Bioinformatics approaches for understanding and predicting protein folding rates

Current Bioinformatics

Volumn 3, Issue 1, 2008, Pages 1-9

  Gromiha, M Michael ^a   Selvaraj, S ^b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b BHARATHIDASAN UNIVERSITY   (India)

Author keywords

value analysis; Amino acid properties; Contact order; Folding rate; Long range order; LRO; Prediction; Regression technique

Indexed keywords

CHYMOTRYPSIN INHIBITOR; PROTEIN S6; PROTEIN SH3; TACROLIMUS;

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; BIOINFORMATICS; CLUSTER ANALYSIS; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; FLUOROMETRY; HYDROPHOBICITY; METHODOLOGY; PHOTOLYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; REGRESSION ANALYSIS; REVIEW; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

EID: 38949121906     PISSN: 15748936     EISSN: None     Source Type: Journal    
DOI: 10.2174/157489308783329832     Document Type: Review

References (54)

1. Eaton WA, Munoz V, Hagen SJ, et al. Fast kinetics and mechanisms in protein folding. Ann Rev Biophys Biomol Struct 2000; 29: 327-59.
2. Maxwell KL, Wildes. D, Zarrine-Afsar A, et al. Protein folding: defining a "standard" set of experimdtal conditions and a preliminary kinetic data set of two-state proteins. Protein Sci 2005; 14: 602-16.
3. Fulton KF, Bate MA, Faux NG, Mahmood K, Betts C, Buckle AM; Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. Nucleic Acids Res 2007; 35: D304-7
4. Gromiha MM, Selvaraj S. Inter-residue interactions in protein folding and stability. Prog Biophys Mol Biol 2004; 86: 235-77.
5. Plaxco KW, Simons KT, Baker D, Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998; 277: 985-94.
6. Gromiha MM, Selvaraj S, Comparison betwein long-range interactions and contact order in determining the folding rate of two-state. proteins: application of long-range order to folding rate prediction. J Mol Biol 2001; 310: 27-32.
7. Miller EJ, Fischer KF, Marqusee, S, Experimental Evaluation of Topological Parameters Determining Protein-Folding Rates. Proc Natl Acad Sci USA 2002; 99: 10359-63.
8. Zhou H, Zhou Y, Folding rate prediction using total contact distance. Biophys J 2002; 82: 458-63.
9. Debe DA, Goddard WA 3rd, First principles prediction of protein folding rates. J Mol Biol 1999; 294: 619-625.
10. Munoz V, Eaton WA, A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci USA 1999; 96: 11311-16.
11. Dinner AR, Karplus M, The roles of stability and contact order in determining protein folding rates. Nat Struct Biol. 2001; 8: 21-22.
12. Makarov DE, Keller CA, Plaxco KW, Metiu H, How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc Natl Acad Sci USA 2002; 99: 3535-39.
13. Makarov DE, Plaxco KW, The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci 2003, 12: 17-26.
14. Dokholyan NV, Li L, Ding F, Shaknovich EI, Topological determinants of protein folding. Proc Natl Acad Sci USA 2002; 99: 8637-41.
15. Zhang L, Li J, Jiang Z, Zia A, folding rate prediction on neural network model. Polymer 2003; 44: 1751-56.
16. Gromiha MM, Importance of native state topology for determining the folding rate of two-state proteins. J Chem Inf Comp Sci 2003; 43: 1481-85.
17. Galzitskaya OV, Garbuzynskiy SO, Ivankov DN, Finkelstein AV, Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Proteins 2003; 51: 162-66.
18. Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV, Contact order revisited: influence of protein size on the folding rate. Protein Sci 2003; 12: 2057-62.
19. Shao H, Peng Y, Zeng ZH, A simple parameter relating sequences with folding rates of small alpha helical proteins. Protein Pept Lett 2003; 10: 277-280.
20. Micheletti C, Prediction of folding rates and transition-state placement from native-state geometry. Proteins 2003; 51: 74-84.
21. Gong H, Isom DG, Srinivasan R, Rose GD, local secondary structure content predicts folding rates for simple, two-state proteins. J Mol Biol 2003; 327: 1149-54.
22. Ivankov DN, Finkelstein AV, Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proc Natl Acad Sci USA 2004; 101: 8942-44.
23. Gromiha MM, A Statistical Model for Predicting Protein Folding Rates from Amino Acid Sequence with Structural Class Information. J Chem Inf Model 2005; 45: 494-501.
24. Punta M, Rost B, Protein folding rates estimated from contact predictions. J Mol Biol 2005; 348: 507-12.
25. Ma BG, Guo JX, Zhang HY, Direct correlation between proteins' folding rates and their amino acid compositions: an ab initio folding rate prediction. Proteins 2006; 65: 362-72
26. Huang JT, Tian J, Amino acid sequence predicts folding rate for middle-size two-state proteins. Proteins 2006; 63: 551-4.
27. Gromiha MM, Thangakani AM, Selvaraj S, FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acids Res 2006; 34: W70-W74.
28. Fersht AR, Matouscheck A, Serrano L, The folding of an enzyme. I. Theory of protein engineering panalysis of stability and pathway of protein folding. J Mol Biol 1992; 224: 771-782.
29. Itzhaki LS, Otzen DE, Fersht AR, The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol 1995; 254: 260-88.
30. Grantcharova VP, Riddle DS, Santiago JV, Baker D, Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol 1998; 5: 714-20.
31. Fulton KF, Main ER, Daggett V, Jackson SE, Mapping the interactions present in the transition state for unfolding/folding of FKBPl2. J Mol Biol 1999; 291: 445-61.
32. Gromiha MM, Selvaraj S. Important amino acid properties for determining the transition state structures of two-state protein mutants. FEBS Lett 2002; 526: 129-34.
33. Selvaraj S, Gromiha MM, Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins. Proteins 2004; 55: 1023-35.
34. Fersht AR, Structure and Mechanism in Protein Science, W.H. Freeman and Company, New York, 1999.
35. Murny L, Shakhnovich E, Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Struct 2001; 30: 361-96.
36. Zhao C, Zhu Y, Zhang H, Liu M, Fan A, Accurate prediction of the folding rate for two-state protein based on amino acid sequences. QSAR Comb Sci 2007; 26: 307-16
37. Capriotti E, Casadio R, K-Fold: a tool for the prediction of the protein folding kinetic order and rate. Bioinformatics 2007; 23: 385-86.
38. Sheinerman FB, Brooks CL 3rd, Molecular picture of folding of a small alpha/beta protein. Proc Natl Acad Sci USA 1998; 95: 1562-67.
39. Zhang L, Sun T, Folding rate prediction using n-order contact distance for proteins with two- and three-state folding kinetics. Biophys Chem 2005; 113: 9-16.
40. Dixit PD, Weikl TR, A simple measure of native-state topology and chain connectivity predicts the folding rates of two-state proteins with and without crosslinks. Proteins 2006; 64: 193-197.
41. Prabhu NP, Bhuyan AK, Prediction of folding rates of small proteins: empirical relations based on length, secondary structure content, residue type, and stability. Biochemistry 2006; 45: 3805-12.
42. Punta M, Rost B, PROFcon: novel prediction of long-range contacts. Bioinformatics 2005; 21: 2960-68.
43. Gromiha, MM, Oobatake M, Sarai A, Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys Chem 1999; 82: 51-67.
44. Gromiha MM, Oobatake M, Kolo H, Uedeira H, Sarai A; Importance of surrounding residues for protein stability of partially buried mutations. J Biomol Struct Dyn 2000; 18: 281-95.
45. Jackson SE, How do small single proteins fold? Fold Des 1998; 3: R81-91.
46. Matouschek A, Kellis JT Jr, Serrano L, Fersht AR, Mapping the transition state and pathway of protein folding by protein engineering. Nature 1989; 340: 122-26.
47. Nolting B, Protein folding kinetics. Springer-Verlag, Heidelberg, 1999
48. van Gunsteren WF, Mark AE, Prediction of the activity and stability effects of site-directed mutagenesis on a protein core. J Mol Biol 1992; 227: 389-95.
49. Main ER, Fulton KF, Jackson SE, Folding pathway of FKBP12 and characterisation of the transition state. J Mol Biol 1999; 291: 429-44
50. Nozaki Y, Tanford C, The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J Biol Chem 1971; 246: 2211-17.
51. Jones DD, Amino acid properties and side-chain orientation in proteins: a cross correlation approach. J Theor Biol 1975, 50: 167-83.
52. Kragelund BB, Osmark P, Neergaard TB, et al. The formation of a native-like structure containing eight conserved hydrophobic residues is rate-limiting in two-state protein folding of ACBP. Nat Struct Biol 1999; 6: 594-601.
53. Kragelund BB, Poulsen K, Andersen K, et al. Conserved residues and their role in the structure, function, and stability of acylcoenzyme A binding protein. Biochemistry 1999; 38: 2386-94.
54. Chu W, Ghahramani Z, Podtelezhnikov A, Wild DL, Bayesian segmental models with multiple sequence alignment profiles for protein secondary structure and contact map prediction. IEEE/ACM Trans Comput Biol Bioinform 2006; 3:98-113.