Publications 2012-2015

2015

1. Parmeggiani F; Huang P-S; Vorobiev S; Xiao R; Park K; Caprari S; Su M; Jayaraman S; Mao L; Janjua H; Montelione GT; Hunt JF; 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  MC4303030. Pubmed.

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 CM; Lee H-W; Grant TD; Luft JR; Xiao R; Acton TB; Snell EH; Montelione GT; Baker D; Lange OF; Sgourakis NG. PROTEINS: Struc. Funct. Bioinformatics. 2015, 83: 309 – 317. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.  suppl. material. PMC5061451. Pubmed.

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 JR; Wolfley JR; Franks EC; Lauricella AM; Gualtieri EJ; Snell EH; Xiao R; Everett JK; Montelione GT. 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 WM; Chanda A; Bushman FD; Montelione GT; Roth MJ. Nucleic Acids Research. 2015, 43: 5647 – 5663. Structural and sequencing analysis of local target DNA recognition by MLV integrase.  PMC4477651. Pubmed.

The C! backbone trace of IN 329–408

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

Genome architecture

6. Gutmanas A; Adams PD; Bardiaux B; Berman HM; Case DA; Fogh RH; Güntert P; Hendrickx PMS; Herrmann T; Kleywegt GJ; Kobayashi N; Lange OF; Markley JL; Montelione GT; Nilges M; Ragan TJ; Schwieters, CD; Tejero R; Ulrich E; Velankar S; Vranken WF; Wedell JR; Westbrook J; Wishart DS; Vuister GW Nature Struct Mol Biol. 2015, 22: 433 – 434. NMR Exchange Format: a unified and open standard for representation of NMR restraint data.  PMC4546829. Pubmed.

Growth in the number of NMR entries in the PDB archive

7. Ragan TJ; Fogh RH; Tejero R; Vranken W; Montelione GT; Rosato A; Vuister GW. 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. Pubmed.

6 Correlation between entry pairwise RMSD and NOE restraint overlap.

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

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 RH; Ragan TJ; Tejero R; Pederson K; Lee HW; Prestegard J; Yee A; Wu B; Lemak A; Houliston S; Arrowsmith C; Kennedy M; Acton TB; Liu G; Xiao R; Montelione GT; Vuister GW. 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. material. PMC4569658.

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 YJ; Hopf TA; Sanders C; Marks DS; Montelione GT. Nature Methods. 2015, 12: 751 – 754. Protein structure determination by combining sparse NMR spectroscopy data with evolutionary couplings.  suppl. material.  PMC4521990. Pubmed.

The EC-NMR approach

11. Aramini JM; Vorobiev SM; Tuberty LM; Janjua H; Campbell ET; Seethraman J; Su M; Huang YJ; Acton TB; Xiao R; Tong L; Montelione GT. 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. Pubmed.

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

12. Choi HW; Tian M; Song F; Venereau E; Preti A; Park SW; Hamilton K; Swapna GVT; Manohar M; Moreau M; Agresti A; Gorzanelli A; De Marchis F; Wang H; Antonyak M; Micikas RJ; Gentile DR; Cerione RA; Schroeder FC; Montelione GT; Bianchi ME; Klessig DF. 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. Pubmed.

Arg24 and Lys28 are required for binding SA

13. Everett JK; Tejero R; Murthy SBK; Acton TB; Aramini JM; Baran MC; Benach J; Cort JR; Eletsky A; Forouhar F; Guan R; Kuzin AP; Lee HW; Liu G; Mani R; Mao B; Mills JL; Montelione AF; Pederson K; Powers R; Ramelot T; Rossi P; Seetharaman J; Snyder D; Swapna GVT; Vorobiev SM; Wu Y; Xiao R; Yang Y; Arrowsmith CH; Hunt JF; Kennedy MA; Prestegard JH; Szyperski T; Tong L; Montelione GT. 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 YR; Koga N; Tatsumi-Koga R; Liu G; Clouser AF; Montelione GT; 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. Pubmed.

Discrete state model of protein local geometry.

15. Wolf C; Siegel JB; Tinberg C; Camarca A; Gianfrani C; Paski S; Guan R; Montelione GT; Baker D; Pultz IS. 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. Pubmed.

Immunogenic gluten epitopes

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

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

1. Mao B; Tejero R; Baker D; Montelione GT. 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. Pubmed.

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 GT; Tong L; Ebright RH; Nickels BE. 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. Pubmed.

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 GT; 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. Pubmed.

. PO4-complexed tetrameric LpcN-II structures

4. Stark JL; Mehla K; Chaika N; Acton TB; Xiao R; Singh PK; Montelione GT; 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. Pubmed.

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 JM; Hamilton K; Ma L-C; Swapna GVT; Leonard PG; Ladbury JE; Krug RM; Montelione GT. Structure (Cell Press). 2014, 22: 515 – 525. F NMR reveals multiple conformations at the dimer interface of the NS1 effector domain from influenza A virus.  suppl. material. PMC4110948. Pubmed.

. 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 GVT; Malani N; Aramini JM; Schneider WM; Plumb MR; Ghanem M; Larue RC; Sharma A; Studamire B; Kvaratskhelia M; Bushman FD; Montelione GT; Roth MJ. 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. Pubmed.

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 YJ; Acton TB; Xiao R; Everett JK; Montelione GT; 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. Pubmed.

8. Xu X; Pulavarti SV; Eletsky A; Huang YJ; Acton TB; Xiao R; Everett JK; Montelione GT; 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. Pubmed.

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

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

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

10. Bruno EB; Ruby AM; Luft JR; Grant TD; Seetharaman J; Montelione GT; Hunt JF; Snell EH. 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 SV; Huang YJ; Pederson K; Acton TB; Xiao R; Everett JK; Prestegard JH; Montelione GT; 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. Pubmed.

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; Zhahttps://pubmed.ncbi.nlm.nih.gov/25010333/ng Q; Daily MD; Xu X; Cui H; Yee A; Lemak A; Wu B; Garcia M; Burnet MC; Meyer KM; Aryal UK; Sanchez O; Ansong C; Xiao R; Acton TB; Adkins JN; Montelione GT; Joachimiak A; Arrowsmith CH; Savchenko A; Szyperski T; Cort J.R. PLoS One. 2014, 9: e101787. Structural and functional characterization of DUF1471 domains of salmonella.  suppl. material. PMC4092069. Pubmed.

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. Pubmed.

Structure of CalU16

14. Yang Y; Ramelot TA; Lee HW; Xiao R; Everett JK; Montelione GT; Prestegard JH; 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. Pubmed.

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

15. Yang Y; Ramelot TA; Lee HW; Xiao R; Everett, JK; Montelione GT; Prestegard JH; 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. Pubmed.

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. Pubmed.

Chemical clustering and visualization applied to macromolecular crystallography

17. Huang YJ; Mao B; Aramini J; Montelione GT. 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. Pubmed.

Comparison of models using distance networks

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

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

19. Snyder DA; Grullon J; Huang Y.J; Tejero R; Montelione GT. 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. Pubmed.

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

2013

1. 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 RJ; Tong L; Moremen KW.  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. Pubmed.

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2. Pulavarti S; He Y; Feldmann EA; Eletsky A; Acton TB; Xiao R; Everett JK; Montelione GT; Kennedy MA; 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. Pubmed.

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3. Kronfel CM; Kuzin AP; Forouhar F; Biswas A; Su M; Lew S; Seetharaman J; Xiao R; Everett JK; Ma LC; Acton TB; Montelione GT; Hunt JF; Paul CEC; Dragomani TM; Boutaghou, MN; Cole RB; Riml C; Alvey RM; Bryant DA; Schluchter WM. Biochemistry. 2013, 52: 8663 – 8676. Structural and biochemical characterization of the bilin lyase CpcS from Thermosynechococcus elongates.  suppl. material. PMC3932240. Pubmed.

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4. Huang Y.J; Acton TB; Montelione GT. Methods in Mol Biol. 2013, 1091: 3 – 16. DisMeta – a meta server for construct design and optimization.  PMC4115584. Pubmed.

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5. Uemura Y; Nakagawa N; WakamatsuT; Kim K; Montelione GT; Hunt JF; 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. Pubmed.

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6. Rossi P; Barbieri CM; Aramini JM; Bini E; Xiao R; Acton TB; Montelione GT. 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. Pubmed.

7. Mills J; Acton TB; Xiao R; Everett JK; Montelione GT; 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. Pubmed.

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

8. Bjelic S; Nivón LG; Celebi-Ölçüm N; Kiss G; Rosewall CF; Lovick HM; Ingalls EL; Gallaher JL; Seetharaman J; Lew S; Montelione GT; 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. Pubmed.

Morita−Baylis−Hillman reaction

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

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

10. Froese DS; Forouhar F; Tran TH; Vollmar M; Kim Y; Lew S; Neely H; Seetharaman J; Shen Y; Xiao R; Acton TB; Everett JK; Cannone G; Puranik S; Savitsky P; Krojer T; Pilka ES; Kiyani W; Lee WH; Marsden BD; von Delft F; Allerston CK; Spagnolo L; Gileadi O; Montelione GT; Oppermann U; Yue WW; 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. Pubmed.

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

11. 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. Pubmed.

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

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

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

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

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

14. Montelione GT; Nilges M; Bax A; Güntert P; Herrmann T; Richardso JS; Schwieters C; Vranken WF; Vuister GW; Wishart DS; Berman H;. Kleywegt GJ; Markley JL. Structure (Cell Press). 2013, 21: 1563 – 1570. Recommendations of the wwPDB NMR validation task force.  PMC3884077. Pubmed.

15. Neklesa TK; Noblin DJ; Kuzin AP; Lew S; Seetharaman J; Acton TB; Kornhaber G; Xiao R; Montelione GT; Tong L; Crews CM. ACS Chem Biol. 2013, 8: 2293 – 2300. A bidirectional system for the dynamic small molecule control of intracellular fusion proteins.  suppl. material. PMC4113957. Pubmed.

Characterization of HALTS1 activity in cells.

16. Pulavarti S; Eletsky A; Lee HW; Acton TB; Xiao R; Everett JK; Prestegard JH; Montelione GT; 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. Pubmed.

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

17. Ramelot TA; Yang Y; Sahu I.D; Lee HW; Xiao R; Lorigan GA; Montelione GT; 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).

18. Xu SY; Kuzin AP; Seetharaman J; Gutjahr A; Chan SH; Chen Y; Xiao R; Acton TB; Montelione GT; 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

19. 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 RJ; Tong L; Moremen KW.  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. Pubmed.

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

20. Pulavarti S; He Y; Feldmann EA; Eletsky A; Acton TB; Xiao R; Everett JK; Montelione GT; Kennedy MA; 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. Pubmed.

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

21. Kronfel CM; Kuzin AP; Forouhar F; Biswas A; Su M; Lew S; Seetharaman J; Xiao R; Everett JK; Ma LC; Acton TB; Montelione GT; Hunt JF; Paul CEC; Dragomani TM; Boutaghou, MN; Cole RB; Riml C; Alvey RM; Bryant DA; Schluchter WM. Biochemistry. 2013, 52: 8663 – 8676. Structural and biochemical characterization of the bilin lyase CpcS from Thermosynechococcus elongates.  suppl. material. PMC3932240. Pubmed.

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

22. Huang Y.J; Acton TB; Montelione GT. Methods in Mol Biol. 2013, 1091: 3 – 16. DisMeta – a meta server for construct design and optimization.  PMC4115584. Pubmed.

Disorder prediction

23. Uemura Y; Nakagawa N; WakamatsuT; Kim K; Montelione GT; Hunt JF; 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. Pubmed.

2012

1. Thompson J; Sgourakis NG; 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. Pubmed.

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 JM; Arrowsmith C; Bagaria A; Baker D; Cavalli A; Doreleijers JF; Eletsky A; Giachetti A; Guerry P; Gutmanas A; Güntert P; He Y; Herrmann T; Huang YJ; Jaravine V; Jonker HRA; Kennedy MA; Lange OF; Liu G; Malliavan TE; Mani R; Mao B; Montelione GT; Nilges M; Possi P; van der Schot G; Schwalbe H; Szyperski TA; Vendruscolo M; Vernon R; Vranken WF; de Vries S; Vuister GW; 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. Pubmed.

Structural Similarity between Reference and CASDNMR2010 Structures

3. Ramelot TA; Yang Y; Xiao R; Acton TB; Everett JK; Montelione GT; Kennedy MA. PROTEINS: Struct Funct Bioinformatics. 2012, 2: 667 – 670. Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron.  suppl. material. PMC3766420. Pubmed.

(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 YJ; Montelione GT; Güntert P. Protein Science. 2012, 21: 229 – 238. Protein structure validation by generalized linear model root-mean-square deviation prediction.  suppl. material. PMC3324767. Pubmed.

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 GVT; Wu KP; Afinogenova Y; Conover K; Mao B; Montelione GT; 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. Pubmed.

Efficiency of expression and solubility of PrS2IN and PrS2IC

6. Eletsky A; Petrey D; Zhang QC; Lee HW; Acton T; Xiao R; Everett J; Prestegard J; Honig B; Montelione GT; 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. Pubmed.

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 GT; 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. Pubmed.

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 GT; 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. Pubmed.

NMR structure of the soluble domain of lipoprotein YxeF.

9. Ertekin A; Aramini JM; Rossi P; Leonard PG; Janjua H; Xiao R; Maglaqui M; Lee HW; Prestegard JH; Montelione GT. 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. Pubmed.

Solution NMR structure of CDK2AP1(61–115).

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

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

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

Solution NMR structure of RP-L35Ae from Pyrococcus furiosus.

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

13. Lange OF; Rossi P; Sgourakis N; Song Y; Lee HW; Aramini JM; Ertekin A; Xiao R; Acton TB; Montelione GT; 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 EA; Seetharaman J; Ramelot TA; Lew S; Zhao L; Hamilton K; Ciccosanti C; Xiao R; Acton TB; Everett JK; Tong L; Montelione GT; Kennedy MA. J Struct Funct Genomics. 2012, 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 SM; Neely H; Yu B; Seetharaman J; Xiao R; Acton TB; Montelione GT; Hunt JF. 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. Pubmed.

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

16. Swapna GVT; Rossi P; Montelione AF; Benach J; Yu B; Abashidze M; Seetharaman J; Xiao R; Acton TB; Tong L; Montelione GT. 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. Pubmed.

. i Least-squares superposition of yozE

17. Aramini JM; Petrey D; Lee DY; Janjua H; Xiao R; Acton TB; Everett JK; 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. Pubmed.

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 JM; Hamilton K; Rossi P; Ertekin A; Lee HW; Lemak A; Wang H; Xiao R; Acton TB; Everett JK; Montelione GT. 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. Pubmed.

) 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 JF; Budamagunta MS; Voss JC; Kuzin AP; Huang YJ; Xiao R; Montelione GT; Fitzgerald PG; Hunt JF. 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. Pubmed.

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

20. Cho EJ; Xia S; Ma LC; Robertus J; Krug RM; Anslyn EV; Montelione GT; Ellington AD. J Biomol Screen. 2012, 17: 448 – 459. Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay. Pubmed.

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

21. Ramelot TA; Rossi P; Forouhar F; Lee HW; Yang Y; Ni S; Unser S; Lew S; Seetharaman J; Xiao R; Acton TB; Everett JK; Prestegard JH; Hunt JF; Montelione GT; Kennedy MA. 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. Pubmed.

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 TB; Montelione GT; Baker D. Nature. 2012, 491: 222 – 227. Principles for designing ideal protein structures.  supplmaterial. PMC3705962. Pubmed.

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

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

24. Lange OF; Rossi P; Sgourakis N; Song Y; Lee HW; Aramini JM; Ertekin A; Xiao R; Acton TB; Montelione GT; 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. Pubmed.

RASREC Rosetta results for maltose-binding protein.

25. Vorobiev SM; Neely H; Yu B; Seetharaman J; Xiao R; Acton TB; Montelione GT; Hunt J. 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. Pubmed.

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 JF; Budamagunta MS; Voss JC; Kuzin AP; Huang Y.J; Xiao R; Montelione GT; Fitzgerald PG; Hunt JF. 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. Pubmed.

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

27. Cho E.J; Xia S; Ma LC; Robertus J; Krug RM; Anslyn EV; Montelione GT; Ellington AD. J Biomol Screen. 2012, 17: 448 – 459. Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay.  PMC in process. Pubmed.

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

28. Koga N; Tatsumi-Koga R; Liu G; Xiao R; Acton TB; Montelione GT; Baker D. Nature. 2012, 491: 222 – 227. Principles for designing ideal protein structures.  suppl. material. PMC3705962. Pubmed.

Comparison of computational models with experimentally determined structures.

29. Kim D; Zheng H; Huang YJ; Montelione GT; Hunt JF. 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. Pubmed.

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 SD; Kiss G; Kuzin AP; Smith AJ; Gallaher JL; Pianowski Z; Helgeson RC; Grjasnow A; Xiao R; Seetharaman J; Su M; Vorobiev S; Lew S; Forouhar F; Kornhaber GJ; Hunt JF; Montelione GT; Tong L; Houk KN; 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. Pubmed.

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

31. Eletsky A; Jeong MY; Kim H; Lee HW; Xiao R; Pagliarini D.J; Prestegard JH; Winge DR; Montelione GT; 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. Pubmed.

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”

32. Thompson J; Sgourakis NG; 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. Pubmed.

Full Text
Cite This Work

33. Rosato A; Aramini JM; Arrowsmith C; Bagaria A; Baker D; Cavalli A; Doreleijers JF; Eletsky A; Giachetti A; Guerry P; Gutmanas A; Güntert P; He Y; Herrmann T; Huang YJ; Jaravine V; Jonker HRA; Kennedy MA; Lange OF; Liu G; Malliavan TE; Mani R; Mao B; Montelione GT; Nilges M; Possi P; van der Schot G; Schwalbe H; Szyperski TA; Vendruscolo M; Vernon R; Vranken WF; de Vries S; Vuister GW; 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. Pubmed.

Full Text
Cite This Work

34. Ramelot TA; Yang Y; Xiao R; Acton TB; Everett JK; Montelione GT; Kennedy MA. PROTEINS: Struct Funct Bioinformatics. 2012, 2: 667 – 670. Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron.  suppl. material. PMC3766420. Pubmed.

Full Text
Cite This Work

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

Full Text
Cite This Work

36. Kobayashi H; Swapna GVT; Wu KP; Afinogenova Y; Conover K; Mao B; Montelione GT; 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. Pubmed.

Full Text
Cite This Work

37. Eletsky A; Petrey D; Zhang QC; Lee HW; Acton T; Xiao R; Everett J; Prestegard J; Honig B; Montelione GT; 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. Pubmed.

Full Text
Cite This Work

38. Eletsky A; Acton T; Xiao R; Everett J; Montelione GT; 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. Pubmed.

Full Text
Cite This Work

39. Wu Y; Punta M; Xiao R; Acton T; Sathyamoorthy B; Dey F; Fischer M; Skerra A; Rost B; Montelione GT; 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. Pubmed.

Full Text
Cite This Work

40. Ertekin A; Aramini JM; Rossi P; Leonard PG; Janjua H; Xiao R; Maglaqui M; Lee HW; Prestegard JH; Montelione GT. 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. Pubmed.

Full Text
Cite This Work

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

Full Text
Cite This Work

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

Full Text
Cite This Work
Full Text
Cite This Work

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

44. Lange OF; Rossi P; Sgourakis N; Song Y; Lee HW; Aramini JM; Ertekin A; Xiao R; Acton TB; Montelione GT; 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.

Full Text
Cite This Work