Integrated prediction of the effect of mutations on multiple protein characteristics

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 1, 2011, Pages 165-178

  Johnston, Michael A ^a   Søndergaard, Chresten R ^a   Nielsen, Jens Erik ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

Binding; pK a values; Site directed mutagenesis; Stability; Structure based energy calculations; Web server

Indexed keywords

BARNASE; GOLGI MANNOSIDASE; HIV REVERSE TRANSCRIPTASE P66; MANNOSIDASE; PROTEINASE; RHODOPSIN; RNA DIRECTED DNA POLYMERASE; SUBTILISIN; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; ENZYME ACTIVITY; LIGAND BINDING; ONLINE SYSTEM; PEAT SA; POINT MUTATION; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEIN STRUCTURE; QUALITY CONTROL; SITE DIRECTED MUTAGENESIS;

ALGORITHMS; COMPUTER SIMULATION; LIGANDS; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEINS; SOFTWARE; SUBTILISINS; THERMODYNAMICS;

EID: 78649763345     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22870     Document Type: Article

References (48)

1. Fersht AR, Sato S. Phi-value analysis and the nature of protein-folding transition states. Proc Natl Acad Sci USA 2004; 101: 7976-7981.
2. Fersht A. Dissection of the structure and activity of the tyrosyl-trna synthetase by sitedirected mutagenesis. Biochemistry 1987; 26: 8031-8037.
3. Bemporad F, Gsponer J, Hopearuoho H, Plakoutsi G, Stati G, Stefani M, Taddei N, Vendruscolo M, Chiti F. Biological function in a non-native partially folded state of a protein. EMBO J 2008; 27: 1525-1535.
4. Horovitz A, Fersht A. Strategy for analysing the co-operativity of intramolecular interactions in peptides and proteins. J Mol Biol 1990; 214: 613-617.
5. Pons J, Rajpal A, Kirsch J. Energetic analysis of an antigen/antibody interface: alanine scanning mutagenesis and double mutant cycles on the hyhel-10/lysozyme interaction. Protein Sci 1999; 8: 958-968.
6. Vajdos F, Adams C, Breece T, Presta L, De Vos A, Sidhu S. Comprehensive functional maps of the antigen-binding site of an anti-erbb2 antibody obtained with shotgun scanning mutagenesis. J Mol Biol 2002; 320: 415-428.
7. Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000; 10: 139-145.
8. Wang W, Donini O, Reyes CM, Kollman PA. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, proteinprotein, and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct 2001; 30: 211-243.
9. Villà J, Warshel A. Energetics and dynamics of enzymatic reactions. J Phys Chem B 2001; 105: 7887-7907.
10. Miller TF, III, Vanden-Eijnden E, Chandler D. Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain. Proc Natl Acad Sci USA 2007; 104: 14559-14564.
11. Berman H, Henrick K, Nakamura H. Announcing the worldwide protein data bank. Nat Struct Biol 2003; 10: 980.
12. Rohl C, Strauss C, Misura K, Baker D. Protein structure prediction using rosetta. Methods Enzymol 2004; 383: 66-93.
13. Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current pdb library. Proc Natl Acad Sci USA 2005; 102: 1029-1034.
14. Mendes J, Guerois R, Serrano L. Energy estimation in protein design. Curr Opin Struct Biol 2002; 12: 441-446.
15. Chakrabarti R, Klibanov AM, Friesner RA. Sequence optimization and designability of enzyme active sites. Proc Natl Acad Sci USA 2005; 102: 12035-12040.
16. Böhm HJ. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 1994; 8: 243-256.
17. Das R, Baker D. Macromolecular modeling with rosetta. Annu Rev Biochem 2008; 77: 363-382.
18. 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.
19. Kwasigroch JM, Gilis D, Dehouck Y, Rooman M. Popmusic, rationally designing point mutations in protein structures. Bioinformatics 2002; 18: 1701-1702.
20. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structurederived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11: 2714-2726.
21. Capriotti E, Fariselli P, Casadio R. I-mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 2005; 33(Web Server issue): W306-W310.
22. Pokala N, Handel TM. Energy functions for protein design: adjustment with proteinprotein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 2005; 347: 203-27.
23. Parthiban V, Gromiha MM, Schomburg D. Cupsat: prediction of protein stability upon point mutations. Nucleic Acids Res 2006; 34(Web Server issue): W239-W242.
24. Yin S, Ding F, Dokholyan NV. Modeling backbone flexibility improves protein stability estimation. Structure 2007; 15: 1567-76.
25. Huang L-T, Gromiha MM, Ho S-Y. iptree-stab: interpretable decision tree based method for predicting protein stability changes upon mutations. Bioinformatics 2007; 23: 1292-1293.
26. Masso M, Vaisman II. Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. Bioinformatics 2008; 24: 2002-2009.
27. Benedix A, Becker CM, de Groot BL, Caflisch A, Böckmann RA. Predicting free energy changes using structural ensembles. Nat Methods 2009; 6: 3-4.
28. Potapov V, Cohen M, Schreiber G. Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 2009; 22: 553-560.
29. 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.
30. Dehouck Y, Grosfils A, Folch B, Gilis D, Bogaerts P, Rooman M. Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics 2009; 25: 2537-2543.
31. Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. Pdb2pqr: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 2007; 35(Web Server issue): W522-W525.
32. Tynan-Connolly BM, Nielsen JE. pkd: re-designing protein pka values. Nucleic Acids Res 2006; 34(Web Server issue): W48-W51.
33. Tynan-Connolly BM, Nielsen JE. Redesigning protein pka values. Protein Sci 2007; 16: 239-249.
34. Dunbrack RLJ, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997; 6: 1661-1681.
35. Petukhov M, Cregut D, Soares CM, Serrano L. Local water bridges and protein conformational stability. Protein Sci 1999; 8: 1982-1989.
36. Wang R, Fang X, Lu Y, Wang S. The pdbbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 2004; 47: 2977-2980.
37. Wang R, Fang X, Lu Y, Yang C-Y, Wang S. The pdbbind database: methodologies and updates. J Med Chem 2005; 48: 4111-4119.
38. Radisky ES, Koshland DE, Jr. A clogged gutter mechanism for protease inhibitors. Proc Natl Acad Sci USA 2002; 99: 10316-10321.
39. DeSantis G, Jones J. Chemical modifications at a single site can induce significant shifts in the ph profiles of a serine protease. J Am Chem Soc 1998; 120: 8582-8586.
40. Herráez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ 2006; 34: 255-261.
41. Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 2006; 25: 247-260.
42. Schuttelkopf AW, van Aalten DMF. Prodrg: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 2004; 60(Pt 8): 1355-1363.
43. Kumar MDS, Bava KA, Gromiha MM, Prabakaran P, Kitajima K, Uedaira H, Sarai A. Protherm and pronit: thermodynamic databases for proteins and proteinnucleic acid interactions. Nucleic Acids Res 2006; 34(Database issue): D204-D206.
44. Wang R, Lu Y, Wang S. Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 2003; 46: 2287-2303.
45. Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002; 99: 14116-14121.
46. Siezen RJ, Leunissen JA. Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci 1997; 6: 501-523.
47. Jaenicke R. Protein stability and molecular adaptation to extreme conditions. Eur J Biochem 1991; 202: 715-728.
48. Jaenicke R. Stability folding of ultrastable proteins: eye lens crystallins and enzymes from thermophiles. FASEB J 1996; 10: 84-92.