Class-Specific Correlations between Protein Folding Rate, Structure-Derived, and Sequence-Derived Descriptors

Proteins: Structure, Function and Genetics

Volumn 54, Issue 2, 2004, Pages 333-341

  Kuznetsov, Igor B ^a   Rackovsky, Shalom ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Contact order; Intrinsic propensity; Protein topology; Secondary structure content; Sequence property; Two state kinetics

Indexed keywords

HELICAL PROTEIN; PROTEIN; SINGLE DOMAIN PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; CORRELATION ANALYSIS; KINETICS; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS;

DATABASES, PROTEIN; KINETICS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 0346458804     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10518     Document Type: Article

References (39)

1. Chiti F, Taddei N, White PM, Bucciantini M, Magherini F, Stefani M, Dobson CM. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat Struct Biol 1999;6:1005-1009.
2. Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol 1999;6:1016-1024.
3. Martinez JC, Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionary conserved. Nat Struct Biol 1999;6:1010-1016.
4. Debe DA, Goddard WA. First principles prediction of protein folding rates. J Mol Biol 1999;294:619-625.
5. Munoz V, Eaton WA. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci USA 1999;96:11311-11316.
6. Fersht A. Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc Natl Acad Sci USA 2000;97:1525-1529.
7. Mirny L, Shakhnovich E. Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Struct 2001;30:361-396.
8. Zhou H, Zhou Y. Folding rate prediction using total contact distance. Biophys J 2002;82:458-463.
9. Makarov DE, Plaxco KW. The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci 2003;12:17-26.
10. Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
11. Koga N, Takada S. Roles of native topology and chain length scaling in protein folding: a simulation study with Go-like model. J Mol Biol 2001;313:171-180.
12. Plaxco KW, Simons KT, Ruczinski I, Baker D. Topology, stability, sequence and length: defining the determinants of two-state protein folding kinetics. Biochemistry 2000;39:11177-11183.
13. Alm E, Baker D. Matching theory and experiment in protein folding. Curr Opin Struct Biol 1999;9:189-196.
14. Baker D. A surprising simplicity to protein folding. Nature 2000;405:39-42.
15. Gong H, Isom DG, Srinivasan R, Rose GD. Local secondary structure content predicts folding rates for simple, two-state proteins. J Mol Biol 2003;327:1149-1154.
16. Goldenberg DP. Finding the right fold. Nat Struct Biol 1999;6:987-990.
17. Jackson SE. How do small single-domain proteins fold? Fold Design 1998;3:R81-R91.
18. Dinner AR, Karplus M. The roles of stability and contact order in predicting protein folding rates. Nat Struct Biol 2001;8:21-22.
19. Roumestand C, Boyer M, Guignard L, Barthe P, Royer CA. Characterization of the folding and unfolding reactions of a small β-barrel protein of novel topology, the MTCP1 oncogene product P13. J Mol Biol 2001;312:247-259.
20. Lindberg MO, Tangrot J, Otzen DE, Dolgikh DA, Finkelstein AV, Olivberg M. Folding of circular permutants with decreased contact order: general trend balanced by protein stabilty. J Mol Biol 2001;314:891-900.
21. Gromiha MM, Selvaraj S. Comparison between 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.
22. Miller EJ, Fischer KF, Marqusee S. Experimental evaluation of topological parameters determining protein-folding rates. Proc Natl Acad Sci USA 2002;99:10359-10363.
23. Freund SMV, Wong K, Fersht A. Initiation sites of protein folding by NMR analysis. Proc Natl Acad Sci USA 1996;93:10600-10603.
24. Munoz V, Serrano L. Local versus nonlocal interactions in protein folding and stability: an experimentalist's point of view. Fold Design 1996;1:R71-R78.
25. Luisi DL, Kuhlman B, Sideras K, Evans PA, Raleigh DP. Effects of varying the local propensity to form secondary structure on the stability and folding kinetics of a rapid folding mixed α/β protein: characterization of a truncation mutant of the N-terminal domain of the ribosomal protein L9. J Mol Biol 1999;289:167-174.
26. Chiti F, Taddei N, Webster P, Hamada D, Fiaschi T, Ramponi G, Dobson C-M. Acceleration of the folding of acylphosphatase by stabilization of local secondary structure. Nat Struct Biol 1999;6:380-387.
27. Makarov DE, Keler 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;99:3535-3539.
28. Grantcharova V, Alm EJ, Baker D, Horwich AL. Mechanisms of protein folding. Curr Opin Struct Biol 2001;11:70-82.
29. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
30. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure 1996;5:1093-1108.
31. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
32. Thornton JM, Sibanda BL. Amino and carboxy-terminal regions in globular proteins. J Mol Biol 1983;167:443-460.
33. Kawashima S, Ogata H, Kanehisa M. AAindex: amino acid index database. Nucleic Acids Res 1999;27:368-369.
34. Snedecor GW, Cochran WG. Statistical methods, 7th edition, Iowa City, IA: The Iowa State University Press; 1980. p385-387.
35. Kanehisa MI, Tsong TY. Local hydrophobicity stabilizes secondary structures in proteins. Biopolymers 1980;19:1617-1628.
36. Ptitsyn OB, Finkelstein AV. Theory of protein secondary structure and algorithm of its prediction. Biopolymers 1983;22:15-25.
37. Munoz V, Serrano L. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Proteins 1994;20:301-311.
38. Luisi DL, Wen-Jin Wu, Raleigh DP. Conformational analysis of a set of peptides corresponding to the entire primary sequence of the N-terminal domain of the ribosomal protein L9: evidence for stable native-like secondary structure in the unfolded state. J Mol Biol 1999;287:395-407.
39. Doyle R, Simons K, Qian H, Baker D. Local interactions and optimization of protein folding. Proteins 1997;29:282-291.