Denatured state is critical in determining the properties of model proteins designed on different folds

Proteins: Structure, Function and Genetics

Volumn 70, Issue 3, 2008, Pages 1047-1055

  Amatori, A ^a,c   Tiana, G ^a   Ferkinghoff Borg, J ^b   Broglia, R A ^a,c  

^a UNIVERSITY OF MILAN   (Italy)

^b NORDITA   (Denmark)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Denatured state; Evolution and design; Protein folding; Simplified model

Indexed keywords

CHYMOTRYPSIN; PROTEIN G;

ARTICLE; CONFORMATIONAL TRANSITION; KINETICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMODYNAMICS;

AMINO ACID SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 38549168016     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21599     Document Type: Article

References (39)

1. Finkelstein AV, Ptitsyn OB. Why do globular proteins fit the limited set of folding patterns? Progr Biophys Mol Biol 1987;50:171-190.
2. Finkelstein AV, Gutin AM, Badretdinov AYa. Why are the same protein folds used to perform different functions? FEBS 1993;325:23-28.
3. Govindarajan S, Goldstein RA. Optimal local propensities for model proteins. Proteins 1995;22:413-418.
4. Govindarajan S, Goldstein RA. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc Natl Acad Sci USA 1996;93:3341-3345.
5. Li H, Helling R, Tang C, Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science 1996;273:666-669.
6. Tiana G, Broglia RA, Provasi D. Designability of lattice model heteropolymers. Phys Rev E 2001;64:11904-11910.
7. England JL, Shakhnovich EI. Structural determinant of protein designability. Phys Rev Lett 2003;90:218101-218104.
8. Tiana G, Shakhnovich BE, Dokholyan NV, Shakhnovich EI. Imprint of evolution on protein structures. Proc Natl Acad Sci USA 2004;101:2846-2851.
9. Abkevich VI, Gutin AM, Shakhnovich EI. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol 1995;252:460-471.
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. Schymkowitz JWH, Rousseau F, Serrano L. Surfing on protein folding energy landscapes. Proc Natl Acad Sci USA 2002;99:15846-15848.
12. Baker D. A surprising simplicity to protein folding. Nature 2000;405:39-42.
13. Alm E, Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Curr Opin Struct Biol 1999;9:189-196.
14. Amatori A, Tiana G, Sutto L, Ferkinghoff-Borg J, Trovato A, Broglia RA. Design of amino acid sequences to fold into Cα-model proteins. J Chem Phys 2005;123:549041-549047.
15. Amatori A, Ferkinghoff-Borg J, Tiana G, Broglia RA. Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model. Phys Rev E 2006;73:61905-1-61905-12.
16. Frauenfelder H, Wolynes PG. Biomolecules: Where the physics of complexity and simplicity meet. Phys Today 1994;47:58-64.
17. Shakhnovich EI, Gutin AM. Engineering of stable and fast-folding sequences of model proteins. Prot Eng 1993;6:793-800.
18. Banavar JR, Hoang TX, Seno F, Maritan A. Unified perspective on proteins: a physics approach. Phys Rev E 2004;70:041905-1-041905-10.
19. Ferkinghoff-Borg J. Optimized Monte Carlo analysis for generalized ensembles. Eur Phys J B 2002;29:481-484.
20. Tiana G, Sutto L, Broglia RA. Use of the Metropolis algorithm to simulate the dynamics of protein chains. Physica A 2007;380:241-249.
21. Irback A, Samuelsson B, Sjunnesson F, Wallin S. Thermodynamics of alpha- and beta-structure formation in proteins. Biophys J 2003; 85:1466-1473.
22. Kaya H, Chan HS. Polymer principles of protein calorimetric two-state cooperativity. Proteins 2000;40, 637-661.
23. McAllister E, Alm E, Baker D. Critical role of beta-hairpin in protein G folding. Nature Struct Biol 2000;7:669-674.
24. 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;254:260-288.
25. Go N, Abe H. Non-interacting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers 1981;20:991-1011.
26. Privalov PL. In Creighton TS, editor. Physical basis of the stability of the folded conformations of proteins in protein folding. W. H. Freeman; 1992.
27. Sherman E, Haran G. Coil-globule transition in the denatured state of a small protein. Proc Natl Acad Sci USA 2006;103:11539-11543.
28. Tanford C, Kawahara K, Lapanje S. Proteins in 6M guanidine hydrochloride. J Biol Chem 1966;8:1921-1923.
29. Kortemme T, Kelly MJS, Kay LE, Forman-Key J, Serrano L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J Mol Biol 2000;297:1217-1229.
30. Yi Q, Scalley-Kim ML, Alm EJ, Baker D. NMR characterization of residual structure in the denatured state of protein L. J Mol Biol 2000;299:1341-1351.
31. Mok Y, Kay CM, Kay LE, Forman-Key J. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions. J Mol Biol 1999;289:619-638.
32. Kazmirski SL, Wong KB, Freund SMV, Tan JJ, Fersht AR, Daggett V. Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution. Proc Natl Acad Sci USA 2001;98:4349-4354.
33. Panchenko AR, Luthey-Schulten Z. Wolynes PG Foldons, protein structural modules, and exons. Proc Natl Acad Sci USA 1996;93:2008-2011.
34. Rao F, Caflisch A. The protein folding network. J Mol Biol 2004; 342:299-306.
35. Krikov SV, Karplus M. Hidden complexity of free energy surfaces for peptide (protein) folding, Proc Natl Acad Sci USA 2004;101: 14766-14770.
36. Broglia RA, Tiana G, Provasi D. Simple model of protein folding and of non-conventional drug design. J Phys Condens Matter 2004; 16:R111-R144.
37. Tiana G, Broglia RA. Statistical analysis of native contact formation in the folding of designed model protein. J Chem Phys 2001;114:2503-2510.
38. Broglia RA, Tiana G. Hierarchy of events in the folding of model proteins. J Chem Phys 2001;114:7267-7273.
39. Klimov DK, Thirumalai D. Cooperativity in protein folding: from lattice models with sidechains to real proteins. Fold Des 1998;3:127-139.