X-ray vs. NMR structures as templates for computational protein design

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 1, 2009, Pages 97-110

  Schneider, Michael ^a   Fu, Xiaoran ^a,b   Keating, Amy E ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MONSANTO COMPANY   (United States)

Author keywords

angle recovery; Native sequence recovery; Packing quality; Side chain packing

Indexed keywords

ARTICLE; CONTROLLED STUDY; INTERMETHOD COMPARISON; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; X RAY;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEINS;

EID: 70349334428     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22421     Document Type: Article

References (59)

1. Pabo C. Molecular technology-designing proteins and peptides. Nature 1983;301:200.
2. Desmet J, Maeyer MD, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992;356:539-542.
3. Dahiyat BI, Mayo SL. Protein design automation. Protein Sci 1996;5:895-903.
4. Dahiyat BI, Sarisky CA, Mayo SL. De novo protein design: towards fully automated sequence selection. J Mol Biol 1997;273:789-796. (Pubitemid 27493719)
5. Ali MH, Taylor CM, Grigoryan G, Allen KN, Imperiali B, Keating AE. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure. Structure 2005;13:225-234. (Pubitemid 40247698)
6. Bolon DN, Mayo SL. Enzyme-like proteins by computational design. Proc Natl Acad Sci U S A 2001;98:14274-14279.
7. Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J Am Chem Soc 2005;127:1346-1347. (Pubitemid 40204489)
8. Fu X, Apgar JR, Keating AE. Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. J Mol Biol 2007;371:1099-1117.
9. Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, 3rd, Hilvert D, Houk KN, Stoddard BL, Baker D. De novo computational design of retro-aldol enzymes. Science 2008;319:1387-1391.
10. Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D. Kemp elimination catalysts by computational enzyme design. Nature 2008;453:190-195. (Pubitemid 351667979)
11. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003;302:1364-1368. (Pubitemid 37452172)
12. Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Biotechnol 2007;25:1171-1176. (Pubitemid 47538113)
13. Lombardi A, Summa CM, Geremia S, Randaccio L, Pavone V, DeGrado WF. Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins. Proc Natl Acad Sci U S A 2000;97:6298-6305. (Pubitemid 30412708)
14. Reina J, Lacroix E, Hobson SD, Fernandez-Ballester G, Rybin V, Schwab MS, Serrano L, Gonzalez C. Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol 2002;9:621-627. (Pubitemid 34816144)
15. Butterfoss GL, Kuhlman B. Computer-based design of novel protein structures. Annu Rev Biophys Biomol Struct 2006;35:49-65. (Pubitemid 43877369)
16. Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, DeGrado WF. De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc 2007;129:10732-10740. (Pubitemid 350067483)
17. Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Jr, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 2006;441:656-659. (Pubitemid 43927299)
18. Joachimiak LA, Kortemme T, Stoddard BL, Baker D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol 2006;361:195-208. (Pubitemid 44041449)
19. Slovic AM, Kono H, Lear JD, Saven JG, DeGrado WF. Computational design of water-soluble analogues of the potassium channel KcsA. Proc Natl Acad Sci U S A 2004;101:1828-1833. (Pubitemid 38228976)
20. Kono H, Saven JG. Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. J Mol Biol 2001;306:607-628. (Pubitemid 33027726)
21. Green DF, Dennis AT, Fam PS, Tidor B, Jasanoff A. Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. Biochemistry 2006;45:12547-12559. (Pubitemid 44583697)
22. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
23. Larson SM, England JL, Desjarlais JR, Pande VS. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci 2002;11:2804-2813.
24. Spronk CA, Linge JP, Hilbers CW, Vuister GW. Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 2002;22:281-289.
25. Snyder DA, Montelione GT. Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins 2005;59:673-686.
26. Ban YE, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures by local density of protons. Proteins 2006;62:852-864. (Pubitemid 43364151)
27. Fan H, Mark AE. Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins 2003;53:111-120. (Pubitemid 37059549)
28. Lee MR, Kollman PA. Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction. Structure 2001;9:905-916.
29. Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A 2000;97:10383-10388. (Pubitemid 30707275)
30. Brunger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992;355:472-475.
31. Brunger AT. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr Sect D 1993;49:24-36.
32. Brunger AT, Clore GM, Gronenborn AM, Saffrich R, Nilges M. Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science 1993;261:328-331. (Pubitemid 23982761)
33. Gronwald W, Kirchhofer R, Gorler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR. RFAC, a program for automated NMR R-factor estimation. J Biomol NMR 2000;17:137-151. (Pubitemid 30452333)
34. Huang YJ, Powers R, Montelione GT. Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 2005;127:1665-1674. (Pubitemid 40229151)
35. Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, Vuister GW. Quantitative evaluation of experimental NMR restraints. J Am Chem Soc 2003;125:12026-12034. (Pubitemid 37175433)
36. Bhattacharya A, Tejero R, Montelione GT. Evaluating protein structures determined by structural genomics consortia. Proteins 2007;66:778-795. (Pubitemid 46273064)
37. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins 1992;12:345-364.
38. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996;8:477-486. (Pubitemid 126706801)
39. Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 2004;32:W615-W619.
40. Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV. Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Proteins 2005;60:139-147.
41. Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA. Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins 2008;75:147-167.
42. Korkegian A, Black ME, Baker D, Stoddard BL. Computational thermostabilization of an enzyme. Science 2005;308:857-860.
43. Dunbrack RL. Rotamer libraries in the 21st century. Curr Opin Struct Biol 2002;12:431-440.
44. Hu X, Wang H, Ke H, Kuhlman B. High-resolution design of a protein loop. Proc Natl Acad Sci U S A 2007;104:17668-17673.
45. Saunders CT, Baker D. Recapitulation of protein family divergence using flexible backbone protein design. J Mol Biol 2005;346:631-644.
46. Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387. (Pubitemid 34722226)
47. Lippow SM, Tidor B. Progress in computational protein design. Curr Opin Biotechnol 2007;18:305-311.
48. Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins 2007;69:449-465. (Pubitemid 47623864)
49. Kelley LA, Gardner SP, Sutcliffe MJ. An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng 1997;10:737-741.
50. Hubbard SJ, Thornton JM. Naccess, computer program. Department of Biochemistry and Molecular Biology, London: University College; 1993.
51. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
52. Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
53. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152. (Pubitemid 29165128)
54. Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. J Mol Biol 2002;322:65-78. (Pubitemid 36132671)
55. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225. (Pubitemid 27192690)
56. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202. (Pubitemid 29435759)
57. Goldstein RF. Efficient rotamer elimination applied to protein sidechains and related spin glasses. Biophys J 1994;66:1335-1340.
58. Dominy BN, Brooks CL. Development of a generalized born model parametrization for proteins and nucleic acids. J Phys Chem B 1999;103:3765-3773.
59. Beroza P, Case DA. Calculations of proton-binding thermodynamics in proteins. Methods Enzymol 1998;295:170-189.