nysgrc-logo Related Publications by the NYSGXRC protein structure initiative

I: Structures- Brief, Electronic

1. K. Rajashankar, M.R. Chance, S.K. Burley, J. Jiang, S.C. Almo, A. Bresnick, R. Huang, G. He, H. Chen, M. Sullivan, J. Toomey, T. Radhakannan, W. Franklin, A. Sali, U. Pieper, and L. McMahan (2002) Structural Genomics at the National Synchrotron Light Source. 2001 National Synchrotron Light Source Activity Report, 2-28 to 2-32.

2. B.D. Danniels, J.-S. Jiang and D. Fu (2004). Crystallization and preminary crystallographic analysis of the Escherichia coli water channel AqpZ. Acta Cryst. D60, 564-566.

3. A. Gogos, Mu, H., Bahna, H., Gomez, C. A., and Shapiro, L. (2004) Crystal Structure of YdcE Protein from Bacillus subtilis. Proteins, in press.

4. A. Gogos, J. Gorman, and L. Shapiro (2004) Structure of Escherichia coli YfdW, a type III CoA transferase, Acta Cryst. D60, 507-511.

5. J. Gorman and L. Shapiro (2004) Structure of Serine Acetyltransferase from Haemophilus influenzae Rd. Acta Cryst. D, in press.

6. M.J. Romanowski, S.A. Gibney, and S.K. Burley (2002) Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17. PROTEINS: Structure, Function and Genetics 15, 403-407.

7. M.J. Romanowski and S.K. Burley (2002) Crystal structure of Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. PROTEINS: Structure, Function and Genetics 47, 558-562.

8. M.J. Romanowski, J.B. Bonanno, and S.K. Burley (2002) Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals amethyltransferase fold. PROTEINS: Structure, Function and Genetics 47, 563-567.

9. M.J. Romanowski, J.B. Bonanno, and S.K. Burley (2002) Crystal structure of Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily. PROTEINS: Structure, Function and Genetics 47, 568-571.

10. S.S. Ray, J.B. Bonanno, H. Chen, S. Wu, H. De Lencastre, A. Tomasz, and S.K. Burley (2003) Crystal structure of a Methanococcus jannaschii DNA-binding protein: Implications for antibiotic resistance in Staphylococcus aureus. PROTEINS: Structure, Function and Genetics 50, 170-173.

11. A.M Deaconescu, A. Roll-Mecak, S.E. Gerchman, H. Kycia, F.W. Studier, J.B. Bonanno, and S.K. Burley (2002) X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1). PROTEINS: Structure, Function and Genetics 48, 431-436.

12. T. Burling, R. Kniewel, J.A. Buglino, T. Chadna, A. Beckwith, and C.D. Lima (2003) Structural analysis of uridine phosphorylase at 2.0A resolution. Acta Cryst D. 59, 73-76.

13. J. Buglino, V. Shen, P. Hakimian, and C.D. Lima (2003) Structural and biochemical analysis of the Obg GTP-binding protein. Structure 10, 1581-1592.

14. R. Kniewel, J.A. Buglino, V. Shen, T. Chadna, A. Beckwith, and C.D. Lima (2002) Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase. Journal of Structural and Functional Genomics 2, 129-134.

II: Structures- Full Length

15. M.R. Chance, A.R. Bresnick, S.K. Burley, J.-S. Jiang, C.D. Lima, A. Sali, S.C. Almo, J.B. Bonanno, J.A. Buglino, S. Boulton, H. Chen, N. Eswar, G. He, R. Huang, V. Ilyin, L. McMahan, U. Pieper, S.S. Ray, M. Vidal, and L.K. Wang (2002) Structural Genomics: A Pipeline for Providing Structures for the Biologist. Protein Science 11, 723-738.

16. T. Dodatko, A.A. Fedorov, M. Grynberg, Y. Patskovsky. D.A. Rozwarski, E. Aronoff-Spencer, E. Kondraskina, T. Irving, A. Godzik, and S.C. Almo (2004) Crystal Structure of the Actin- Binding Domain of the Cyclase Associated Protein (CAP), Biochemistry, in the press.

17. S. Eswaramoorthy, S. Gerchman, V. Graziano, H. Kycia, F.W. Studier, and S. Swaminathan (2003) Structure of a yeast hypothetical protein selected by structural genomics approach. Acta Crystallographica D 59, 127-135.

18. D. Kumaran, S. Eswaramoorthy, S. Gerchman, H. Kycia, F.W. Studier, and S. Swaminathan (2003) Crystal structure of a putative CN-hydrolase from yeast, Proteins 52, 283-291.

19. A. Gogos and L. Shapiro (2002) Large conformational changes in the catalytic cycle of glutathione synthase. Structure 10, 1669-1676.

20. S.D. Patel, M.W. Rajala, L. Rossetti, P.E. Scherer, and L. Shapiro (2004) Disulfide-dependent multimeric assembly of resistin family hormones, Science 304, 1154-1158.

21. C.E. Groft, R. Beckmann, A. Sali, and S.K. Burley (2000) Crystal structure of ribosome antiassociation factor eIF6. Nature Structural Biology 7, 1156-1164.

22. K. Kamada, F. Shu, H. Chen, S. Malik, G. Stelzer, R.G. Roeder, M. Meisterernst, and S.K. Burley (2001) Crystal structure of Negative Cofactor 2 Recognizing the TPB-DNA Transcription Complex. Cell 106, 71-81.

23. J.B. Bonanno, C. Edo, N. Easwar, U. Pieper, M.J. Romanowski, V. Ilyin, S.E. Gerchman, H. Kycia, F.W. Studier, A. Sali, and S.K. Burley (2001) Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proceedings of the National Academy of Sciences USA 98, 12896-12901.

24. C.L. Kielkopf and S.K. Burley (2002) X-ray structures of threonine aldolase complexes: Structural bases of substrate recognition. Biochemistry 41, 11711-11720.

25. M.J. Romanowski, R.E. Soccio, J.L. Breslow, and S.K. Burley (2002) Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StARrelated lipid transfer domain. Proceedings of the National Academy of Sciences USA 99, 6949-6954.

26. S.S. Ray, J.B. Bonanno, K.R. Rajashankar, M.G. Pinho, G. He, H. De Lencastre, A. Tomasz, and S.K. Burley (2002) Co-crystal structures of diaminopimelate decarboxylase: Mechanism, evolution, and inhibition of an antibiotic resistance factor from Staphylococcus aureus. Structure 10, 1499-1508.

27. K. Kamada and S.K. Burley (2003) Crystal structure of the MazE/MazF complex: Molecular bases of antidote-toxin recognition. Mol. Cell 11, 875-884.

28. A.K. Padyana and S.K. Burley (2003) Crystal Structure of Shikimate Dehydrogenase with Bound Cofactor Nadp+: Insights Into Function and Evolution, Structure 11, 1005-1013.

29. C.D. Lima (2002) Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation. J. Mol. Biol. 315, 1199-1208.

30. J. Buglino, V. Shen, P. Hakimian, and C.D. Lima (2003) Structural and biochemical analysis of the Obg GTP-binding protein. Structure 10, 1581-1592.

31. R. Beckmann, C.M.T. Spahn, N. Eswar, J. Helmers, P.A. Penczek, A. Sali, J. Frank, and G. Blobel (2001) Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361-372.

32. C.M.T. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, and J. Frank (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae - tRNARibosome and subunit-subunit interactions. Cell 107, 373-386.

33. C.D. Lima (2002) Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation. Journal of Molecular Biology 315, 1199-1208.

34. Fabrega, C., Hausmann, S., Shen, V., Shuman, S., and Lima, C.D. (2004) Structure and mechanism of the mRNA (guanine-N7) cap methyltransferase. Mol. Cell 13, 77-89.

35. Buglino, J., Onwueme, K.C., Ferreras, J.A., Quadri, L.E., and Lima, C.D. (2004) Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from mycobacterium tuberculosis. J. Biol. Chem. May 3 [Epub ahead of print].

36. Deo, R.C., Schmidt, E.F., Elhabazi, A., Togashi, H., Burley, S.K., and Strittmatter, S.M. (2004) Cellular and Structural Basis for CRMP Function In Plexin-Dependent Semaphorin3A Signaling. EMBO J. 23, 9-22.

III: Methodology/Technology Development

37. H. Gao, J. Sengupta, M. Valle, A. Korostelev, N. Eswar, S.M. Stagg, P. VanRoey, R.K. Angrawal, S.C. Harvey, A. Sali, M.S. Chapman, and J. Frank (2003) Study of the Structural Dynamics of the E. Coli 70S Ribosome Using Real Space Refinement. Cell 113, 789-801.

38. Y. Yang, L. Li, G.W. Wong, S.A. Krilis, M.S. Madhusudhan, A. Sali, and R.L. Stevens (2002) RasGRP4: a new mast cell-restricted, ras guanine nucleotide releasing protein with calcium- and diacylglycerol-binding motifs. J. Biol. Chem. 277, 25756-25774.

39. R. Beckmann, C.M.T. Spahn, N. Eswar, J. Helmers, P.A. Penczek, A. Sali, J. Frank, and G. Blobel (2001) Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361-372.

40. C.M.T. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, and J. Frank (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae - tRNA-Ribosome and subunit- subunit interactions. Cell 107, 373-386.

41. Huang, R. Y., Boulton, S., Vidal, M., Almo, S. C., Bresnick, A.R., and Chance, M.R., (2003) High-Throughput Expression, Purification, and Characterization of Recombinant C. elegans Proteins. Biochem. Biophys. Res. Comm. 307, 928-934.

42. Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong C, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR Jr, Hartley JL, Brasch MA, Vandenhaute J, Boulton S, Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, and Vidal M. (2003) C. elegans ORFeome verson 1.1: experimental verification of the genome annotation and resource for proteome- scale protein expression. Nature Gen. 34, 35-41.

43. J.-S. Jiang and R.M. Sweet (2004), Protein Data Bank depositions from synchrotron sources, J. Synchrotron Rad. 11, 319-327.

44. Mancia, F., Patel, S.D., Rajala, M.W., Scherer, P.E., Nemes, A., Ira Schieren, I., Hendrickson, W.A. and Shapiro, L. (2004) Optimization of protein production in mammalian cells with a co- expressed fluorescent marker. Structure, in press.

45. C.S. Gunther and T. Gaasterland (2001) Characterizing the relationship between proteinfusion and gene co-expression. Genome Informatics Workshop Special Issue, Genome Informatics 12, 34-43.

46. S. Gopal, M. Schoreder, U. Pieper, A. Sczyrba, G. Ayetkin-Kurban, S. Bekiranov, J.E. Fajardo, N. Eswar, R. Sanchez, A. Sali, and T. Gaasterland (2001) Homology-based annotation yields 1042 new candidate genes in the Drosophila melanogaster genome. Nature Genetics 27, 337-340.

47. M.H. Serres, S. Gopal, L.A. Nahum, P. Liang, T. Gaasterland, and M. Riley (2001) A functional update of the Escherichia coli K-12 genome. Genome Biology 2, 0035.1- 0035.7.

48. B. John, and A. Sali. (2003) Comparative Protein Structure Modeling by Iterative Alignment, Model Building, and Model Assessment. Nucl. Acids Res. 31, 3982-3992.

49. V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Martí-Renom, and A. Sali. (2003) ModView, a web application for visualization of multiple protein sequences and structures. Bioinformatics 19, 165-166.

50. F. Melo, R. Sánchez, and A. Sali (2002) Statistical potentials for fold assessment. Protein Science 11, 430-448.

51. U. Pieper, N. Eswar, A.C. Stuart, V.A. Ilyin, and A. Sali. (2002) MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research 30, 255-259.

52. A. Fiser, M. Feig, C.L. Brooks III, and A. Sali (2002) Evolution and physics in comparative protein structure modeling. Accounts of Chemical Research 35, 413-421.

53. M.A. Martí-Renom, V.A. Illyin, and A. Sali. (2002) DBAli: A database of alignments and tools for benchmarking protein sequence--structure comparison. Bioinformatics 17, 746-747.

54. A.C. Stuart, V.A. Illyin, and A. Sali. (2002) LigBase: A Database of Families of Aligned Ligand Binding Sites in Known Protein Sequences and Structures. Bioinformatics 18, 200-201.

IV: Othert

55. J.B. Bonanno and S.K. Burley (2002) Structural genomics of proteins contributing to conserved biochemical pathways/processes. Curr. Opin. Struct. Biol. 12, 383-391.

56. S.K. Burley and J.B. Bonanno (2003) "Structural Genomics" in Structural Bioinformatics, Methods of Biochemical Analysis, H. Weissig and P. Bourne, eds., Academic Press, New York, New York, 44, 591-612.

57. S.K. Burley and J.B. Bonanno (2002) Structuring the Universe of Proteins, Ann. Rev. Gen. and Hum. Genet. 3, 243-262.

58. C.E. Groft, R. Beckmann, A. Sali, and S.K. Burley (2001) Response to Paoli. Nature Struct. Biol. 8, 745.

59. R.E. Soccio, R.M. Adams, M.J. Romanowski, E. Sehayek, S.K. Burley, and J.L. Breslow (2002) The novel cholesterol-regulated StarD4 gene encodes a StAR-related lipid transfer protein with two closely related homologues. Proc. Natl. Acad.Sci. USA 99, 6943-6948.

60. S.K. Burley (2000) An overview of structural genomics. Nature Struct. Biol. 7, 932-934.

61. D. Pilloff, K. Dabovic, M.J. Romanowski, J.B. Bonanno, M. Doherty, S.K. Burley, and T.S. Leyh (2003) The kinetic mechanism of phosphomevaloante kinase. J. Biol. Chem. 278, 4510-4514.

62. T. Gaasterland and M. Oprea (2001) Whole-genome analysis: annotations and updates. Current Opinion in Structural Biology 11, 377-381.

63. R. Sanchez, U. Pieper, F. Melo, N. Eswar, M.A. Martí-Renom, M.S. Madhusudhan, N. Mirkovic, and A. Sali (2000) Protein structure modeling for structural genomics. Nature Struct. Biol. 7, 986-990.

64. S. Jin, S. Martinek, W.S. Joo, J.R. Wortman, N. Mirkovic, A. Sali, M.D. Yandell, N.P. Pavletich, M.W. Young, and A.J. Levine (2000) Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc. Natl. Acad.Sci. USA 97, 7301-7306.

65. A. Sali (2001) Target practice. Nature Struct. Biol. 8, 482-484.

66. A. Fiser and A. Sali (2001) "MODELLER: generation and refinement of homology models" in Methods in Enzymology. Carter, C.W. and Sweet, R.M., eds. Academic Press, San Diego, in the press.

67. M.A. Martí-Renom, B. Yerkovich, and A. Sali (2002) Comparative protein structure prediction. Ed: John Wiley & Sons, Inc. Curr. Protocol. Prot. Sci. 1, 2.9.1-2.9.22.

68. M.A. Martí-Renom, M.S. Madhusudhan, A. Fiser, B. Rost, and A. Sali (2002). Reliability of assessment of protein structure prediction methods. Structure 10, 435-440.

69. A. Sali, M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, and B. Rost (2002) Reply to Moult et al. Structure 10, 292-293.

70. M.A. Marti-Renom, A. Fiser, M.S. Madhusudhan, B. John, A. Stuart, N. Eswar, P. Pieper, M-Y. Shen, A. Sali. Modeling protein structure from its sequence. Current Protocols in Bioinformatics John Wiley & Sons, Inc., V. 5 November Issue, Pages 5.1.1-5.1.32, 2003.

71. A. Sali, R. Glaeser, T. Ernst, and W. Baumeister (2003) Structural Proteomics: From words to literature. Nature 422, 216-225, 2003.

72. A. Fiser, A. Sali. Comparative Protein Structure Modeling. In: Protein Structure. Ed: Daniel Chasman. Marcel Dekker, Inc., New York, 167-206, 2003.

73. I.Y.Y. Koh, V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, E. Narayanan, O. Grana, F. Pazos, A. Valencia, A. Sali, and B. Rost. (2003) EVA: evaluation of protein structure prediction servers. Nucl. Acids Res. 31, 3311-3315.

74. N. Mirkovic, M.A. Marti-Renom, B.L. Weber, A. Sali, and A.N.A. Monteiro. (2004) Structure- based assessment of missence mutations in human BRCA1: Implications for breast and ovarian cancer predisposition. Cancer Res. 64, 3790-3797.

75. N. Eswar, B. John, N. Mirkovic, A. Fiser, V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich, and A. Sali. (2003) Tools for comparative protein structure modeling and analysis. Nucl. Acids Res. 31, 3375-3380.

76. A. Rossi, Q. Deveraux, B. Turk, and A. Sali. (2004) Comprehensive search for cysteine cathepsins in the human genome. J. Biol. Chem. 385, 363-372.

77. W. Shi, D. Ostrov, S. Gerchman, H. Kycia, F.W. Studier, W. Edstrom, A. Bresnick, J. Ehrlich, J. Blanchard, S. Almo, and M.R. Chance (2003) "High-Throughput Structural Biology and Proteomics" in Protein Arrays, Biochips and Proteomics: The Next Phase of Genomics Discovery, Marcel Dekker, Inc., New York, Chapter 12, 299-324.

78. Chance, M.R., Fiser, A., Sali, A. Pieper, U., Eashwar, N., Xu, G., Radahakanan, T., and Marinkovic, N. (2004) High throughput computational and experimental techniques in structural genomics, Genome Research, in press.

 
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