Protein side-chain rearrangement in regions of point mutations

Proteins: Structure, Function and Genetics

Volumn 50, Issue 2, 2003, Pages 272-282

  Eyal, Eran ^a   Najmanovich, Rafael ^a   Edelman, Marvin ^a   Sobolev, Vladimir ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

B factor; Protein Data Bank; Side chain flexibility; Side chain prediction

Indexed keywords

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; HYDROPHILICITY; HYDROPHOBICITY; POINT MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ELECTROSTATICS; LIGANDS; MODELS, MOLECULAR; PLIABILITY; POINT MUTATION; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; SOLVENTS;

EID: 0037296382     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10276     Document Type: Article

References (60)

1. Shortle D. Mutational studies of protein structures and their stabilities. Rev Biophys 1992;25:205-250.
2. Eigenbrot C, KossiakoffAA. Structural consequences of mutation. Curr Opin Biotech 1992;333-337.
3. Rejto PA, Freer ST. Protein conformational substates from X-ray crystallography. Progr Biophys Mol Biol 1996;66:167-196.
4. De Filippis V, Sander C, Vriend G. Predicting local structural changes that result from point mutations. Protein Eng 1994;7:1203-1208.
5. Janin J, Wodak S, Levitt M, Maigret B. Conformation of amino acid side-chains in proteins. J Mol Biol 1978;125:357-386.
6. Schrauber H, Eisenhaber F, Argos P. Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 1993;230:592-612.
7. MArthur MW, Thornton JM. Protein side-chain conformations: A systematic variations of χ1 mean values with resolution - A consequence of multiple rotameric states? Acta Crystallogr 1999;D55:994-1004.
8. Dunbrack RL, Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Struct Biol 1994;1:334-340.
9. Hutchinson EG, Thornton JM. A revised set of potentials for β-turn formation in proteins. Protein Sci 1994;3:2207-2216.
10. Street AG, Mayo SL. Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone. Proc Natl Acad Sci USA 1999;96:9074-9076.
11. Eswar N, Ramakrishnan C. Secondary structures without backbone: An analysis of backbone mimicry by polar side chains in protein structures. Protein Eng 1999;12:447-455.
12. Eswar N, Ramakrishnan C. Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Eng 2000;13:227-238.
13. Tuffery P, Etchebest C, Hazout S, Lavery R. A new approach to the rapid determination of protein side chain conformations. J Biomol Struct Dyn 1991;8:1267-1289.
14. Dunbrack RL, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol 1993;230:543-574.
15. Koehl P, Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 1994;239:249-275.
16. Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001;311:421-430.
17. Lee C, Subbiah S. Prediction of protein side-chain conformation by packing optimization. J Mol Biol 1991;217:373-388.
18. Holm L, Sander C. Fast and simple Monte Carlo algorithm for side chain optimization in proteins: Application to model building by homology. Proteins 1992;14:213-223.
19. Hwang, JK, Liao, WF. Side-chain prediction by neural networks and simulated annealing optimisation. Protein Eng 1995;8:363-370.
20. Shenkin PS, Farid H, Fetrow JS. Prediction and evaluation of side-chain conformations for protein backbone structures. Proteins 1996;26:323-352.
21. Kussell E, Shimada J, Shakhnovich EI. Excluded volume in protein side-chain packing. J Mol Biol 2001;311:183-193.
22. Sutcliffe MJ, Hayes FRF, Blundel TL. Knowledge based modeling of homologous proteins, part II: Rules for the conformations of substituted side chains. Protein Eng 1987;1:385-392.
23. Laughton CA. Prediction of protein side-chain conformations from local three-dimensional homology relationships. J Mol Biol 1994;235:1088-1097.
24. Chinea G, Padron G, Hooft RWW, Sander C, Vriend G. The use of position-specific rotamers in model-building by homology. Proteins 1995;23:415-421.
25. Bower MJ, Cohen FE, Dunbrack RL. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J Mol Biol 1997;267:1268-1282.
26. Mendes J, Bapitista AM, Carrondo MA, Soares CM. Improved modeling of side chains in proteins with rotamer-based method: A flexible rotamer model. Proteins 1999;37:530-543.
27. Feig M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CL. Accurate reconstruction off all-atom protein representations from side-chain-based low-resolution models. Proteins 2000;41:86-97.
28. Samudrala R, Moult J. Determinants of side-chain conformational preferences in protein structures. Protein Eng 1998;11:991-997.
29. Summers NL, Carlson WD, Karplus M. Analysis of side-chain orientations in homologous proteins. J Mol Biol 1987;196:175-198.
30. α coordinates: A test study. Proteins 1989;5:170-182.
31. Levitt M. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992;226:507-533.
32. Eisenmenger F, Argos P, Abagyan R. A method to configure protein side-chains from the main-chain trace in homology modelling. J Mol Biol 1993;231:849-860.
33. Wilson C, Gregoret LM, Agard DA. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 1993;229:996-1006.
34. Cheng B, Nayeem A, Scheraga HA. From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins. J Comput Chem 1996;17:1453-1480.
35. Desmet J, De Maeyer M, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992;356:539-542.
36. Goldstein RF. Efficient rotamer elimination applied to protein side-chains and related spin-glasses. Biophys J 1994;66:1335-1340.
37. Lasters I, De Maeyer M, Desmet J. Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains. Protein Eng 1995;8:815-822.
38. De Maeyer M, Lasters I. All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of side-chains by dead-end elimination. Fold Des 1997;2:53-66.
39. Lee C. Predicting protein mutant energetics by self-consistent ensemble optimization. J Mol Biol 1994;236:918-939.
40. Vasquez M. An evaluation of discrete and continuum search techniques for conformational analysis of side-chains in proteins. Biopolymers 1995;36:53-70.
41. Voigt CA, Gordon DB, Mayo SL. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J Mol Biol 2000;299:789-803,
42. Lasters I, Desmet J. The fuzzy-end elimination theoremcorrectly implementing the side-chain placement algorithm based on the dead-end elimination theorem. Protein Eng 1993;6:717-722.
43. Keller DA, Shibata M, Marcus E, Ornstein RL, Rein R. Finding the global minimum: A fuzzy end elimination implementation. Protein Eng 1995;8:893-904.
44. Liang SD, Grishin NV. Side-chain modeling with an optimized scoring function. Protein Sci 2002;11:322-331.
45. Eyal E, Najmanovich R, Sobolev V, Edelman M. MutaProt: A Web interface for structural analysis of point mutations. Bioinformatics 2001;17:381-382.
46. Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M. Automated analysis of interatomic contacts in proteins. Bioinformatics 1999;15:327-332.
47. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: A computer based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
48. 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.
49. Najmanovich R, Kuttner J, Sobolev V, Edelman M. Side-chain flexibility in proteins upon ligand binding. Proteins 2000;39:261-268.
50. Petrella R, Lazaridis T, Kurplus M. Protein side chain conformer prediction: A test of the energy function. Fold Des 1998;3:353-377.
51. Flores TP, Orengo CA, Moss DS, Thornton JM. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 1993;2:1811-1826.
52. Betts MJ, Sternberg MJE. An analysis of conformational changes on protein-protein association: Implications for predictive docking. Protein Eng 1999;12:271-283.
53. Lee B, Richards FM. The interpretation of protein structure: Estimation of static accessibility. J Mol Biol 1971;55:379-400.
54. Parthasarathy S, Murthy MRN. Analysis of temperature factor distribution in high-resolution protein structures. Protein Sci 1997;6:2561-2567.
55. Dunbrack RL, Cohen FE. Bayesian statistical analysis of protein side chain rotamer preferences. Protein Sci 1997;6:1661-1681.
56. Petsko GA, Ringe D. Fluctuations in protein structure from x-ray diffraction. Annu Rev Biophys Bioeng 1984;13:331-371.
57. Carugo O, Argos P. Correlation between side-chain mobility and conformation in protein structures. Protein Eng 1997;10:777-787.
58. Kamphuis IG, Drenth J, Baker EN. Comparative studies based on the high-resolution structures of papain and actinidin, and on amino acid sequence information for cathepsins B and H, and stem bromelain. J Mol Biol 1985;182:317-329.
59. Zhao SR, Goodsell DS, Olson AJ. Analysis of a data set of paired uncomplexed protein structures: New metrics for side-chain flexibility and model evaluation. Proteins 2001;43:271-279.
60. Hooft RWW, Sander C, Vriend G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 1996;26:363-376.