Importance of Sequence Specificity for Predicting Protein Folding Pathways: Perturbed Gaussian Chain Model

Proteins: Structure, Function and Genetics

Volumn 53, Issue 3, 2003, Pages 616-628

  Kameda, Tomoshi ^a  

^a KOBE UNIVERSITY   (Japan)

Author keywords

value analysis; Gaussian chain; G model; Protein folding; Topology

Indexed keywords

ACYLPHOSPHATASE; ALBUMIN BINDING PROTEIN; APOMYOGLOBIN; BARNASE; CARBOXYPEPTIDASE; CHYMOTRYPSIN INHIBITOR; FIBRONECTIN; FODRIN; LEGHEMOGLOBIN; PROTEIN; PROTEIN G; PROTEIN L; PROTEIN TYROSINE KINASE; REPRESSOR PROTEIN; SPLICEOSOME PROTEIN U1A; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; CORRELATION COEFFICIENT; ENERGY; GAUSSIAN CHAIN MODEL; PHASE TRANSITION; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN LOCALIZATION; QUANTITATIVE ANALYSIS; THEORETICAL MODEL;

BACTERIAL PROTEINS; DNA-BINDING PROTEINS; MODELS, MOLECULAR; PEPTIDES; PLANT PROTEINS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SEQUENCE ANALYSIS, PROTEIN; TENASCIN; VIRAL PROTEINS;

EID: 0242267529     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10427     Document Type: Article

References (44)

1. Fersht AR. Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. New York: Freeman; 1999.
2. Onuchic JN, Luthey-Schulten ZA, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 1997;48:545-600.
3. Grantcharova V, Alm EJ, Baker D, Horwich AL. Mechanisms of protein folding. Curr Opin Struct Biol 2001;11:70-82.
4. Baker D. A surprising simplicity to protein folding. Nature 2000;405:39-42.
5. Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
6. 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.
7. Itzhaki LA, Otzen DE, Fersht AR. The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol 1995;254:260-288.
8. Martinez JC, Serrano L. The folding transition state between SH3 domains is conformation ally restricted and evolutionarily conserved. Nat Struct Biol 1999;6:1010-1016.
9. Riddle DS, Grantcharova VA, Santiago JD, 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.
10. Chiti F, Taddei N, White PM, et al. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat Struct Biol 1999;6:1005-1009.
11. Villegas V, Martinez JC, Aviles FX, Serrano L. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J Mol Biol 1998;283:1027-1036.
12. Kim DE, Fisher C, Baker D. A breakdown of symmetry in the folding transition state of protein L. J Mol Biol 2000;298:971-984.
13. McCallister EL, Alm E, Baker D. Critical role of β-hairpin formation in protein G folding. Nat Struct Biol 2000;7:669-673.
14. Ternstrom T, Mayor U, Akke M, Oliveberg M. From snapshot to movie: φ analysis of protein folding transition states taken one step further. Proc Natl Acad Sci USA 1999;96:14854-14859.
15. Shoemaker BA, Wang J, Wolynes PG. Structural correlations in protein folding funnels. Proc Natl Acad Sci USA 1997;94:777-782.
16. Portman JJ, Takada S, Wolynes PG. Variational theory for site resolved protein folding free energy surfaces. Phys Rev Lett 1998;81:5237-5240.
17. Portman JJ, Takada S, Wolynes PG. Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach. J Chem Phys 2001;114:5069-5081.
18. Galzitskaya OV, Finkelstein AV. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci USA 1999;96:11299-11304.
19. Alm E, Baker D. Prediction of protein folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci USA 1999;96:11305-11310.
20. 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.
21. Guerois R, Serrano L. The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J Mol Biol 2000;304:967-982.
22. Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? J Mol Biol 2000;298:937-953.
23. Clementi C, Jennings PA, Onuchic JN. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1 β. Proc Natl Acad Sci USA 2000;97:5871-5876.
24. Cieplak M, Hoang TX. Scaling of folding properties in Gō models of proteins. J Biol Phys 2000;26:273-294.
25. Koga N, Takada S. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model. J Mol Biol 2001;313:171-180.
26. Takada S. Gō-ing for the prediction of protein folding mechanisms. Proc Natl Acad Sci USA 1999;96:11698-11700.
27. Go N. Theoretical studies of protein folding. Annu Rev Biophys Bioeng 1983;12:183-210.
28. Bryngelson JD, Wolynes PG. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 1987;84:7524-7528.
29. Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744.
30. Burton RE, Huang GS, Daugherty MA, Calderone TL, Oas TG. The energy landscape of a fast-folding protein mapped by Ala → Gly substitutions. Nat Struct Biol 1997;4:305-310.
31. Ferguson N, Johnson CM, Macias M, Oschkinat H, Fersht A. Ultra fast folding of WW domains without structured aromatic clusters in the denatured state. Proc Natl Acad Sci USA 2000;98:13002-13007.
32. Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading. J Mol Biol 1996;256:623-644.
33. Bixon M, Zwanzig R. Rouse-Zimm theory for stiff polymers. J Chem Phys 1978;68:1896-1902.
34. Cantor CR, Schimmel PR. Biophysical chemistry. Vol, 3. New York: WH Freeman; 1980. 1013 p.
35. Feynmann RP. Statistical mechanics. Benjamin; 1972. p 39-71.
36. 55 clusters. J Chem Phys 1994;101:3750-3762.
37. Shea JE, Onuchic JN, Brooks CL III. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci USA 1999;96:12512-12517.
38. Go M, Nosaka M. Protein architecture and the origin of intron. Cold Spring Harbor Symp Quant Biol 1987;LII:915-924.
39. 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.
40. Matouschek A, Serrano L, Fersht AR. The folding of an enzyme. IV. Structure of an intermediate in the refolding of Barnase analyzed by a protein engineering procedure. J Mol Biol 1992;224:819-835.
41. Hamill SJ, Steward A, Clarke J. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology. J Mol Biol 2000;297:165-178.
42. Li A, Daggett V. Identification and characterization of the unfolding transition state of chymotripsin inhibitor 2 by molecular dynamics simulations. J Mol Biol 1996;257:412-429.
43. Lazaridis T, Karplus M. New view of protein folding reconciled with the old through multiple unfolding simulations. Science 1997;278:1928-1931.
44. Kraulis PJ. A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.