Constraining local structure can speed up folding by promoting structural polarization of the folding pathway

Protein Science

Volumn 20, Issue 6, 2011, Pages 959-969

  Buck, Patrick M ^a   Bystroff, Christopher ^a  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

G model; Protein folding; Rigid body constraints; Structure prediction

Indexed keywords

CHYMOTRYPSIN INHIBITOR; CHYMOTRYPSIN INHIBITOR 2; PROTEIN SH3; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; HYPOTHESIS; POLARIZATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN POLYMORPHISM; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SIMULATION; STRUCTURAL PROTEOMICS;

KINETICS; MODELS, MOLECULAR; PEPTIDES; PLANT PROTEINS; PLANTS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SRC HOMOLOGY DOMAINS; SRC-FAMILY KINASES;

EID: 79956188915     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.619     Document Type: Article

References (42)

1. Fersht AR (1995) Characterizing transition states in protein folding: an essential step in the puzzle. Curr Opin Struct Biol 5:79-84.
2. Karplus M, Weaver DL (1976) Protein-folding dynamics. Nature 260:404-406.
3. Daggett V, Fersht A (2003) The present view of the mechanism of protein folding. Nat Rev Mol Cell Biol 4: 497-502. (Pubitemid 36648595)
4. Wetlaufer DB (1973) Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 70:697-701.
5. Wolynes PG, Onuchic JN, Thirumalai D (1995) Navigating the folding routes. Science 267:1619-1620.
6. Dill KA (1999) Polymer principles and protein folding. Protein Sci 8:1166-1180.
7. Clementi C, Nymeyer H, Onuchic JN (2000) Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298:937-953.
8. Plaxco KW, Simons KT, Baker D (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277:985-994. (Pubitemid 28195995)
9. Baker D (2000) A surprising simplicity to protein folding. Nature 405:39-42.
10. Larson SM, Snow CD, Shirts M, Pande VS (2009) Folding@Home and Genome@ Home: Using distributed computing to tackle previously intractable problems in computational biology. Arxiv preprint arXiv:0901.0866.
11. Hills R Jr, Brooks C III (2009) Insights from coarse-grained G models for protein folding and dynamics. Int J Mol Sci 10:889.
12. Das P, Matysiak S, Clementi C (2005) Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. Proc Natl Acad Sci USA 102:10141-10146. (Pubitemid 41023339)
13. Klimov DK, Thirumalai D (2001) Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins 43:465-475. (Pubitemid 32476441)
14. Yap EH, Fawzi NL, Head-Gordon, T (2008) A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins 70:626-638. (Pubitemid 351161925)
15. Koga N, Takada S (2001) Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. J Mol Biol 313:171-180. (Pubitemid 33001173)
16. Klimov DK, Thirumalai D (2002) Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol 317: 721-737. (Pubitemid 34722160)
17. Spagnolo L, Ventura S, Serrano L (2003) Folding specificity induced by loop stiffness. Protein Sci 12: 1473-1482. (Pubitemid 36759351)
18. Buck PM, Bystroff C (2009) Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field. Proteins 76:331-342.
19. Grantcharova VP, Riddle DS, Santiago JV, Baker D (1998) Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol 5:714-720. (Pubitemid 28359808)
20. Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D (1999) Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol 6:1016-1024. (Pubitemid 29519594)
21. Itzhaki LS, Otzen DE, Fersht AR (1995) 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 254:260-288.
22. Martinez JC, Pisabarro MT, Serrano L (1998) Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol 5: 721-729. (Pubitemid 28359809)
23. Jackson SE, Fersht AR (1991) Folding of chymotrypsin inhibitor 2. 2. Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition state of folding. Biochemistry 30: 10436-10443.
24. Jackson SE, Fersht AR (1991) Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30:10428-10435.
25. Otzen DE, Fersht AR (1995) Side-chain determinants of beta-sheet stability. Biochemistry 34:5718-5724.
26. Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268: 209-225. (Pubitemid 27192690)
27. Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34:82-95. (Pubitemid 29019533)
28. Skolnick J, Kolinski A, Ortiz AR (1997) MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 265: 217-241. (Pubitemid 27110659)
29. Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 85:1145-1164. (Pubitemid 36909676)
30. Srinivasan R, Rose GD (1995) LINUS: a hierarchic procedure to predict the fold of a protein. Proteins 22: 81-99.
31. Voelz VA, Shell MS, Dill KA (2009) Predicting peptide structures in native proteins from physical simulations of fragments. PLoS Comput Biol 5:e1000281.
32. Ozkan SB, Wu GA, Chodera JD, Dill KA (2007) Protein folding by zipping and assembly. Proc Natl Acad Sci USA 104:11987-11992. (Pubitemid 47185617)
33. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: A linear constraint solver for molecular simulations. J Comp Chem 18:1463-1472. (Pubitemid 127637344)
34. Ryckaert J, Ciccoitt G, Berendsen H (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys 23:327-341.
35. Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA (2009) Blind test of physics-based prediction of protein structures. Biophys J 96:917-924.
36. Wang T, Xu Y, Du D, Gai F (2004) Determining beta-sheet stability by Fourier transform infrared difference spectra. Biopolymers 75:163-172. (Pubitemid 39330023)
37. McCallister EL Alm E, Baker D (2000) Critical role of beta-hairpin formation in protein G folding. Nat Struct Biol 7:669-673.
38. Grantcharova VP, Baker D (1997) Folding dynamics of the src SH3 domain. Biochemistry 36:15685-15692. (Pubitemid 28027367)
39. Viguera AR, Serrano L, Wilmanns M (1996) Different folding transition states may result in the same native structure. Nat Struct Biol 3:874-880. (Pubitemid 26330639)
40. Portman JJ (2010) Cooperativity and protein folding rates. Curr Opin Struct Biol 20:11-15.
41. Grantcharova VP, Baker D (2001) Circularization changes the folding transition state of the src SH3 domain. JMol Biol 306:555-563. (Pubitemid 33027722)
42. Berendsen HC Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.