Publications 2001-2011

2011

1. Vaiphei ST; Tang Y; Montelione GT; 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 EJ; Leavitt J; Ma LC; Montelione GT; Anslyn EV; Krug RM; Ellington A; Robertus JD. Bioorg Med Chem Lett. 2011, 21: 3007 – 3011. Synthesis and evaluation of quinoxaline derivatives as potential NS1A protein inhibitors.  suppl. material.  PMC3114437. Pubmed.

3. Schauder C; Ma LC; Krug RM; Montelione GT; 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. Pubmed.

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

4. Vorobiev SM; Huang YJ; Seetharaman J; Xiao R; Acton TB; Montelione GT; Tong L. Protein Peptide Letts. 2011, 19: 194 – 197. Human retinoblastoma binding protein 9, a serine hydrolase implicated in pancreatic cancers.  PMC3677193. Pubmed.

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

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

The NESG Disorder Prediction Server (DisMeta)

6. Mao L; Inoue K; Tao Y; Montelione GT; McDermott AE; 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 TA; Smola MJ; Lee HW; Ciccosanti C; Hamilton K; Acton TB; Xiao R; Everett JK; Prestegard JH; Montelione GT; Kennedy MA. 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. Pubmed.

) 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 JM; Ma LC; Cort JR; Swapna GVT; Krug RM; Montelione GT. 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. Pubmed.

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 JE; Chen I; Joachimiak LA; Dym O; Peck SH; Albeck S; Unger T; Hu W; Liu G; Delbecq S; Montelione GT; Spiegel CP; Liu DR; Baker D. Molecular Cell. 2011, 42: 250 – 260. A de novo protein binding pair by computational design and directed evolution.  suppl. material. PMC3102007. Pubmed.

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 JR; Wolfley JR; Tsuruta H; Martel A; Montelione GT; Snell E. Biopolymers. 2011, 95: 517 – 530. Small angle x-ray scattering as a complementary tool for high-throughput structural studies.  PMC3124082. Pubmed.

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 NG; Lange OF; DiMaio F; André I; Fitzkee NC; Rossi P; Montelione GT; 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. Pubmed.

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

12. Barb AW; Cort JR; Seetharaman J; Lew S; Lee HW; Acton T; Xiao R; Kennedy MA; Tong L; Montelione GT; Prestegard JH. Protein Science. 2011, 20: 396 – 405. Structures of domains I and IV from YbbR are representative of a widely distributed protein family.  PMC3048424. Pubmed.

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

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

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 GT. Structure (Cell Press). 2011, 19: 757 – 766. Improved technologies now routinely provide protein NMR structures useful for molecular replacement.  suppl. material. PMC3612016.

15. Aramini JM; Ma LC; Zhou L; Schauder CM; Hamilton K; Amer BR; Mack TR; Lee HW; Ciccosanti CT; Zhao L; Xiao R; Krug RM; Montelione GT. 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. Pubmed.

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

16. Aramini JM; Rossi P; Fischer M; Xiao R; Acton TB; Montelione GT. 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. Pubmed.

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

17. Guan R; Ma LC; Leonard PG; Amer BR; Sridharan H; Zhao C; Krug RM; Montelione GT. 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. Pubmed.

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 WT; Xiao R; Acton TB; Montelione GT; 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. Pubmed.

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 GT; Tong L. Acta Crystallographica Section F. 2011, 67: 1323 – 1327. A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding.  PMC3212444. Pubmed.

Crystal structure of the P. furiosus PF0828 homodimer

20. Lowery J; Szul T; Seetharaman J; Xiaoying J; Su M; Forouhar F; Xiao R; Acton TB; Montelione GT; Lin H; Wright JW; Lee E; Holloway ZG; Randazzo PA; 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. Pubmed.

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 TA; Cort JR; Wang D; Ciccosanti C; Jiang M; Acton TB; Xiao R; Everett JK; Montelione GT; 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. Pubmed.

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

23. Feldmann EA; Ramelot TA; Yang Y; Xiao R; Acton TB; Everett JK; Montelione GT; Kennedy MA. 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. Pubmed.

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

1. Singarapu KK; Mills J; Xiao R; Acton T; Punta M; Fischer M; Honig B; Rost B; Montelione GT; 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. Pubmed.

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

2. Mao L; Vaiphei ST; Shimazu T; Schneider WM; Tang Y; Mani R; Roth MJ; Montelione GT; 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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

. (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. Pubmed.

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. Pubmed.

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. material. PMC3057626. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

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. Pubmed.

. (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 KK; Xiao R; Acton T; Su M; Bansal S; Prestegard JH; Hunt J; Montelione GT; 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 WN. 2nd; Chen Y; Handelman SK; Neely H; Manor P; Karlin R; Nair R; Liu R; Baran M; Everett J; Tong SN; Forouhar F; Swaminathan SS; Acton T; Xiao R; Luft JR; Lauricella A; DeTitta GT; Rost B; Montelione GT; Hunt JF. Nature Biotechnology. 2009, 27: 51 – 57. Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data.  suppl. material. PMC2746436. Pubmed.

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 HS; Aramini JM; Xiao R; Huang YJ; Abashidze M; Seetharaman J; Liu J; Rost B; Acton T.; Montelione GT; Hunt JF; SzyperskiT. 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. Pubmed.

X-ray crystal structure of human Ufc1

8. Bertonati C; Punta M; Fischer M; Yachdav G; Forouhar F; Zhou W; Kuzin AP; Seetharaman J; Abashidze M; Ramelot TA; Kennedy MA. 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 TT; Acton TB; Everett J; Kouranov A; Fiser A; Godzik A; Jaroszewski L; Orengo C; Montelione GT; Rost B. J Struct Funct Genomics. 2009, 10: 181 – 191. Structural genomics is the largest contributor of novel structural leverage.  PMC2705706. Pubmed.

Per-structure estimates of novel leverage

10. Schwede T; Sali A; Honig B; Levitt M; Berman HM; Jones D; Brenner SE; Burley SK; Das R; Dokholyan NV; Dunbrack RL; Fidelis K; Fiser A; Godzik A; Huang YJ; Humblet C; Jacobson MP; Joachimiak A; Krystek SR Jr; Kortemme T; Kryshtafovych A; Montelione GT; Moult J; Murray D; Sanchez R; Sosnick TR; Standley DM; Stouch T; Vajda S; Vasquez M; Westbrook JD; Wilson IA. Structure (Cell Press). 2009, 17: 151 – 159. Outcome of workshop on applications of protein models in biomedical research.  PMC2739730. Pubmed.

11. Montelione GT; Arrowsmith CA; Girvin M; Kennedy MA; Markley JL; Powers R; Prestegard JH; Szyperski T. J Struct Funct Genomics. 2009, 10: 101-106. Unique opportunities for NMR methods in structural genomics. PMC2705713. Pubmed.

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 YJ; Ertekin A; Hamuro Y; Rossi P; Tejero R; Acton T; Xiao R; Jiang M; Zhao L; Ma LC; Swapna GVT; Aramini JM; Montelione GT. 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 SG; Mani R; Fakhoury E; White E; Montelione GT; 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. Pubmed.

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 DK; Xiao R; Acton T; Rost B; Montelione GT; 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. Pubmed.

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

15. Schneider WM; Inouye M; Montelione GT; Roth MJ. 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 JF; Giachetti A; Guerry P; Güntert P; Herrmann T; Huang YJ; Jonker HRA; Mao B; Malliavin TE; Montelione GT; Nilges M; Raman S; van der Schot G; Vranken WF; Vuister GW; Bonvin AMJJ. Nature Methods. 2009, 6: 625 – 626. CASD-NMR: Critical assessment of automated structure determination by NMR.  PMC2841015. Pubmed.

Performance of various automated structure calculation methods.

17. Mercier KA; Mueller GA; Acton TB; Xiao R; Montelione GT; 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 SK; Joachimiak A; Montelione GT; Wilson IA. Structure (Cell Press). 2008, 16: 5 – 11. Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI production centers.  PMC2678832. Pubmed.

2. Singarapu KK; Xiao R; Sukumaran DK; Acton T; Montelione GT; 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. Pubmed.

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 HW; Savchenko A; Yee A; Edwards A; Vincentelli R; Cambillau C; Kim R; Kim SH; Rao Z; Shi Y; Terwilliger TC; Kim CY; Hung LW; Waldo GS; Peleg Y; Albeck S; Unger T; Dym O; Prilusky J; Sussman JL; Stevens RC; Lesley SA; Wilson IA; Joachimiak A; Collart F; Dementieva I; Donnelly MI; Eschenfeldt WH; Kim Y; Stols L; Wu R; Zhou M; Burley SK; Emtage JS; Sauder JM; Thompson D; Bain K; Luz J; Gheyi T; Zhang F; Atwell S; Almo SC; Bonanno JB; Fiser A.; Swaminathan S; Studier FW; Chance MR; Sali A; Acton TB; Xiao R; Zhao L; Ma LC; Hunt JF; Tong L; Cunningham K; Inouye M; Anderson S; Janjua H; Shastry R; Ho C.K.; Wang, H; Jiang M; Montelione GT; Stuart DI; Owens RJ; Daenke S; Schütz A; Heinemann U; Yokoyama S; Büssow K; Gunsalus KC. Nature Methods. 2008, 5: 135 – 146. Protein production and purification.  PMC3178102. Pubmed.

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 KK; Xiao R; Acton T; Rost B; Montelione GT; 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. Pubmed.

NMR structure of the P. syringae PTH domain.

5. Aramini JM; Sharma S; Huang YJ; Swapna GVT; Ho CK; Shetty K; Cunningham K; Ma LC; Zhao L; Owens LA; Jiang M; Xiao R; Liu J; Baran MC; Acton TB; Rost B; Montelione GT. PROTEINS: Struct Funct Bioinformatics. 2008, 72: 526 – 530. Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis.  suppl. material. Pubmed.

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 LL; Seetharaman J; Hussain M; Kuzin A; Chen Y; Zhou W; Xiao R; Acton TB; Montelione GT; Galinier A; White RH; Tong L. J Biol Chem. 2008, 17: 11832 – 11840. Molecular insights into the biosythesis of the F420 coenzyme.  PMC2431047. Pubmed.

, 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. ShenY; Lange O; Delaglio F; Rossi P; Aramini JM; Liu G; Eletsky A; Wu Y; Singarapu KK; Lemak A; Ignatchenko A; Arrowsmith CH; Szyperski T; Montelione GT; 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. Pubmed.

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

8. Huang YJ; Hang D; Lu LJ; Tong L; Gerstein MB; Montelione GT. Mol. Cell. Proteomics. 2008, 7: 2048 – 2060. Targeting the human cancer pathway protein interaction network by structural genomics.  PMC2559933. Pubmed.

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 YJ; Ramelot TA; Cort JR; Semesi A; Jung JW; Lee W; Montelione GT; Kennedy MA; Arrowsmith CH. 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 LC; Xiao R; Radvansky B; Aramini J; Zhao L; Marklund J; Kuo RL; Twu KY; Arnold E; Krug RM; Montelione GT. 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. Pubmed.

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 JM; Rossi P; Huang YJ; Zhao L; Jiang M; Maglaqui M; Xiao R; Locke J; Nair R; Rost B; Acton TB; Inouye M; Montelione GT. 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. Pubmed.

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 GT; 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 SM; Su M; Seetharaman J; Huang YJ; Chen XC; Cunningham K; Maglaqui M; Owens L; Proudfoot M; Yakunin A; Xiao R; Acton TB; Montelione GT; 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 JR; Ramelot TA; Murray D; Acton TB; Ma LC; Xiao R; Montelione GT; Kennedy MA. 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 TA; Raman S; Kuzin AP; Xiao R; Ma LC; Acton TB; Hunt JF; Montelione GT; Baker D; Kennedy MA. PROTEINS: Struct Funct Bioinformatics. 2008, 75: 147 – 167. Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study.  suppl. material. PMC2878636. Pubmed.

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 JM; Xiao R; Chen CX; Nwosu C; Owens LA; Maglaqui M; Nair R; Fischer M; Acton TB; Honig B; Rost B; Montelione GT. 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. Pubmed.

(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 KK; Xiao R; Acton T; Su M; Bansal S; Prestegard JH; Hunt J; Montelione GT; 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 KA; Baran M; Ramanathan V; Revesz P; Xiao R; Montelione GT; Powers R. J Amer Chem Soc. 2006, 128: 15292 – 15299. FAST-NMR – Functional Annotation Screening Technology using NMR spectroscopy.  PMC2529462. Pubmed.

(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 GT. PROTEINS: Struct Funct Bioinformatics. 2007, 66: 778 – 795. Evaluating protein structures determined by structural genomics consortia.  Pubmed.

MAR30

3. Forouhar F; Anderson JL; Mowat CG; Vorobiev SM; Hussain A; Abashidze M; Bruckmann C; Thackray SJ; Seetharaman J; Tucker T; Xiao R; Ma L; Zhao L; Acton TB; Montelione GT; Chapman SK; 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. Pubmed.

The structure of TDO.

4. Vorobiev SM; Neely H; Seetharaman J; Ma L; Xiao R; Acton TB; Montelione GT; Tong L. Protein Science. 2007, 16: 535 – 538. Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens.  PMC2203313. Pubmed.

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

(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 GT. Nature Methods. 2007, 4: 491 – 493. Microgram scale protein structure determination by NMR.  suppl. material. Pubmed.

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 JA; Swapna GVT; Ertekin A; Krug RM; Tong L; Montelione GT. 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. Pubmed.

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

8. Aramini J; Y. Huang YJ; Swapna GVT; Cort JR; Rajan PK; Xiao R; Shastry R; Acton TB; Liu J; Rost B; Kennedy MA; Montelione GT. 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. Pubmed.

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 GT; Rost B. Nature Biotechology. 2007, 25: 849 – 851. Novel leverage of structural genomics.  suppl. material. Pubmed.

10. Andrec M; Snyder D A; Zhou Z; Young J; Montelione GT; 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. Pubmed.

11. Lu LJ; Sboner A; Huang Y J; Lu H.X.; Gianoulis T.A.; Yip KY; Kim PM; Montelione GT; Gerstein MB. TIBS. 2007, 32: 320 – 331. Comparing classical pathways and modern networks: Towards the development of an edge ontology.  suppl. material. Pubmed.

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

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 TB; Pichersky E; Klessig DF; Porter CW; Montelione GT; Tong L. J Struct Funct Genomics. 2007, 8: 37 – 44. Functional insights from structural genomics.  Pubmed.

14. Benach J; Wang L; Chen Y; Ho CK; Lee S; Seetharaman J; Xiao R; Acton TB; Montelione GT; 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.  Pubmed.

. 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 GT; 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. Pubmed.

2. Baran M; Moseley HNB; Aramini JM; Bayro MJ; Monleon D; Locke J; Montelione GT. 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. Pubmed.

3. Forouhar F; Hussain M; Farid R; Benach J; Abashidze M; Edstrom WC; Vorobiev SM; Xiao R; Acton TB; Fu Z; Kim J; Miziorko HM; Montelione GT; Hunt JF. 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. Pubmed.

4. Kornhaber GJ; Snyder D; Moseley HNB; Montelione GT. J Biomol NMR. 2006, 34: 259 – 269. Identification of zinc-ligated cysteine residues based on 13Cα and 13Cβ chemical shift data.  Pubmed.

5. Berman HM; Burley SK; Chiu W; Sali A; Adzhubei A; Bourne PE; Bryant SH; Dunbrack Jr, RL; 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.  Pubmed.

6. Greenfield NJ; Huang YJ; Swapna GVT; Bhattacharya A; Rapp B; Singh A; Montelione GT; Hitchcock-DeGregori SE. J Mol Biol. 2006, 364: 80 – 96. Solution NMR structure of the junction between tropomyosin molecules: Implications for actin binding and regulation.  suppl. material. Pubmed.

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

(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 YJ; Moseley HNB; Baran MC; Arrowsmith C; Powers R; Tejero R; Szyperski T; Montelione GT. Methods in Enzymology. 2005, 394: 111 – 141. An integrated platform for automated analysis of protein NMR structures. Pubmed.

2. Acton TB; Gunsalus KC; Xiao R; Ma LC; Aramini JM; Baran MC; Chiang YW; Climent T; Cooper B; Denissova N; Douglas SM; Everett JK; Ho CK; Macapagal D; Rajan PK; Shastry R; Shih LY; Swapna GVT; Wilson M; Wu M; Gerstein M; Inouye M; Hunt JF; Montelione GT. Methods in Enzymology. 2005, 394: 210 – 243. Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium.  Pubmed.

3. Shen Y; Goldsmith-Fischman S; Atreya HS; Acton TB; Ma LC; Xiao R; Honig B; Montelione GT; 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 DA; Montelione GT.  PROTEINS: Struct Funct Bioinformatics. 2005, 59: 673 – 686.  Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Pubmed.

5. Huang YJ; Powers R; Montelione GT. 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. Pubmed.

6. Liu G; Li Z; Chiang Y; Acton TB; Montelione GT; 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. Pubmed.

7. Forouhar F; Yang Y; Kumar D; Chen Y; Fridman E; Park SW; Chiang Y; Acton TB; Montelione GT; Pichersky E; Klessig DF; 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. Pubmed.

8. Liu G; Shen Y; Atreya HS; Parish D; Shao Y; Sukumaran DK; Xiao R; Yee A; Lemak A; Bhattacharya A; Acton TB; Arrowsmith CH; Montelione GT; Szyperski T.  Proc Natl Acad Sci USA. 2005, 102: 10487 – 10492.  NMR data collection and analysis protocol for high-throughput protein structure determination. suppl. material. PMC1180791. Pubmed.

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

10. Huang YJ; Tejero R; Powers R; Montelione GT. PROTEINS: Struct Funct Bioinformatics. 2006, 62: 587 – 603. A topology- constrained distance network algorithm for protein structure determination from NOESY data. suppl. material. Pubmed. 

11. Snyder DA; Bhattacharya A; Huang YJ.; Montelione GT. PROTEINS: Struct Funct Bioinformatics. 2005, 59: 655 – 661. Assessing precision and accuracy of protein structures derived from NMR data.  suppl. material. Pubmed.

12. Snyder DA; Chen Y; Denissova NG; Acton T; Aramini JM; Ciano M; Karlin R; Liu J; Manor P; Rajan PA; Rossi P; Swapna GVT; Xiao R; Rost B; Hunt J; Montelione GT. 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. Pubmed.

13. Benach J; Edstrom WC; Lee I; Das K; Cooper B; Xiao R; Liu J; Rost B; Acton TB; Montelione GT; Hunt JF. 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. Pubmed.

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

15. Aramini JM; Swapna GVT; Huang YJ; Rajan PK; Xiao R; Shastry R; Acton TB; Cort JR; Kennedy MA; Montelione GT. 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. Pubmed.

16. Liu G; Aramini J; Atreya HS; Eletsky A; Xiao R; Acton TB; Ma LC; Montelione GT; 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. Pubmed.

17. Forouhar F; Lee IS; Vujcic J; Vujcic S; Shen J; Vorobiev SM; Xiao R; Acton TB; Montelione GT; Porter CW; 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). Pubmed.

18. Bachhawat P; Swapna GVT; Montelione GT; Stock AM. 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. Pubmed.

19. Powers R; Mirkovic N; Goldsmith-Fischman S; Acton TB; Chiang Y; Huang YJ; Ma L; Rajan RK; Cort JR; Kennedy MA; Liu J; Rost B; Honig B; Murray D; Montelione GT. 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 eukaryotes. PMC2253226. Pubmed.

20. Huang YJ; Montelione GT. Nature. 2005, 438: 36 – 37. News and Views: Proteins flex to function. Pubmed.

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 JM; Swapna GVT; Macapagal D; Gunsalus KC; Kim S; Szyperski T; Montelione GT.  J. Biomol. NMR. 2004, 28: 91 – 92.  Backbone 1H, 15N and 13C assignments for the 21 kDa Caenorhabditis elegans homologue of ‘brain-specific’ protein. Pubmed.

2. Zheng D; Aramini J; Montelione GT.  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 CS; Lan N; Douglas SM; Wu B; Echols N; Smith A; Milburn D; Montelione GT; 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. Pubmed.

4. Chien CY; Xu Y; Xiao R; Aramini JM; Sahasrabudhe PV; Krug RM; Montelione GT.  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. Pubmed.

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

6. Das K; Acton TB; Chiang Y; Shih L; Arnold E; Montelione GT. 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. Pubmed.

7. Liu G; Sukumaran DK; Xu D; Chiang Y; Acton TB; Goldsmith- Fischman, S; Honig B; Montelione GT; 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. Pubmed.

8. Herve Du Penhoat C; Atreya HS; Shen Y; Liu G; Acton TB; Xiao R; Li Z; Murray D; Montelione GT; 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 GT; 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. Pubmed.

10. Forouhar F; Lee IS; Benach J; Kulkarni K; Xiao R; Acton TB; Montelione GT; 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). Pubmed.

11. Makokha M; Huang YJ; Montelione GT; Edison AS; Barbar E. Protein Science   2004 13: 727 – 734.  The solution structure of the pH-induced monomer of dynein light-chain LC8 from Drosophila.  PMC2286742. Pubmed.

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

13. Adams M; Joachimiak A; Kim R; Montelione GT; 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). Pubmed.

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

15. Shen Y; Atreya HS; Xiao R; Acton TB; Shastry R; Ma L; Montelione GT; 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 TB; Montelione GT; Rost B.  PROTEINS: Struct. Funct. Bioinformatics. 2004, 56: 188 – 200.  Automatic target selection for structural genomics on eukaryotes. 

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

18. Baran MC; Huang YJ; Moseley HN; Montelione GT.  Chemical Reviews. 2004, 104: 3451 – 3556.  Automated analysis of protein NMR assignments and structures. Pubmed.

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

20. Powers R; Acton TB; Chiang Y; Rajan PK; Cort JR; Kennedy MA; Liu J; Ma LC; Rost B; Montelione GT.  J. Biomol. NMR. 2004, 30: 107-108.  1H, 13C, and 15N assignments for the Archaeglobus fulgidis protein AF2095. Pubmed.

21. Ramelot TA; Cort JR; Goldsmith-Fischman S; Kornhaber GJ; Xiao R; Shastry R; Acton TB; Honig B; Montelione GT; Kennedy MA.  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. Pubmed.

22. Goldsmith-Fischman S; Kuzin A; Edstrom WC; Benach J; Shastry R; Xiao R; Acton TB; Honig B; Montelione GT; Hunt JF. 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. Pubmed.

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 GT; 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. Pubmed.

2. Yuan E; Aramini JM; Montelione GT; Krug RM. 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. Pubmed.

3. Swapna GVT; Huang Y; Palm T; Graboski S; Montelione GT; Hitchcock-DeGregori SE.  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. Pubmed.

4. Huang YJ; Swapna GVT; Rajan PK; Ke H; Xia B; Shukla K; Inouye M; Montelione GT. 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. Pubmed.

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

6. Zheng D; Huang YJ; Moseley HNB; Xiao R; Aramini J; Swapna GVT; Montelione GT. Protein Science. 2003, 12: 1232 – 1246.  Automated protein fold determination using a minimal NMR constraint strategy.  PMC2323888.

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

8. Goh CS; Lan N; Echols N; Douglas S; Milburn D; Bertone P; Xiao R; Ma LC; Zheng D; Wunderlich Z; Acton T; Montelione GT; Gerstein M.  Nucleic Acids Res.  2003, 31: 2833 – 2838.  SPINE 2: A system for collaborative structural proteomics within a federated database framework. PMC156730. Pubmed.

9. Bayro MJ; Mukhopadhyay J; Swapna GVT; Huang JY; Ma LC; Sineva E; Dawson P; Montelione GT; Ebright RH.  J. Amer. Chem. Soc. 2003, 125: 12382 – 12383.  Structure of antibacterial peptide microcin J25: A 21-residue lariat protoknot.  suppl. material. Pubmed.

10. Forouhar F; Shen J; Xiao R; Acton TB; Montelione GT; 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. Pubmed.

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

12. Aramini JM; Mills JL; Xiao R; Acton TB; Wu MJ; Szyperski T; Montelione GT.  J. Biomol. NMR. 2003, 27: 285 – 286.  Resonance assignments for the hypothetical protein yggU from Escherichia coli. Pubmed.

13. Benach J; Lee I; Edstrom WC; Kuzin A; Chiang Y; Acton TB; Montelione GT; Hunt JF.  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. Pubmed.

14. Aramini JM; Huang YJ; Cort JR; Goldsmith-Fischman S; Xiao R; Shih LY; Ho CK; Liu J; Rost B; Honig B; Kennedy MA; Acton TB; Montelione GT.  Protein Science. 2003, 12: 2823 – 2830.  Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. PMC2366990. Pubmed.

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

1. McFeeters RL; Swapna GVT; Montelione GT; Oswald RE. 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 TB; Basu SK; Montelione GT; Inouye M.  J. Molec. Microbiol. Biotech. 2002, 4: 519 – 524.  Enhancement of the solubility of proteins overexpressed in Escherichia coli by heat shock. Pubmed.

3. Monleón D; Colson K; Moseley HNB; Anklin C; Oswald R; Szyperski T; Montelione GT.  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. Pubmed.

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

5. Szyperski T; Yeh DC; Sukumaran DK; Moseley HNB; Montelione GT.  Proc. Natl. Acad. Sci. 2002, 99: 8009 – 8014.  Reduced- dimensionality NMR spectroscopy for high-throughput protein resonance assignment.  suppl. material.  PMC123011. Pubmed.

6. Cort JR; Chiang Y; Zheng D; Montelione GT; Kennedy MA.  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 MA; Montelione GT; Arrowsmith CH; Markley JL.  J. Struct. Funct. Genomics. 2002, 2: 155 – 169.  Role for NMR in structural genomics. Pubmed.

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

9. Lan N; Montelione GT; 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. Pubmed.

10. Yuan E; Aramini JM; Montelione GT; Krug RM. 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. Pubmed.

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 HNB; Monleon D; Montelione GT. Meth. Enzymology. 2001, 339: 91 – 108. Automatic determination of protein backbone resonance assignments from triple-resonance NMR data. Pubmed.

2. Sahasrabudhe PV; Xiao R; Montelione GT. 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 AM; Arrowsmith CH; Montelione GT; 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. Pubmed.

4. Kulikowski CA; Muchnik I; Yun HJ; Dayanik AA; Zheng D; Song Y; Montelione GT.  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. Pubmed.

5. Greenfield NJ; Huang Y; Palm T; Swapna GVT.; Monleon D; Montelione GT; Hitchcock-DeGregori SE. 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 CA; Montelione GT; 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 GT.  Proc. Natl. Acad. Sci. U.S.A. 2001, 98: 13488 – 13489.  Structural genomics: An approach to the protein folding problem.  PMC61067.

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

9. Cassetti MC; Noah DL; Montelione GT; Krug RM. Virology. 2001, 289: 180 – 185.  Efficient translation of mRNAs in Influenza A virus-infected cells is independent of the viral 5′ untranslated region. Pubmed.

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