) ConSurf images of SSP0609 for identical size and orientation as (A) ConSurf analysis was conducted for the entire CHAP protein domain family, standard ConSurf residue coloring
reflecting the degree of residue conservation over the entire family were used (color scheme: magenta, highly conserved; cyan, variable). (C) Electrostatic potential surface diagrams for SSP0609 shown in the same
orientation as (A) and (B).

5. Parish, D.; Benach, J.; Liu, G.; Singarapu, K.K.; Xiao, R.; Acton, T.; Su, M.; Bansal, S.; Prestegard, J.H.; Hunt, J.; Montelione, G.T.; Szyperski, T. J Struct Funct Genomics 2008, 9: 41 – 49. Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif.  PMC2850599

a Superposition of the 20 conformers representing the NMR solution structure of Q8ZP25_SALTY, b NMR structure of Q8ZP25_SALTY
(in orange) superimposed on the X-ray structure of Q8ZP25_SALTY (in grey), c ribbon drawing of the NMR
structure of HYAE_ECOLI

6. Price, W.N. 2nd; Chen, Y.; Handelman, S.K.; Neely, H.; Manor, P.; Karlin, R.; Nair, R.; Liu, R.; Baran, M.; Everett, J.; Tong, S.N.; Forouhar, F.; Swaminathan, S.S.; Acton, T.; Xiao, R.; Luft, J.R.; Lauricella, A.; DeTitta, G.T.; Rost, B.; Montelione, G.T.; Hunt, J.F. Nature Biotechnology 2009, 27: 51 – 57. Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data.  suppl. material  PMC2746436

Protein stability does not strongly influence success in crystalstructure solution. Denaturation experiments were performed on
biochemically well-behaved NESG proteins drawn from the set of 679 used in the data mining studies

7. Liu, G.; Forouhar, F.; Eletsky, A.; Atreya, H.S.; Aramini, J.M.; Xiao, R.; Huang, Y.J.; Abashidze, M.; Seetharaman, J.; Liu, J.; Rost, B.; Acton, T.; Montelione, G.T.; Hunt, J.F.; Szyperski, T. J Struct Funct Genomics 2009, 10: 127 – 136. NMR and X-ray structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquitination pathway.  PMC2850604

X-ray crystal structure of human Ufc1

8. Bertonati, C.; Punta, M.; Fischer, M.; Yachdav, G.; Forouhar, F.; Zhou, W.; Kuzin, A.P.; Seetharaman, J.; Abashidze, M.; Ramelot, T.A.; Kennedy, Rost, B. PROTEINS: Struct Funct Bioinformatics 2009, 75: 760 – 773. Structural genomics reveals EVE as a new ASCH/PUA-related domain.  suppl. material PMC4080787

PUA-like domain topologies. In blue and orange, we denote strands and helices, respectively. Insertions (INS0, INS1, and INS2) characteristic of specific domains are marked in red and additional strands (i.e. strands within insertions, namely 6 and 20) in lavender.

9. Nair, R.; Liu, J.; Soong, T-T.; Acton, T.B.; Everett, J.; Kouranov, A.; Fiser, A.; Godzik, A.; Jaroszewski, L.; Orengo, C.; Montelione, G.T.; Rost, B. J Struct Funct Genomics 2009, 10: 181 – 191. Structural genomics is the largest contributor of novel structural leverage.  PMC2705706

Per-structure estimates of novel leverage

10. Schwede, T.; Sali, A.; Honig, B.; Levitt, M.; Berman, H.M.; Jones, D.; Brenner, S.E.; Burley, S.K.; Das, R.; Dokholyan, N.V.; Dunbrack, R.L.; Fidelis, K.; Fiser, A. Godzik, A.; Huang, Y.J.; Humblet, C.; Jacobson, M.P.; Joachimiak, A.; Krystek, S.R. Jr.; Kortemme, T.; Kryshtafovych, A.; Montelione, G.T.; Moult, J.; Murray, D.; Sanchez, R.; Sosnick, T.R.; Standley, D.M.; Stouch, T.; Vajda, S.; Vasquez, M.; Westbrook, J.D.; Wilson, I.A. Structure (Cell Press) 2009, 17: 151 – 159. Outcome of workshop on applications of protein models in biomedical research.  PMC2739730

11. Montelione, G.T.; Arrowsmith, C.A.; Girvin, M.; Kennedy, M.A.; Markley, J.L. ; Powers, R.; Prestegard, J.H.; Szyperski, T. J Struct Funct Genomics 2009, 10: 101-106. Unique opportunities for NMR methods in structural genomics. PMC2705713.

MW distributions for protein NMR structures ([50 residues) determined by PSI groups and non SG groups in the same time period are similar.

12. Sharma, S.; Zheng, H.; Huang, Y.J.; Ertekin, A.; Hamuro, Y.; Rossi, P.; Tejero, R.; Acton, T.; Xiao, R.; Jiang, M.; Zhao, L.; Ma, L-C.; Swapna, G.V.T.; Aramini, J.M.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2009, 76: 882 – 894. Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry.  suppl. material  PMC2739808

NMR solution structures of full length (blue; PDB ID, 2HEP) and truncated (red; PDB ID, 2JVD) protein YnzC from B. subtilis (NESG targets SR384 and SR384-1–46, respectively)

13. Mao, L.; Tang, Y.; Vaiphei, T.; Shimazu, T.; Kim, S-G.; Mani, R.; Fakhoury, E.; White, E.; Montelione, G.T.; Inouye, M. J Struct Funct Genomics 2009, 10: 281 – 289. Production of membrane proteins for NMR studies using the condensed single protein (cSPP) production system.  suppl. material 1  suppl. material 2  PMC2923930

Schematic representation of the concept of SPP production of a membrane protein. Only a single targeted membrane protein
is produced, allowing specific enrichment with isotopes (e.g., 13C, 15N, etc.), as indicated in green

14. Eletsky, A.; Sukumaran, D.K.; Xiao, R.; Acton, T.; Rost, B.; Montelione, G.T.; Szyperski, T. PROTEINS: Struct Funct Bioinformatics 2009, 76: 1037 – 1041 NMR structure of protein YvyC from Bacillus subtilis reveals unexpected structural similarity between two PFAM families.  suppl. material  PMC2735722

Surface representation of the conformer with the lowest CYANA target function.

15. Schneider, W.M.; Inouye, M.; Montelione, G.T.; Roth, M.J. J Struct Funct Genomics 2009, 10: 219 – 225. Independently inducible system of gene expression for condensed single protein production (cSPP) suitable for high efficiency isotope enrichment.  PMC4898478

A pColdI(tet) vector map where the region shown in bold containing TEE (translation enhancing element), His Tag, and Factor Xa vary among the different pCold(tet) vectors

16. Rosato, A.; Bagaria, A.; Baker, D.; Bardiaux, B.; Cavalli, A.; Doreleijers, J.F.; Giachetti, A.; Guerry, P.; Güntert, P.; Herrmann, T.; Huang, Y.J.; Jonker, H.R.A.; Mao, B.; Malliavin, T.E.; Montelione, G.T.; Nilges, M.; Raman, S.; van der Schot, G.; Vranken, W.F.; Vuister, G.W.; Bonvin, A.M.J.J. Nature Methods 2009, 6: 625 – 626. CASD-NMR: Critical assessment of automated structure determination by NMR.  PMC2841015

Performance of various automated structure calculation methods.

17. Mercier, K.A.; Mueller, G.A.; Acton, T.B.; Xiao, R.; Montelione, G.T.; Powers, R. J Biomol NMR Assignments 2009, 3: 191 – 194. 1H, 13C, and 15N NMR assignments for the Bacillus subtilis yndB START domain.  PMC4991356

The 15N, 13Ca, and 13Cb chemical shift index

2008

1. Burley, S.K.; Joachimiak, A.; Montelione, G.T.; Wilson, I.A. Structure (Cell Press) 2008, 16: 5 – 11. Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI production centers.  PMC2678832

2. Singarapu, K.K.; Xiao, R.; Sukumaran, D.K.; Acton, T.; Montelione, G.T.; Szyperski, T. PROTEINS: Struct Funct Bioinformatics 2008, 70: 1650 – 1654. NMR structure of protein Cgl2762 from Corynebacterium glutamicum implicated in DNA transposition reveals a helix-turn-helix motif attached to a flexibly disordered leucine zipper.  suppl. material 

NMR structure of the HTH domain (1–50) of protein Cgl2762.

3. Gräslund,S.; Nordlund, P.; Weigelt, J.; Bray, J.; Gileadi, O.; Knapp, S.; Oppermann, U.; Arrowsmith, C.; Hui, R.; Ming, J.; Park, H-w.; Savchenko, A.; Yee, A.; Edwards, A.; Vincentelli, R.; Cambillau, C.; Kim, R.; Kim, S-H.; Rao, Z.; Shi, Y.; Terwilliger, T.C.; Kim, C-Y.; Hung, L-W.; Waldo, G.S.; Peleg, Y.; Albeck, S.; Unger, T.; Dym, O.; Prilusky, J.; Sussman, J.L.; Stevens, R.C.; Lesley, S.A.; Wilson, I.A.; Joachimiak, A.; Collart, F.; Dementieva, I.; Donnelly, M.I.; Eschenfeldt, W.H.; Kim, Y.; Stols, L.; Wu, R.; Zhou, M.; Burley, S.K.; Emtage, J S.; Sauder, J.M.; Thompson, D.; Bain, K.; Luz, J.; Gheyi, T.; Zhang, F.; Atwell, S.; Almo, S.C.; Bonanno, J.B.; Fiser, A.; Swaminathan, S.; Studier, F.W.; Chance, M.R.; Sali, A.; Acton, T.B.; Xiao, R.; Zhao, L.; Ma, L-C.; Hunt, J.F.; Tong, L.; Cunningham, K.; Inouye, M.; Anderson, S.; Janjua, H.; Shastry, R.; Ho, C.K.; D.; Wang, H.; Jiang, M.; Montelione, G.T.; Stuart, D.I.; Owens, R.J.; Daenke, S.; Schütz, A.; Heinemann, U.; Yokoyama, S.; Büssow, K.; Gunsalus, K.C. Nature Methods 2008, 5: 135 – 146. Protein production and purification.  PMC3178102

 Solubility as a function of construct length. Fraction of successful
purifications and structure determinations as a function of protein length (data from New York Structural GenomiX Research Center).

4. Singarapu, K.K.; Xiao, R.; Acton, T.; Rost, B.; Montelione, G.T.; Szyperski, T. PROTEINS: Struct Funct Bioinformatics 2008, 71: 1027 – 1031. NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors. 

NMR structure of the P. syringae PTH domain.

5. Aramini, J.M.; Sharma, S.; Huang, Y.J.; Swapna, G.V.T.; Ho, C.K.; Shetty, K.; Cunningham, K.; Ma, L-C.; Zhao, L.; Owens, L.A.; Jiang, M.; Xiao, R.; Liu, J.; Baran, M.C.; Acton, T.B.; Rost, B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2008, 72: 526 – 530. Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis.  suppl. material 

Electrostatic potential surface diagrams of the interhelical surfaces made by helix 1 and 2 in YnzC. For clarity, the unstructured C-terminal region of the protein has been omitted and only the structured residues (1–42) are shown. (E) ConSurf images of the same interhelical faces of
YnzC based on the multiple sequence alignment of the entire DUF896 (PF05979) protein domain family. Residue coloring, reflecting the degree of residue conservation
over the entire family, ranges from magenta (highly conserved) to cyan (variable)

6. Forouhar, F.; Abashidze, M.; Xu, H.; Grochowski, L.L.; Seetharaman, J.; Hussain, M.; Kuzin, A.; Chen, Y.; Zhou, W.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Galinier, A.; White, R.H.; Tong, L. J Biol Chem 2008, 17: 11832 – 11840. Molecular insights into the biosythesis of the F420 coenzyme.  PMC2431047

, schematic drawing of the interactions between GDP and CofD. C, overlay of the structure of the ternary complex with Fo and GDP (in purple) and that with Fo and Pi (in yellow). The Pi is located about 1 Å from the -phosphate of GDP, but there is a large difference in the conformation of the glycine-rich
loop, indicated with the red star.

7. Shen,Y.; Lange, O.; Delaglio, F.; Rossi, P.; Aramini, J.M.; Liu, G.; Eletsky, A.; Wu, Y.; Singarapu, K.K.; Lemak, A.; Ignatchenko, A.; Arrowsmith, C.H.; Szyperski, T.; Montelione, G.T.; Baker, D.; Bax, A. Proc Natl Acad Sci USA 2008, 105: 4685 – 4690. Consistent blind protein structure generation from NMR chemical shift data.  suppl. material  PMC2290745

Plots of ROSETTA all atom energy versus C rmsd relative to the experimental structures for four representative test proteins.

8. Huang, Y.J.; Hang, D.; Lu, L.J.; Tong, L.; Gerstein, M.B.; Montelione, G.T. Mol. Cell. Proteomics 2008, 7: 2048 – 2060. Targeting the human cancer pathway protein interaction network by structural genomics.  PMC2559933

Cross-talk between pathways. A, frequency of observing one protein in one or more of the seven KEGG signaling pathways. !20%
of HCPIN pathway proteins are associated with two or more pathways. B, frequency of observing one HCPIN protein in one or more of seven pathway interaction subnets.

9. Wu, B.; Yee, A.; Huang, Y.J.; Ramelot, T.A.; Cort, J.R.; Semesi, A.; Jung, J-W.; Lee, W.; Montelione, G.T.; Kennedy, M.A.; Arrowsmith, C.H. Protein Science 2008, 17: 583 – 588. The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: A structural homolog of the FF domain.  PMC2248302

(B) Ribbon representation of the lowest energy structure of S17E. (C) Stereoview of an ensemble of 15 refined structures represented in an orientation similar to B.

10. Das, K.; Ma, L-C.; Xiao, R.; Radvansky, B.; Aramini, J.; Zhao, L.; Marklund, J.; Kuo, R-L.; Twu, K.Y.; Arnold, E.; Krug, R.M.; Montelione, G.T. Proc Natl Acad Sci USA 2008, 105: 13092 – 13097. Structural basis for suppression by influenza A virus of a host antiviral response.  suppl. material  PMC2522260

C) F3-binding pocket on NS1A (85-215). A hydrophobic pocket on the NS1A surface binds to the F3 Zn finger of F2F3. Both
chains of NS1A in the head-to-head dimer interact with each F2F3 molecule. (D) Expanded view of the F3-binding pocket. The NS1A amino acid residues labeled in red interact with the aromatic side chains of residues Y97, F98, and F102 of the F3 Zn finger of F2F3.

11. Aramini, J.M.; Rossi, P.; Huang, Y.J.; Zhao, L.; Jiang, M.; Maglaqui, M.; Xiao, R.; Locke, J.; Nair, R.; Rost, B.; Acton, T.B.; Inouye, M.; Montelione, G.T. Biochemistry (Rapid Report) 2008, 47: 9715 – 9717. Solution NMR structure of the NIpC/P60 domain of lipoprotein Spr from Escherichia coli: Structural evidence for a novel cysteine peptidase catalytic triad.  suppl. material 

View into the active site of E. coli Spr[37-162] showing the conserved Cys-His-His catalytic triad and flanking tyrosine. Juxtaposed heavy atoms in the triad and secondary structural elements are labeled.

12. Vila, J.; Aramini, J.; Rossi, P.; Kuzin, A.; Su, M.; Seetharaman, J.; Xiao, R.; Tong, L.; Montelione, G.T.; Scheraga, H. Proc Natl Acad Sci USA 2008, 105: 14389 – 14394. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation.  suppl. material  PMC2567219

Ribbon diagrams of the superposition of 10 conformations obtained in Set-bt (A), the superposition of 20 conformations of 2JVD (B), and the x-ray structure (three monomers in the asymmetric unit) (C).

13. Vorobiev, S.M.; Su, M.; Seetharaman, J.; Huang, Y.J.; Chen, X.C.; Cunningham, K.; Maglaqui, M.; Owens, L.; Proudfoot, M.; Yakunin, A.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L. PROTEINS: Struct Funct Bioinformatics 2009, 74: 526 – 529. Crystal structure of human retinoblastoma binding protein 9 (RBBP9).  PMC2684859

Structure of RBBP9. A: Ribbon representation of the RBBP9 structure. The secondary structure is depicted as red (a-helixes), yellow (b-strands), and green (loops). The LxCxE residues are shown in magenta.

14. Cort, J.R.; Ramelot, T.A.; Murray, D.; Acton, T.B.; Ma, L-C.; Xiao, R.; Montelione, G.T.; Kennedy, M.A. PROTEINS: Struct Funct Bioinformatics 2008, 9: 7 – 20. Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5- related N -acetyltransferase-like proteins. 

Portion
of the space-filling model near the bound acetyl-CoA, which is colored as in Fig. 3a, but with hydrogen atoms shown. F77
atoms are shown in tan, and the sulfur of C75 is yellow. The
acetyl group of acetyl-CoA is just right of the sulfur; the CoA sulfur is orange

15. Ramelot, T.A.; Raman, S.; Kuzin, A.P.; Xiao, R.; Ma, L.-C.; Acton, T.B.; Hunt, J.F.; Montelione, G.T.; Baker, D.; Kennedy, M.A. PROTEINS: Struct Funct Bioinformatics 2008, 75: 147 – 167. Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study.  suppl. material  PMC2878636

B: Ribbon representation of X-ray structure of HSPC034, residues
4–139. The Ca12 ion is shown in yellow and a Sm13 ion in green. C: Backbone atoms for 20 NMR structures optimally superimposed with respect the N, Ca, and C0 coordinates of the X-ray structure residues 6–138. NMR residues 2–141 are shown. D: NOE violations indicated on X-ray structure. Red violations are >2 A˚ , orange are 1–2 A˚ , and yellow are 0.5–1 A˚ . Violations are not show for residues 1–3 and 140–141. Figures (B–D) were generated using PyMOL (DeLano Scientific)

16. Rossi, P.; Aramini, J.M.; Xiao, R.; Chen, C.X.; Nwosu, C.; Owens, L.A.; Maglaqui, M.; Nair, R.; Fischer, M.; Acton, T.B.; Honig, B.; Rost, B.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2009, 74: 515 – 519. Structural elucidation of the Cys-His-Glu-Asn proteoytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus.  suppl. material  PMC2735724

(A) Stereoview of the ribbon representation of the lowest energy
conformer (lowest CNS energy) from the ensemble of deposited
solution NMR structures of full length SSP0609 (PDB_ID: 2K3A). Only residues 50–155 are shown. The secondary structural elements are labeled and the triad sidechain residues (Cys57, His109, Glu126) are highlighted as red sticks. (B) ConSurf images of SSP0609 for identical
size and orientation as (A) ConSurf analysis was conducted for the entire CHAP protein domain family, standard ConSurf residue coloring reflecting the degree of residue conservation over the entire family were
used (color scheme: magenta, highly conserved; cyan, variable). (C) Electrostatic potential surface diagrams for SSP0609 shown in the same orientation as (A) and (B).

17. Parish, D.; Benach, J.; Liu, G.; Singarapu, K.K.; Xiao, R.; Acton, T.; Su, M.; Bansal, S.; Prestegard, J.H.; Hunt, J.; Montelione, G.T.; Szyperski, T. J Struct Funct.Genomics 2008, 9: 41 – 49. Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif.  PMC2850599

1 a Superposition of the 20 conformers representing the NMR solution structure of Q8ZP25_SALTY, b NMR structure of Q8ZP25_SALTY (in orange) superimposed on the X-ray structure of Q8ZP25_SALTY (in grey), c ribbon drawing of the NMR
structure of HYAE_ECOLI
2007

1. Mercier, K.A.; Baran, M.; Ramanathan, V.; Revesz, P.; Xiao, R.; Montelione, G.T.; Powers, R. J Amer Chem Soc 2006, 128: 15292 – 15299. FAST-NMR – Functional Annotation Screening Technology using NMR spectroscopy.  PMC2529462

(i) SAV1430-pTyr binding site to the (j) Src SH2 domain’s pTyr-peptide binding site (PDB ID:1004). The sequence alignment is shown below the structure where the aligned residues are colored blue. The pTyr and pTyr-peptide ligands are colored
yellow.

2. Bhattacharya, A.; Tejero, R.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2007, 66: 778 – 795. Evaluating protein structures determined by structural genomics consortia. 

MAR30

3. Forouhar, F.; Anderson, J.L.; Mowat, C.G.; Vorobiev, S.M.; Hussain, A.; Abashidze, M.; Bruckmann, C.; Thackray, S.J.; Seetharaman, J.; Tucker, T.; Xiao, R.; Ma, L.; Zhao, L.; Acton, T.B.; Montelione, G.T.; Chapman. S.K.; Tong, L. Proc Natl Acad Sci USA 2007, 104: 473 – 478. Molecular insights into substrate recognition and catalysis by tryptophan 2,3- dioxygenase.  suppl. material 

The structure of TDO.

4. Vorobiev, S.M.; Neely, H.; Seetharaman, J.; Ma, L.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L. Protein Science 2007, 16: 535 – 538. Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens.  PMC2203313

. (D) A close up of the heme binding site in Y. enterocolitica HemS (in green) and comparison with the equivalent region in AGR_C_4470p (in magenta). The proximal ligand in HemS does not have a counterpart in AGR_C_4470p.

5. Singarapu, K.K.; Liu, G.; Xiao, R.; Bertonati, C.; Honig, B.; Montelione, G. T.; Szyperski T. PROTEINS: Struct Funct Bioinformatics. 2007, 67: 501 – 504. NMR structure of protein yjbR from Escherichia coli reveals ‘double-wing’ DNA binding motif. 

(a) Model of the MotCF-DNA complex.22 Residues which are putatively mediating specific DNA binding (Lys 129, Lys 130, Tyr 134, Arg 135, Lys 144, Arg 145, Arg 150, Arg 161, Phe 163, Tyr 165, Lys 166, Lys 183, Lys 186, Tyr 191, Lys 195) are shown in yellow. (b) Ribbon drawing of the NMR structure of protein
yjbR in which conserved residues of the exposed b-sheet are highlighted.

6. Aramini, J.; Rossi, P.; Anklin, C.; Xiao, R.; Montelione, G.T. Nature Methods 2007, 4: 491 – 493. Microgram scale protein structure determination by NMR.  suppl. material 

Assessment of structural accuracy. (a,b) Backbone superimposition
(ordered residues in red; a) and ribbon diagrams of the solution structures of Q8PX65 solved using conventional (left) and microcoil-probe (right) data (b).
(c) Stereo view of the superimposition of the lowest energy conventional (blue) and microprobe (green) solution structures of Q8PX65.

7. Yin, C.; Khan, J.A.; Swapna, G.V.T.; Ertekin, A.; Krug, R.M.; Tong, L.; Montelione, G.T. J Biol Chem 2007, 282: 20584 – 20592. Conserved surface features form the double-stranded RNA-binding site of non-structural protein 1 (NS1) from Influenza A and B viruses.  suppl. material 

NMR chemical shift perturbation data for the NS1A-(1–73)dsRNA complex.

8. Aramini, J; Y. Huang, Y.J.; Swapna, G.V.T.; Cort, J.R.; Rajan, P.K.; Xiao, R.; Shastry, R.; Acton, T.B.; Liu, J.; Rost, B.; Kennedy, M.A.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2007, 68: 789 – 795. The solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family.  suppl. material 

Stereoview of the ribbon representation of a representative conformer (lowest CNS energy) from the ensemble generated using MOLMOL.5 The
secondary structural elements are labeled

9. Liu, J.; Montelione, G. T.; Rost, B. Nature Biotechology 2007, 25: 849 – 851. Novel leverage of structural genomics.  suppl. material 

10. Andrec, M.; Snyder, D. A.; Zhou, Z.; Young, J.; Montelione, G. T.; Levy, R. PROTEINS: Struct Funct Bioinformatics 2007, 69: 449 – 465. A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing.  suppl. material 

11. Lu, L.J.; Sboner, A.; Huang, Y. J.; Lu, H.X.; Gianoulis; T.A.; Yip, K.Y.; Kim, P.M.; Montelione, G.T.; Gerstein, M.B. TIBS 2007, 32: 320 – 331. Comparing classical pathways and modern networks: Towards the development of an edge ontology.  suppl. material 

12. Bhattacharya, A.; Wunderlich, Z.; Monleon, D.; Tejero, R.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2007, 70: 105 – 118. Assessing model accuracy using the homology modeling automatically (HOMA) software.  suppl. material 

13. Forouhar, F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Yong, W.; Janjua, H.; Fang, Y.; Wang, D.; Cunningham, K.; Xiao, R.; Acton, T.B.; Pichersky, E.; Klessig, D.F.; Porter, C.W.; Montelione, G.T.; Tong, L. J Struct Funct Genomics 2007, 8: 37 – 44. Functional insights from structural genomics. 

14. Benach, J.; Wang, L.; Chen, Y.; Ho, C.K.; Lee, S.; Seetharaman, J.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Deng, H.; Sun, R.; Tong, L. J Biol Chem 2007, 43: 31534 – 31541. Structural and functional studies of the abundant tegument protein ORF52 from murine gammaherpesvirus-68. 

. C, molecular surface of the ORF52 tetramer, in the same view as A, colored by electrostatic potentials. D, molecular surface of the ORF52 tetramer in the same view as B. E, conserved molecular surface features of the ORF52 tetramer. A, B, and E created with Pymol (44), and C and D were created with Grasp (45).
2006

1. Liu, G.; Shen, Y.; Xiao, R.; Acton, T.; Ma, L.; Joachimiak, A.; Montelione, G.T.; Szyperski, T. PROTEINS: Struct Funct Bioinformatics 2006, 62: 288 – 291. NMR structure of protein yqbG from Bacillus subtilis reveals a novel α-helical protein fold.

2. Baran, M.; Moseley, H.N.B.; Aramini, J.M.; Bayro, M.J.; Monleon, D.; Locke, J.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2006, 62: 843 – 851. SPINS: A laboratory information management system for organizing and archiving intermediate and final results from NMR protein structure determinations.  suppl. material 

3. Forouhar. F.; Hussain, M.; Farid, R.; Benach, J.; Abashidze, M.; Edstrom, W.C.; Vorobiev, S.M.; Xiao, R.; Acton, T.B.; Fu, Z.; Kim, J.; Miziorko, H.M.; Montelione, G.T.; Hunt, J.F. J Biol Chem 2006, 281: 7533 – 45. Crystal structures of two bacterial 3-hydroxy- 3methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM-barrel metalloenzymes cleaving carbon-carbon bonds.

4. Kornhaber, G.J.; Snyder, D.; Moseley, H.N.B.; Montelione, G.T. J Biomol NMR 2006, 34: 259 – 269. Identification of zinc-ligated cysteine residues based on 13Cα and 13Cβ chemical shift data. 

5. Berman, H.M.; Burley, S.K.; Chiu, W.; Sali, A.; Adzhubei, A.; Bourne, P.E.; Bryant, S.H.; Dunbrack, Jr., R.L.; Fidelis, K.; Frank, J.; Godzik, A.; Henrick, K.; Joachimiak, A.; Heymann, B.; Jones, D.; Markley, J.L.; Moult, J.; Montelione, G.T.; Orengo, C.; Rossman, M.T.; Rost, B.; Saibil, H.; Schwede, T.; Standley, D.M.; Westbrook, J.D. Structure (Cell Press) 2006, 14: 1211 – 1217. Outcome of a workshop on archiving structural models of biological macromolecules. 

6. Greenfield, N.J.; Huang, Y.J.; Swapna, G.V.T.; Bhattacharya, A.; Rapp, B.; Singh, A.; Montelione, G.T.; Hitchcock-DeGregori, S.E. J Mol Biol 2006, 364: 80 – 96. Solution NMR structure of the junction between tropomyosin molecules: Implications for actin binding and regulation.  suppl. material 

7. Mercier, K.A.; Baran, M.; Ramanathan, V.; Revesz, P.; Xiao, R.; Montelione, G.T.; Powers, R. J Amer Chem Soc 2006, 128: 15292 – 15299. FAST-NMR – Functional Annotation Screening Technology using NMR spectroscopy.  PMC2529462

(c) Chemical structure of O-phospho-L-tyrosine shown to bind SAV1430. (d) Illustration of the use of the NMR-defined ligand binding site to direct a protein-ligand co-structure determination with AutoDock.20 SAV1430 surface where residues that incur a chemical shift change are colored blue. (e) GRASP33 electropotential surface where positive and negative regions are blue and red, respectively. (f) NMR-based ligand-defined SAV1430 binding site where residues that incur a chemical shift change upon binding pTyr are colored blue. (g) Mapping of functionally conserved residues (colored blue) identified
by ConSurf22 on the SAV1430 surface. (h) Molecular model of SAV1430-SE0630 (structural homologue of SAV0936) complex determined by Hex.42 SE0630 is shown as a ribbon. Sequence and structural alignment of (i) SAV1430-pTyr binding site to the (j) Src SH2 domain’s pTyr-peptide binding site (PDB ID:
1004). The sequence alignment is shown below the structure where the aligned residues are colored blue. The pTyr and pTyr-peptide ligands are colored yellow.
2005

1. Huang, Y.J.; Moseley, H.N.B.; Baran, M.C.; Arrowsmith, C.; Powers, R.; Tejero, R.; Szyperski, T.; Montelione, G.T. Methods in Enzymology 2005, 394: 111 – 141. An integrated platform for automated analysis of protein NMR structures. 

2. Acton, T.B.; Gunsalus, K.C.; Xiao, R.; Ma, L-C.; Aramini, J.M.; Baran, M.C.; Chiang, Y-W.; Climent, T.; Cooper, B.; Denissova, N.; Douglas, S.M; Everett, J.K.; Ho, C.K.; Macapagal, D.; Rajan, P.K.; Shastry, R.; Shih, L-Y.; Swapna, G.V.T.; Wilson, M.; Wu, M.; Gerstein, M.; Inouye, M.; Hunt, J.F.; Montelione, G.T. Methods in Enzymology 2005, 394: 210 – 243. Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium. 

3. Shen, Y.; Goldsmith-Fischman, S.; Atreya, H.S.; Acton, T.B.; Ma, L-C.; Xiao, R.; Honig, B.; Montelione, G.T.; Szyperski, T.  PROTEINS: Struct. Funct. Bioinformatics 2005, 58: 747 – 750.  NMR structure of the 18 kDa protein CC1736 from Caulobacter crescentus identifies a member of the “START” domain superfamily and suggests residues mediating substrate specificity. 

4. Snyder, D.A.;  Montelione, G.T.  PROTEINS: Struct Funct Bioinformatics 2005, 59: 673 – 686.  Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles.

5. Huang, Y.J.; Powers, R.; Montelione, G.T. J. Amer Chem Soc 2005, 127: 1665 – 1674. Protein NMR Recall, Precision, and F-measure scores (RPF Scores): Structure quality assessment measures based on information retrieval statistics.  suppl. material 

6. Liu, G.; Li, Z.; Chiang, Y.; Acton, T.B.; Montelione, G.T.; Murray, D.; Szyperski, T.  Protein Science 2005, 14:1597 – 1608. High-quality homology derived from NMR and X-ray structures of E. coli. proteins YgdK and SufE suggest that all members of the YgdK/SufE protein family are enhancers of cysteine desulfurases.  PMC2253389

7. Forouhar, F.; Yang, Y.; Kumar, D.; Chen, Y.; Fridman, E.; Park, S.W.; Chiang, Y.; Acton, T.B.; Montelione, G.T.; Pichersky, E.; Klessig, D.F.; Tong, L. Proc Natl Acad Sci USA 2005, 102: 1773 – 1778. Structure and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity.  suppl. material  PMC547883

8. Liu, G.; Shen, Y.; Atreya, H.S.; Parish, D.; Shao, Y.; Sukumaran, D.K.; Xiao, R.; Yee, A.; Lemak, A.; Bhattacharya, A.; Acton, T.B.; Arrowsmith, C.H.; Montelione, G.T.; Szyperski, T.  Proc Natl Acad Sci USA  2005, 102: 10487 – 10492.  NMR data collection and analysis protocol for high-throughput protein structure determinationsuppl. material  PMC1180791

9. Douglas, S.M.; Montelione, G.T.; Gerstein, M.  Genome Biology 2005, 6:R80.  PubNet: A flexible system for visualizing literature-derived networks.  PMC1242215

10. Huang, Y-J.; Tejero, R.; Powers, R.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2006 62: 587 – 603. A topology- constrained distance network algorithm for protein structure determination from NOESY datasuppl. material 

11. Snyder, D.A.; Bhattacharya, A.; Huang, Y.J.; Montelione, G.T. PROTEINS: Struct Funct Bioinformatics 2005, 59: 655 – 661. Assessing precision and accuracy of protein structures derived from NMR data.  suppl. material 

12. Snyder, D.A.; Chen, Y.; Denissova, N.G.; Acton, T.; Aramini, J.M.; Ciano, M.; Karlin, R.; Liu, J.; Manor, P.; Rajan, P.A.; Rossi, P.; Swapna, G.V.T.; Xiao, R.; Rost, B.; Hunt, J.; Montelione, G.T. J Amer Chem Soc 2005, 127: 16505 – 16511. Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and x-ray crystallography are complementary methods for small protein structure determination.  suppl. material 

13. Benach, J.; Edstrom, W.C.; Lee, I.; Das, K.; Cooper, B.; Xiao, R.; Liu, J.; Rost, B.; Acton, T.B.; Montelione, G.T.; Hunt, J.F. Acta Cryst D: Biol Cryst 2005, D61: 589 – 598. The 2.35 Å structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism. 

14. Rossi, P; Ramelot, T.; Xiao, R.; Ho, C.K.; Ma, L.; Acton, T.B.; Kennedy, M.A.; Montelione, G.T. J Biomol NMR 2005, 33: 197. 1H, 13C, 15N resonance assignments for the protein coded by gene locus BB0938 of Bordetella bronchiseptica.

15. Aramini, J. M.; Swapna, G.V.T.; Huang, Y.J.; Rajan, P.K.; Xiao, R.; Shastry, R.; Acton, T.B.; Cort, J.R.; Kennedy, M.A.; Montelione, G.T. J Biomol NMR 2005, 33: 197. 1H, 13C, 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family.

16. Liu, G.; Aramini, J.; Atreya, H.S.; Eletsky, A.; Xiao, R.; Acton, T.B.; Ma, L-C.; Montelione, G.T., Szyperski, T. J Biomol NMR 2005, 32: 261. Letter to the Editor: GFT NMR based resonance assignment for the 21 kDa human protein UFC1.  suppl. material 

17. Forouhar, F.; Lee, I.-S.; Vujcic, J.; Vujcic, S.; Shen, J.; Vorobiev, S.M.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Porter, C.W.; Tong, L. J Biol Chem 2005, 280: 40328 – 40336. Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase (SSAT).

18. Bachhawat, P.; Swapna, G.V.T.; Montelione, G.T.; Stock, A.M. Structure (Cell Press). 2005, 13: 1353 – 1363. Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states. PMC3685586

19. Powers, R.; Mirkovic, N.; Goldsmith-Fischman, S.; Acton, T.B.; Chiang, Y.; Huang, Y.J.; Ma, L.; Rajan, R.K.; Cort, J.R.; Kennedy, M.A.; Liu, J.; Rost, B.; Honig, B.; Murray, D.; Montelione, G.T. Protein Science 2005, 14: 2849 – 2861. Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria and eukaryotesPMC2253226

20. Huang, Y.J.; Montelione, G.T. Nature 2005, 438: 36 – 37. News and Views: Proteins flex to function. 

The intrinsic
dynamics of a protein are fundamental to its structure and contribute to how it works. The double arrows indicate interconverting states, with the larger arrows showing the direction that is most favoured energetically. Percentages give rough populations for each state.
2004

1. Monleon, D.; Chiang, Y.; Aramini, J.M.; Swapna, G.V.T.; Macapagal, D.; Gunsalus, K.C.; Kim, S.; Szyperski, T; Montelione, G.T.  J. Biomol. NMR 2004, 28: 91 – 92.  Backbone 1H, 15N and 13C assignments for the 21 kDa Caenorhabditis elegans homologue of ‘brain-specific’ protein. 

2. Zheng, D.; Aramini, J.; Montelione, G.T.  Protein Science  2004, 13: 549 – 554.  Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.  PMC2286702

3. Goh, C.-S.; Lan, N.; Douglas, S.M.; Wu, B.; Echols, N.; Smith, A.; Milburn, D.; Montelione, G.T.; Zhao, H.; Gerstein, M.   J. Mol. Biol. 2004, 336: 115 – 130.  Mining the structural genomics pipeline: Identification and analysis of protein properties that affect high-throughput experimental analysis. 

4. Chien, C.-Y.; Xu, Y.; Xiao, R.; Aramini, J.M.; Sahasrabudhe, P.V.; Krug, R.M.; Montelione, G.T.  Biochemistry 2004, 43: 1950 – 1962.  Biophysical characterization of the complex between double-stranded RNA and the N-terminal domain of the NS1 protein from Influenza A virus: Evidence for a novel RNA-binding mode. 

5. Moseley, H.N.B.; Sahota, G.; Montelione, G.T.  J. Biomol. NMR 2004, 28: 341 – 355.  Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. 

6. Das, K.; Acton, T.B.; Chiang, Y.; Shih, L.; Arnold, E.; Montelione, G.T. Proc. Natl. Acad. Sci. U.S.A.  2004, 101: 4041 – 4046.  Crystal structure of E. coli RlmAI: Implications for understanding 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.  PMC384692

7. Liu, G.; Sukumaran, D.K.; Xu, D.; Chiang, Y.; Acton, T.B.Goldsmith- Fischman, S.; Honig, B.; Montelione, G.T.; Szyperski, T.  PROTEINS: Struct. Funct. Genetics  2004, 55: 756 – 758.  NMR structure of the hypothetical protein NMA1147  from Neisseria meningitidis reveals a distinct 5-helix bundle. 

8. Herve Du Penhoat, C.; Atreya, H.S.; Shen Y.; Liu, G.; Acton, T.B.; Xiao, R.; Li, Z.; Murray, D.; Montelione, G.T.; Szyperski, T., Protein Sci. 2004, 13: 1407 – 1416.  The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold.  PMC2286747

9. Xu, D.; Liu, G.; Xiao, R.; Acton, T.; Goldsmith-Fischman, S.; Honig, B.; Montelione, G.T.; Szyperski, T.  PROTEINS: Struct. Funct. Genetics  2004, 54: 794 – 796.  NMR structure of the hypothetical protein AQ- 1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold. 

10. Forouhar, F.; Lee, I-S.; Benach, J.; Kulkarni, K.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L.  J. Biol. Chem.  2004, 279: 13148 – 13155.  A novel NAD binding protein revealed by the crystal structure of E. coli 2,3-diketogulonate reductase (YiaK).

11. Makokha, M.; Huang, Y.J.; Montelione, G.T.; Edison, A.S.; Barbar, E.  Protein Science   2004, 13: 727 – 734.  The solution structure of the pH-induced monomer of dynein light-chain LC8 from Drosophila.  PMC2286742

12. Everett, J.K.; Acton, T.B.; Montelione, G.T.  J. Struct. Funct. Genomics  2004, 5: 13 – 21.  Primer Prim’ər: A web based server for automated primer design.

13. Adams, M.; Joachimiak, A.; Kim, R.; Montelione, G.T.; Norvell, J.  J. Struct. Funct. Genomics 2004, 5: 1 – 2.  2003 NIH protein structure initiative workshop in protein production and crystallization for structural and functional genomics (Meeting Review). 

14. Wunderlich, Z.; Acton, T.B.; Liu, J.; Kornhaber, G.; Everett, J.; Carter, P.; Lan, N.; Echols, N.; Gerstein, M.; Rost, B.; Montelione, G.T.  PROTEINS: Struct. Funct. Bioinformatics  2004, 56: 181 – 187.  The protein target list of the Northeast Structural Genomics Consortium. 

15. Shen, Y.; Atreya, H.S.; Xiao, R.; Acton, T.B.; Shastry, R.; Ma, L.; Montelione, G.T.; Szyperski, T.  J. Biomol. NMR 2004, 29: 549 – 550.  Resonance assignments for the 18kDa protein CC1736 from Caulobacter crescentus. 

16. Liu, J.; Hegyi, H.; Acton, T.B.; Montelione, G.T.; Rost, B.   PROTEINS: Struct. Funct. Bioinformatics 2004, 56: 188 – 200.  Automatic target selection for structural genomics on eukaryotes. 

17. Qing, G; Ma, L.-C.; Khorchid, A; Swapna, G. V. T.;  Mal, T.K.; Takayama, M.M.; Xia, B.; Phadtare, S.; Ke, H.; Acton, T.; Montelione, G.T.; Ikura, M.; Inouye, M.   Nature Biotechnology 2004, 22: 877 – 882. Cold-shock induced high-yield protein production in Escherichia coli.  suppl. material 

18. Baran, M.C.; Huang, Y.J.; Moseley, H.N.; Montelione, G.T.  Chemical Reviews  2004, 104: 3451 – 3556.  Automated analysis of protein NMR assignments and structures.

19. Moseley, H.N.B.; Riaz, N.; Aramini, J.M.; Szyperski, T.; Montelione,  G.T.  J. Magn. Reson. 2004, 170: 263-277.  A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra.

20. Powers. R.; Acton, T.B.; Chiang, Y.; Rajan, P.K.; Cort, J.R.; Kennedy, M.A.; Liu, J.; Ma, L.-C.; Rost, B.; Montelione, G.T.  J. Biomol. NMR  2004, 30: 107-108.  1H, 13C, and 15N assignments for the Archaeglobus fulgidis protein AF2095. 

21. Ramelot, T.A.; Cort, J.R.; Goldsmith-Fischman,S.; Kornhaber, G.J.  Xiao, R.; Shastry, R.; Acton, T.B.; Honig, B.; Montelione, G.T.; Kennedy, M.A.  J. Mol. Biol.  2004, 344: 567-583.  Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site.

22. Goldsmith-Fischman, S.; Kuzin, A.; Edstrom, W.C.; Benach, J.; Shastry, R.; Xiao, R.; Acton, T.B.; Honig, B.; Montelione, G.T.; Hunt, J.F. J. Mol. Biol.  2004, 344: 549 – 565.  The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexes.

The structure of E. coli SufE. A, MOLSCRIPT/Raster3D75,76 stereo ribbon diagram of the E. coli SufE crystal structure.
2003

1. Lan, N.; Montelione, G.T.; Gerstein, M.  Curr. Opin. Chem. Biol. 2003, 7: 44 – 54.  Ontologies for proteomics – Towards a systematic definition  of structure and function that scales to the genome level.

2. Yuan, E.; Aramini, J.M.; Montelione, G.T.; Krug, R. M.  Virology 2002, 304: 291 – 301. Structural basis for ubiquitin-like ISG 15 protein binding to the NS1 protein of influenza B virus: A protein–protein interaction function that is not shared by the corresponding N-terminal domain of the NS1 protein of influenza A virus.

3. Greenfield, N.J.; Swapna, G.V.T.; Huang, Y.; Palm, T.; Graboski, S.; Montelione, G.T.; Hitchcock-DeGregori, S.E.  Biochemistry 2003, 42: 614 – 619.  The structure of the carboxyl terminus of striated α-tropomysosin in solution reveals an unusual parallel arrangement of interacting α-helices. 

4. Huang, Y.P.; Swapna, G.V.T.; Rajan, P.K.; Ke, H.; Xia, B.; Shukla, K.; Inouye, M.; Montelione, G. T.  J. Molec. Biol. 2003, 327: 521 – 536.  Solution NMR structure of ribosome binding factor A (RbfA), A cold-shock adaptation protein from Escherichia coli.  suppl. material 

5. Gerstein, M.; Edwards, A.; Arrowsmith, C.; Montelione, G.T.  Science 2003, 299: 1663. Structural Genomics: Current progress 

6. Zheng, D.; Huang, Y.J.; Moseley, H.N.B.; Xiao, R.; Aramini, J.; Swapna, G.V.T.; Montelione, G.T.  Protein Science  2003, 12: 1232 – 1246.  Automated protein fold determination using a minimal NMR constraint strategy.  PMC2323888

7. Zheng, D.; Cort, J.R.; Chiang, Y.; Acton, T.; Kennedy, M.A.; Montelione, G.T.  J. Biomol. NMR  2003, 27: 183 – 184.  1H, 13C and 15N resonance assignments for methionine sulfoxide reductase B from Bacillus subtilis. 

8. Goh, C.-S.; Lan, N.; Echols, N.; Douglas, S.; Milburn, D.; Bertone, P.; Xiao, R.; Ma, L.-C.; Zheng, D.; Wunderlich, Z.; Acton, T. ; Montelione, G.T.; Gerstein, M.  Nucleic Acids Res.  2003, 31: 2833 – 2838.  SPINE 2: A system for collaborative structural proteomics within a federated database frameworkPMC156730

9. Bayro, M.J.; Mukhopadhyay, J.; Swapna, G.V.T.; Huang, J.Y.; Ma, L.-C.; Sineva, E.; Dawson, P.; Montelione, G.T.; Ebright, R.H.  J. Amer. Chem. Soc. 2003, 125: 12382 – 12383.  Structure of antibacterial peptide microcin J25: A 21-residue lariat protoknot.  suppl. material 

10. Forouhar, F.; Shen, J.; Xiao, R.; Acton, T.B.; Montelione, G.T.; Tong, L.  PROTEINS: Struct. Funct. Genetics 2003, 53: 329 – 332.  Functional assignment based on structural analysis: The yggJ protein (HI0303) of Haemophilus influenzae is an RNA methyltransferase with a deep trefoil knot. 

11. Li, W.; Zhang, Y.; Kihara, D.; Huang, Y.J.; Zheng, D.; Montelione, G.T.; Kolinski, A.; Skolnick, J.  PROTEINS: Struct. Funct. Genetics  2003, 53: 290 – 306.  TOUCHSTONEX: Protein structure prediction with sparse NMR data. 

12. Aramini, J.M.; Mills, J.L.; Xiao, R.; Acton, T.B.; Wu, M.J.; Szyperski, T. Montelione, G.T.  J. Biomol. NMR  2003, 27: 285 – 286.  Resonance assignments for the hypothetical protein yggU from Escherichia coli. 

13. Benach, J.; Lee, I.; Edstrom, W.C.; Kuzin, A.; Chiang, Y.; Acton, T.B.; Montelione, G.T.; Hunt, J.F.  J. Biol. Chem.  2003, 278: 19176 – 19182.  The 2.3 Å crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from E. coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase.

14. Aramini, J.M.; Huang, Y.J.; Cort, J.R.; Goldsmith-Fischman, S.; Xiao, R.; Shih, L.-Y.; Ho, C.K.; Liu, J.; Rost, B.; Honig, B.; Kennedy, M.A.; Acton, T.B.; Montelione, G.T.  Protein Science 2003, 12: 2823 – 2830.  Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. PMC2366990

Electrostatic potential surfaces (Nicholls et al. 1991) showing the “positive” (blue) and “negative” (red) faces of S28E.
2002

1. McFeeters, R.L.; Swapna, G.V.T.; Montelione, G.T.; Oswald, R.E.  J. Biomol. NMR  2002, 22: 297 – 298.  Semi- automated backbone resonance assignments of the extracellular ligand-binding domain of an ionotropic glutamate receptor. 

2. Chen, J.; Acton, T.B.; Basu, S.K.; Montelione, G.T.; Inouye, M.  J. Molec. Microbiol. Biotech.  2002, 4: 519 – 524.  Enhancement of the solubility of proteins overexpressed in Escherichia coli by heat shock. 

3. Monleón, D.; Colson, K.; Moseley, H.N.B.; Anklin, C.; Oswald, R.; Szyperski, T.; Montelione, G.T.  J. Struct. Funct. Genomics 2002, 2: 93 – 101.  Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools. 

4. Mueller, L.; Montelione, G.T.  J. Struct. Funct. Genomics 2002, 2: 67 – 70.  Structural genomics in pharmaceutical design (Meeting Review). 

5. Szyperski, T.; Yeh, D.C.; Sukumaran, D.K.; Moseley, H.N.B.; Montelione, G.T.  Proc. Natl. Acad. Sci. 2002, 99: 8009 – 8014.  Reduced- dimensionality NMR spectroscopy for high-throughput protein resonance assignment.  suppl. material  PMC123011

6. Cort, J.R.; Chiang, Y.; Zheng, D.; Montelione, G.T.; Kennedy, M.A.  PROTEINS: Struct. Funct. Genetics 2002, 48, 733 – 736.  NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: A ubiquitin-like fold. 

7. Kennedy, M.A.; Montelione, G.T.; Arrowsmith, C.H.; Markley, J.L.  J. Struct. Funct. Genomics 2002, 2: 155 – 169.  Role for NMR in structural genomics. 

8. Baran, M.; Moseley, H.N.B.; Sahota, G.; Montelione, G.T.  J. Biomol. NMR 2002, 24: 113 – 121.  SPINS: Standardized ProteINMR Storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.  suppl. material 

9. Lan, N.; Montelione, G.T.; Gerstein, M.  Curr. Opin. Chem. Biol. 2003, 7: 44 – 54.  Ontologies for proteomics – Towards a systematic definition  of structure and function that scales to the genome level.

10. Yuan, E.; Aramini, J.M.; Montelione, G.T.; Krug, R. M.  Virology 2002, 304: 291 – 301. Structural basis for ubiquitin-like ISG 15 protein binding to the NS1 protein of influenza B virus: A protein–protein interaction function that is not shared by the corresponding N-terminal domain of the NS1 protein of influenza A virus.

Loop 1/1', but not loop 2/2' or R50/R53, comprises part of the ISG15
protein-binding site. GST-ISG15 (1 g) was added to each of the following 35S-labeled NS1B(1-103) proteins: wild-type (Lane 1), loop 1/1' mutant (Lane 2), loop 2/2' mutant (Lane 3), or the 50/53 mutant (40,000 cpm each).
2001

1. Moseley, H.N.B.; Monleon, D.; Montelione, G.T. Meth. Enzymology 2001, 339: 91 – 108. Automatic determination of protein backbone resonance assignments from triple-resonance NMR data. 

2. Sahasrabudhe, P.V.; Xiao, R.; Montelione, G.T. J. Biomol. NMR  2001, 19: 285 – 286.  Resonance assignments for the N-terminal domain from human RNA-binding protein with multiple splicing (RBP-MS). 

3. Bertone, P.; Kluger, Y.; Lan, N.; Zheng, D.; Christendat, D.; Yee, A.; Edwards, A.M.; Arrowsmith, C.H.; Montelione, G.T.; Gerstein, M.  Nucleic Acids Res. 2001, 29: 2884 – 2898.  SPINE: An integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.  PMC55760

4. Kulikowski, C.A.; Muchnik, I.; Yun, H.J.; Dayanik, A.A.; Zheng, D.; Song, Y.; and Montelione, G.T.  MedInfo 2001 – 10th World Congress on Health and Medicinal Informatics 2001, 965 – 969.  Protein structural domain parsing by consensus reasoning over multiple knowledge sources and methods. 

5. Greenfield, N.J.; Huang, Y.; Palm, T.; Swapna, G.V.T.; Monleon, D.; Montelione, G.T.; Hitchcock-DeGregori, S.E. J. Mol. Biol.  2001, 312: 833 – 847.  Solution NMR structure and folding dynamics of the N-terminus of a rat non-muscle α-tropomyosin in an engineered chimeric protein.  suppl. material 

6. Das, K.; Xiao, R.; Wahlberg, E.; Hsu, F.; Arrowsmith, C.A.; Montelione, G.T.; Arnold, E.  PROTEINS: Struct. Func. Genetics 2001, 45: 486 – 488.  X-ray crystal structure of MTH938 from Methanobacterium thermoautotrophicum at 2.2 Å resolution reveals a novel tertiary protein fold.

7. Montelione, G.T.  Proc. Natl. Acad. Sci. U.S.A. 2001, 98: 13488 – 13489.  Structural genomics: An approach to the protein folding problem.  PMC61067

8. Swapna, G.V.T.; Shukla, K.; Huang, Y.J.; Ke, H.; Xia, B.; Inouye, M.; Montelione, G.T.  J. Biomol. NMR  2001, 21: 389 – 390.  Resonance assignments for cold-shock protein ribosome-binding factor A (RbfA) for Escherichia coli. 

9. Cassetti, M.C.; Noah, D.L.; Montelione; G.T.; Krug, R.M.  Virology 2001, 289: 180 – 185.  Efficient translation of mRNAs in Influenza A virus-infected cells is independent of the viral 5′ untranslated region. 

Influenza virus infection does not inhibit the translation of vaccinia virus specific mRNAs
2000

1. Xiong, Y.; Juminaga, D.; Swapna, G. V. T.; Wedemayer, W. J.; Scheraga, H. A.; Montelione, G. T.  Protein Science 2000, 9: 421 – 426. Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A.  PMC2144552

2. McDermott, A.; Polenova, T.; Bockmann, A.; Zilm, K.W.; Paulson, E.K.;Martin, R.W.; Montelione, G. T. J. Biomol. NMR 2000, 16: 209 – 219. Partial NMR resonance assignments of uniformly (13C,15N)-labeled BPTI in the solid state. 

3. Montelione, G.T. & Anderson, S. The Investigational Drugs Database (IDdb) March 15, 2000.  Quantitative challenges in the post-genomic sequence era.

4. Andrec, M.; Inman, K. G.; Weber, D. J.; Levy, R. M.; Montelione, G. T.  J. Magn. Reson. 2000, 146: 66 – 80. A Bayesian statistical method for the detection and qualification of rotational diffusion anistropy from NMR relaxational data. 

5. Andrec, M.; Montelione, G.T.; and Levy, R.  J. Biomol. NMR 2000, 18: 83 – 100.  Lipari-Szabo mapping: A graphical approach to Lipari-Szabo analysis of NMR relaxation data using reduced spectral density mapping. (pdf)

6. Montelione, G.T.; Zheng, D.; Huang, Y.J.; Gunsalus, K.C; Szyperski, T.  Nature Struct. Biol. 2000, 7: 982 – 985. Protein NMR spectroscopy in structural genomics.

1999

1. Montelione, G. T. and Anderson, S. Nature Struct. Biol. 1999, 6: 11 – 12. Structural genomics: Keystone for a human proteome project.

2. Wang, W.; Riedel, K.; Lynch, P.; Chien, C.-Y.; Montelione, G. T.; and Krug, R. M. RNA 1999, 5: 195 – 205. RNA-binding by the novel helical domain of the Influenza virus NS1 protein requires its dimer structure and a small number of specific basic amino acids.  PMC1369752

3. Swapna, G.V.T.; Montelione, G.T. J. Magn. Reson. 1999, 137: 437 – 442. Sensitivity-enhanced Sim-CT HMQC PFG-HBHA(CO)NH and PFG-CBCA(CO)NH triple-resonance experiments. 

4. Andrec, M.; Montelione, G. T.; Levy, R. M. J. Magn. Reson. 1999, 139: 408 – 421. Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo Model-free approach and Bayesian statistical methods. (pdf)

5. Moseley, H. N. B. and Montelione, G. T.  Curr. Opin. Struct. Biol. 1999, 9: 635 – 642.  Automated analysis of NMR assignments and structures for proteins. 

6. Tejero, R.; Monleon, D.; Celda, B.; Montelione, G.T. J. Biomol. NMR 1999, 15: 251 – 264. HYPER: A hierarchical algorithm for automatic determination of protein dihedral-angle constraints and stereospecific C βH2 resonance assignments from NMR data. 

7. Laity, J. H.; Montelione, G. T.; Scheraga, H. A. Biochemistry 1999, 38: 16432 – 16442.  Comparison of local and global stability of an analogue of a disulfide-folding intermediate with those of the wild-type protein in bovine pancreatic ribonuclease A: Identification of specific regions of stable structure along the oxidative folding pathway.  suppl. material 

8. Montelione, G.T.; Rios, C.B.; Swapna, G.V.T.; Zimmerman, D.E. in Berliner and N.R. Krishna, Eds. 1999, Biological Magnetic Resonance, v 17: Structural Computation and Dynamics in Protein NMR, pp. 81 – 130. NMR pulse sequences and computational approaches for automated analysis of sequence- specific backbone resonance assignments in proteins. ‘

1998

1. Sahasrabudhe, P. V.; Tejero, R.; Kitao, S.; Furuichi, Y.; Montelione, G. T. PROTEINS: Struct. Funct. Genetics 1998, 33: 558 – 566. Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments. 

2. Feng, W.; Tejero, R.; Zimmerman, D.E.; Inouye, M.; Montelione, G.T. Biochemistry 1998, 37: 10881 – 10896. Solution NMR structure and backbone dynamics of the major cold shock protein (CspA) from Escherichia coli Evidence for conformational dynamics in the ssRNA- binding site.  suppl. material 

3. Greenfield, N. J.; Montelione, G. T.; Farid, R. S.; Hitchcock-DeGregori, S. E. Biochemistry 1998, 37: 7834 – 7843. The structure of the N-terminus of striated muscle α-tropomyosin in a chimeric peptide: Solution NMR structure and circular dichroism studies.  suppl. material 

4. Mullenbach, G. T.; Chiu, C. Y.; Gyenes, A.; Blaney, J.; Rosenberg, S.; Marlowe, C. K.; Brown, S.; Stratton-Thomas, J.; Montelione, G. T.; George- Nascimento, C.; Stauber, G.  Protein Engineering 1998, 11: 473 – 480. Modification of a receptor-binding surface of epidermal growth factor (EGF): Analogs with enhanced receptor affinity at low pH or at neutrality.

5. Jin, D.; Andrec, M.; Montelione, G. T.; Levy, R. M. J. Biomol. NMR 1998, 12: 471 – 492. Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics. 

6. Kulikowski, C.A.; Zimmerman, D.; Montelione, G.T.; Anderson, S. Stud. Health Technol. Inform. 1998, 52 Pt. 1: 365-366.  Structural- functional bioinformatics: Knowledge-based NMR interpretation. 

1997

1. Swapna, G.V.T.; Ríos, C.B.; Shang, Z.; Montelione, G.T. J. Biomol. NMR 1997, 9: 105 – 111. Application of multiple-quantum line narrowing with simultaneous 1H and 13C constant-time scalar- coupling evolution in PFG-HACANH and PFG-HACA(CO)NH triple-resonance experiments.

2. Li, H.; Tejero, R.; Monleon, D.; Bassolino-Klimas, D.; Abate-Shen, C.; Bruccoleri, R.E.; Montelione, G.T.  Protein Science 1997, 6: 956 – 970. Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three-dimensional structure of murine homeodomain Msx-1.  PMC2143703

3. Zimmerman, D.E.; Kulikowski, C.A.; Huang, Y.; Feng, W.; Tashiro, M.; Shimotakahara, S.; Chien, C-Y.; Powers, R.; Montelione G.T. J. Mol. Biol. 1997, 269: 592 – 610. Automated analysis of protein NMR assignments using methods from artificial intelligence. 

4. Shimotakahara, S.; Ríos, C.B.; Laity, J.H.; Zimmerman, D.E.; Scheraga, H.A.; Montelione, G.T. Biochemistry 1997, 36 : 6915 – 6929.  NMR structural analysis of an analog of an intermediate formed in the rate-determining step of one pathway in the oxidative folding of bovine pancreatic ribonuclease A: Automated analysis of 1H, 13C, and 15N resonance assignments for wild-type and [C65S, C72S] mutant forms.  suppl. material 

5. Laity, J.H.; Lester, C.; Shimotakahara, S.; Zimmerman, D.E.; Montelione, G.T.; Scheraga, H.A. Biochemistry 1997, 36: 12683 – 12699. Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A.  suppl. material 

6. Shang, Z.; Swapna, G.V.T.; Ríos, C.B.; Montelione, G.T. J. Am. Chem. Soc. 1997, 119: 9274 – 9278. Sensitivity enhancement of triple-resonance protein NMR spectra by proton evolution of multiple-quantum coherences using a simultaneous 1H and 13C constant-time evolution period.

7. Tashiro, M.; Tejero, R.; Zimmerman, D.E.; Celda, B.; Nilsson, B.; Montelione, G.T. J. Mol. Biol. 1997, 272: 573 – 590. High resolution solution NMR structure of the Z domain of staphylococcal protein A.

8. Chien, C.-Y.; Tejero, R.; Huang, Y.; Zimmerman, D.E.; Krug, R.M.; Montelione, G.T.  Nature Struct. Biol. 1997, 4: 891 – 895.  A novel RNA-binding motif in influenza A virus non-structural protein 1. 

9. Liu, J.; Lynch, P.; Chien, C.-Y; Montelione, G.T.; Krug, R.M.; Berman, H. Nature Struct. Biol. 1997, 4: 896 – 899. Crystal structure of the unique RNA- binding domain of the influenza virus NS1 protein.

10. Jin, D.; Figueirido, F.; Montelione, G.T.; Levy, R.M. J. Am. Chem. Soc. 1997, 119: 6923 – 6924. Impact of the precision in NMR relaxation measurements on the interpretation of protein dynamics.

1996

1. Jendeberg, L.; Tashiro, M.; Tejero, R.; Lyons, B.A.; Uhlén, M.; Montelione, G.T.; Nilsson, B. Biochemistry 1996, 35: 22 – 31. The mechanism of binding staphylococcal protein A to immunoglobulin G does not involve helix unwinding. 

2. Jansson, M.; Li, Y.-C.; Jendeberg, L.; Anderson, S.; Montelione, G.T.; Nilsson, B. J. Biomol. NMR 1996, 7: 131 – 141. High- level production of uniformly 15N-and 13C-enriched fusion proteins in Escherichia coli. 

3. Bassolino-Klimas, D.; Tejero, R.; Krystek, S.R.; Metzler, W.J.; Montelione, G.T.; Bruccoleri, R.E.  Protein Science 1996, 5: 593 – 603. Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints.  PMC2143380

4. Tejero, R.; Bassolino-Klimas, D.; Bruccoleri, R.E.; Montelione, G.T.  Protein Science 1996, 5: 578 – 592. Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type-α transforming growth factors.  PMC2143379

5. Feng, W.; Ríos, C.B.; Montelione, G. T. J. Biomol. NMR 1996, 8: 98 – 104. Phase labeling of C-H and C-C spin-system topologies: Applications in PFG-HACANH and PFG-HACA(CO)NH triple-resonance experiments for determining backbone resonance assignments in proteins.

6. Ríos, C.B.; Feng, W.; Tashiro, M.; Shang, Z.; Montelione, G.T. J. Biomol. NMR 1996, 8: 345 – 350. Phase labeling of C-H and C-C spin system topologies: Application in constant-time PFG-CBCA(CO)NH experiments for discriminating amino-acid spin-system types.

1995

1. Tashiro, M.; Montelione, G. T. Current Opin. In Struct. Biol. 1995, 5: 471 – 481. Structures of bacterial immunoglobulin-binding domains and their complexes with immunoglobulins.

2. Zimmerman, D.E.; Montelione, G. T. Current Opin. in Struct. Biol. 1995, 5: 664 – 673. Automated analysis of nuclear magnetic resonance assignments for proteins.

3. Celda, B.; Biamonti, C.; Arnau, M. J.; Tejero, R.; Montelione, G.T. J. Biomol. NMR 1995, 5: 161 – 172. Combined use of 13C chemical shift and 1Hα13Cα heteronuclear NOE data in monitoring a protein NMR structure refinement.

4. Li, Y.-C.; Montelione, G. T. Biochemistry 1995, 34: 2408 – 2423. Human type- α transforming growth factor undergoes slow conformational exchange between multiple backbone conformations as characterized by 15N relaxation measurements. 

5. Tashiro, M.; Ríos, C. B., Montelione, G. T. J. Biomol. NMR 1995, 6: 211 – 216.  Classification of amino acid spin systems using PFG HCC(CO)NH-TOCSY with constant-time aliphatic carbon-13 frequency labeling.

6. Fadel, A. R.; Jin, D. Q.; Montelione, G. T.; Levy, R. M. J. Biomol. NMR 1995, 6: 221 – 226. Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor.

7. Qian, X.-Y.; Chien, C.-Y.; Lu, Y.; Montelione, G.T.; Krug, R.M. RNA 1995, 1: 948 – 956. An amino-terminal polypeptide fragment of the influenza virus NS1 protein possesses specific RNA-binding activity and largely helical backbone structure.  PMC1369343

1994

1. Campion, S.R.; Biamonti, C.; Montelione, G.T.; Niyogi, S.K. Protein Engineering 1993, 6: 651 – 659. The role of asparagine-32 in forming the receptor-binding epitope of human epidermal growth factor. (featured on cover of August 1994 issue of Protein Engineering).

2. Lyons, B.A.; Tashiro, M; Cedergren, L., Nilsson, B.; Montelione, G.T. Biochemistry 1993, 32: 7839 – 7845.  An improved strategy for determining resonance assignments for isotopically enriched proteins and its application on an engineered domain of staphylococcal Protein A.

3. Li, Y.-C.; Montelione, G.T. J. Magn. Reson. 1993, B101: 315 – 319. Solvent saturation-transfer effects in pulsed-field-gradient heteronuclear single- quantum coherence (PFG-HSQC) spectra of polypeptides and proteins. (pdf)

4. Zimmerman, D.; Kulikowski, C.; Montelione, G.T. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1993, 1: 447 – 455. A constraint reasoning system for automating sequence-specific resonance assignments in multidimensional protein NMR spectra.

5. Zimmerman, D.; Kulikowski, C.; Wang, L.; Lyons, B.; Montelione, G.T. J. Biomol. NMR 1994, 4: 241 – 256. Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence.

6. Li, Y.-C.; Montelione, G.T. J. Magn. Reson. 1994, 105: 45 – 51. Overcoming solvent saturation-transfer artifacts in protein NMR at neutral pH: Application of pulsed-field gradients in measurements of1H- 15N Overhauser effects.

7. Newkirk, K.; Feng, W.; Jiang, W.; Tejero, R.; Emerson, S.D.; Inouye, M.; Montelione, G.T. Proc. Natl. Acad. Sci. U.S.A. 1994, 91: 5114 – 5118. Solution NMR structure of the major cold-shock protein (CspA) from Escherichia coli : Identification of a binding epitope for DNA.  PMC43942

8. Shang, Z.; Isaac, V.E.; Li, H.; Patel, L.; Catron, K.M.; Curran, T.; Montelione, G.T.; Abate, C. Proc. Natl. Acad. Sci. U.S.A. 1994, 91: 8373 – 8377. Design of a “minimA1” homeodomain: the N- terminal arm modulates DNA binding affinity and stabilizes homeodomain structure.  PMC44608

9. Biamonti, C.; Ríos, C. B.; Lyons, B.A.; Montelione, G.T. Advances in Biophysical Chemistry 1994, 4: 51 – 120. Multidimensional NMR experiments and analysis techniques for determining homo- and heteronuclear scalar coupling constants in proteins and nucleic acids. 

1993

1. Lyons, B.A.; Montelione, G.T. J. Magn. Reson. 1993, B101: 206 – 209. An HCCNH triple-resonance experiment using carbon-13 isotropic mixing for correlating backbone amide and side-chain aliphatic resonances in isotopically enriched proteins.

2. Celda, B.; Montelione, G.T. J. Magn. Reson. 1993, B101: 189 – 193. Total correlation spectroscopy (TOCSY) of proteins using coaddition of spectra recorded with several mixing times.

3. Moy, F.J.; Li, Y.-C.; Rauenbuehler, P; Winkler, M.E.; Scheraga, H.A.; Montelione, G.T. Biochemistry 1993, 32: 7334 – 7353. Solution structure of human type-α transforming growth factor determined by heteronuclear NMR spectroscopy and refined by energy minimization with restraints.  suppl. material 

4. Campion, S.R.; Biamonti, C.; Montelione, G.T.; Niyogi, S.K. Protein Engineering 1993, 6: 651 – 659. The role of asparagine-32 in forming the receptor-binding epitope of human epidermal growth factor. (featured on cover of August 1994 issue of Protein Engineering).

5. Lyons, B.A.; Tashiro, M; Cedergren, L., Nilsson, B.; Montelione, G.T. Biochemistry 1993, 32: 7839 – 7845.  An improved strategy for determining resonance assignments for isotopically enriched proteins and its application on an engineered domain of staphylococcal Protein A.

6. Li, Y.-C.; Montelione, G.T. J. Magn. Reson. 1993, B101: 315 – 319. Solvent saturation-transfer effects in pulsed-field-gradient heteronuclear single- quantum coherence (PFG-HSQC) spectra of polypeptides and proteins.

7. Zimmerman, D.; Kulikowski, C.; Montelione, G.T. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1993, 1: 447 – 455. A constraint reasoning system for automating sequence-specific resonance assignments in multidimensional protein NMR spectra.

1992

1. Montelione, G.T.; Wüthrich, K.; Burgess, A.W.; Nice, E.C.; Wagner, G.; Gibson, K.D.; Scheraga, H.A. Biochemistry 1992, 31: 236 – 249. Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints. 

2. Emerson, S.D.; Montelione, G.T. J. Amer. Chem. Soc. 1992, 114: 354 – 356. Accurate measurements of proton scalar coupling constants using carbon-13 isotropic mixing spectroscopy. 

3. Montelione, G.T.; Emerson, S.D.; Lyons, B.A. Biopolymers 1992, 32: 327 – 334. A general approach for determining scalar coupling constants in polypeptides and proteins.

4. Moy, F.J.; Scheraga, H.A.; Patt, S.L.; Montelione, G.T. J. Magn. Reson. 1992, 98: 451 – 457. Application of frequency-shifted shaped pulses for overcoming solvent-saturation transfer and pre-irradiation associated spin-diffusion effects in aqueous solutions of polypeptides and proteins. 

5. Emerson, S.D.; Montelione, G.T. J. Magn. Reson. 1992, 99: 413 – 420. 2D and 3D HCCH TOCSY experiments for determining 3J(Hα-Hβ) coupling constants of amino acid residues. 

6. Montelione, G.T.; Lyons, B.A.; Emerson, S.D.; Tashiro, M. J. Amer. Chem. Soc. 1992, 114: 10974 – 10975. An efficient triple resonance experiment using carbon-13 isotropic mixing for determining sequence-specific resonance assignments of isotopically enriched proteins. (pdf) suppl. material 

1990

1. Wagner, G.; Nirmala, N.R.; Montelione, G.T.; Hyberts, S. “Frontiers of NMR in Molecular Biology” pp. 129 – 143.  1990. A.R. Liss, Inc., New York, NY. Static and dynamic aspects of protein structure. 

2. Montelione, G.T.; Wagner, G. J. Magn. Reson. 1990, 87: 183 – 188. Conformation-independent sequential NMR connections in isotope-enriched polypeptides by 1H-13C- 15N triple-resonance experiments. 

3. Engler, D.A.; Montelione, G.T.; Niyogi, S.K. FEBS Lett. 1990, 271: 47 – 50. Human epidermal growth factor: Distinct roles of Tyr-37 and Arg-41 in receptor binding as determined by site-directed mutagenesis and nuclear magnetic resonance spectroscopy. 

1989

1. Montelione, G.T.; Winkler, M.E.; Burton, L.E.;Rinderknecht, E.; Sporn, M.B.; Wagner, G. Proc. Natl. Acad. Sci. U.S.A. 1989, 86: 1519 – 1523. Sequence-specific 1H-NMR assignments and identification of two small anti-parallel β-sheets in the solution structure of recombinant human transforming growth factor-α.  PMC286729

2. Montelione, G.T.; Wagner, G. J. Amer. Chem. Soc. 1989, 111: 3096 – 3098. 2D chemical exchange NMR spectroscopy by proton-detected heteronuclear correlation. 

3. Montelione, G.T.; Winkler, M.; Rauenbuehler, P.; Wagner,G. J. Magn. Reson. 1989, 82: 198 – 204. Accurate measurements of long-range heteronuclear coupling constants from homonuclear 2D NMR spectra of isotope- enriched proteins. 

4. Montelione, G.T.; Wagner, G. J. Amer. Chem. Soc. 1989, 111: 5474 – 5475. Accurate measurements of homonuclear HN-Hα coupling constants in polypeptides using heteronuclear 2D NMR experiments. (pdf)

5. Moy, F.J.; Scheraga, H.A.; Liu, J.-F.; Wu, R.; Montelione, G.T. Proc. Natl. Acad. Sci. U.S.A. 1989, 86: 9836 – 9840. Conformational characterization of a single-site mutant of murine epidermal growth factor (EGF) by 1H-NMR provides evidence that leucine-47 is involved in interactions with the EGF receptor.  PMC298597

6. Montelione, G.T.; Scheraga, H.A.  Accts. Chem. Research 1989, 22: 70 – 76. Formation of local structures in protein folding. 

1988

1. Montelione, G.T.; Wüthrich, K.; Scheraga, H.A. Biochemistry 1988, 27: 2235 – 2243. Sequence-specific 1H-NMR assignments and identification of slowly exchanging amide protons in murine epidermal growth factor. suppl. material 

2. Ray, P.; Moy, F.; Montelione, G.T.; Liu, J.-F.; Narang, S.A.; Scheraga, H.A.; Wu, R. Biochemistry 1988, 27: 7289 – 7295. Structure- function studies of murine epidermal growth factor: Expression and site- directed mutagenesis of the epidermal growth factor gene. 

1986

1. Stimson, E.R.; Meinwald, Y.C.; Montelione, G.T.; Scheraga, H.A. Intl. J. Peptide Protein Res. 1986, 27: 569 – 582. Conformational properties of trans Ac- Asn-Pro-Tyr-NHMe and trans Ac-Tyr-Pro-Asn-NHMe in dimethylsulfoxide and in water determined by multinuclear NMR spectroscopy. 

2. Montelione, G.T.; Hughes, P.; Clardy, J.; Scheraga, H.A. J. Amer. Chem. Soc. 1986, 108: 6765 – 6773. Conformational properties of 2,4-methanoproline (2-carboxy-2,4-methanopyrrolidine) in peptides: Determination of preferred peptide bond conformations in aqueous solution by proton Overhauser measurements.

3. Montelione, G.T.; Wüthrich, K.; Nice, E.C.; Burgess, A.W.; Scheraga, H.A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83: 8594 – 8598. Identification of two anti-parallel beta-sheet conformations in the solution structure of murine epidermal growth factor by proton magnetic resonance.  PMC386977

1984

1. Montelione, G.T.; Arnold, E.; Meinwald, Y.C.; Stimson, E.R.; Denton, J.B.; Huang, S.-G.; Clardy, J.; Scheraga, H.A. J. Amer. Chem. Soc. 1984, 106: 7946 – 7958. Chain-folding initiation structures in ribonuclease A: Conformational analysis of trans Ac-Asn-Pro-Tyr-NHMe and trans Ac-Tyr-Pro-Asn-NHMe in water and in the solid state.  suppl. material  addition/correction 

2. Oka, M.; Montelione, G.T.; Scheraga, H.A. J. Amer. Chem. Soc. 1984, 106: 7959 – 7969. Chain-folding initiation structures in ribonuclease A: Conformational free energy calculations on Ac-Asn-Pro-Tyr- NHMe, Ac-Tyr-Pro-Asn-NHMe, and related peptides.  suppl. material 

3. Swadesh, J.K.; Montelione, G.T.; Thannhauser, T.W.; Scheraga, H.A. Proc. Natl. Acad. Sci. U.S.A. 1984, 81: 4606 – 4610. Local structure involving histidine-12 in reduced S-sulfonated ribonuclease A detected by proton NMR spectroscopy under folding conditions.  PMC345642

1982

1. Stimson, E.R.; Montelione, G.T.; Meinwald, Y.C.; Rudolph, R.K.E.; Scheraga, H.A. Biochemistry 1982, 21: 5252 – 5262. Equilibrium ratios of cis– and trans-proline conformers in fragments of ribonuclease A from nuclear magnetic resonance spectra of adjacent tyrosine ring resonances.  suppl. material 

1981

1. Montelione, G.T.; Callahan, S.; Podleski, T.R. Biochim. Biophys. Acta 1981 , 670: 110 – 123. Physical and chemical characterization of the major lactose-blockable lectin activity from fetal calf skeletal muscle.