A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding

Proteins: Structure, Function and Genetics

Volumn 70, Issue 3, 2008, Pages 626-638

  Yap, Eng Hui ^a   Fawzi, Nicolas Lux ^a   Head Gordon, Teresa ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California at Berkeley   (United States)

Author keywords

Anisotropic hydrogen bonding; Coarse grained protein models; Kinetics; Multiscale models; Protein folding; Simulation

Indexed keywords

CARBON; POLYPEPTIDE; PROTEIN; PROTEIN G; PROTEIN L; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; ANISOTROPY; ARTICLE; BETA SHEET; HYDROGEN BOND; KINETICS; MEASUREMENT; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; THERMODYNAMICS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; HYDROGEN BONDING; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 38549133951     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21515     Document Type: Article

References (47)

1. Bryngelson JD, Wolynes PG. Intermediates and barrier crossing in a random energy-model (with applications to protein folding). J Phys Chem 1989;93:6902-6915.
2. Onuchic JN, LutheySchulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annual Rev Phys Chem 1997;48:545-600.
3. Cheung MS, Finke JM, Callahan B, Onuchic JN. Exploring the interplay between topology and secondary formation in the protein folding problem. J Phys Chem B 2003;107:11193-11200.
4. 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.
5. Honeycutt JD, Thirumalai D. Metastability of the folded states of globular-proteins. Proc Natl Acad Sci USA 1990;87:3526-3529.
6. Guo ZY, Thirumalai D, Honeycutt JD. Folding kinetics of proteins - a model study. J Chem Phys 1992;97:525-535.
7. Guo ZY, Thirumalai D. Kinetics of protein-folding - nucleation mechanism, time scales, and pathways. Biopolymers 1995;36:83-102.
8. Guo Z, Thirumalai D. Kinetics and thermodynamics of folding of a de Novo designed four-helix bundle protein. J Mol Biol 1996;263:323-343.
9. Go N. Theoretical-studies of protein folding. Ann Rev Biophys Bioeng 1983;12:183-210.
10. Sorenson JM, Head-Gordon T. Protein engineering study of protein L by simulation. J Computat Biol 2002;9:35-54.
11. Sorenson JM, Head-Gordon T. Matching simulation and experiment: a new simplified model for simulating protein folding. J Computat Biol 2000;7(3/4):469-481.
12. Brown S, Head-Gordon T. Intermediates and the folding of proteins L and G. Protein Sci 2004;13:958-970.
13. Brown S, Fawzi NJ, Head-Gordon T. Coarse-grained sequences for protein folding and design. Proc Natl Acad Sci USA 2003;100:10712-10717.
14. Sorenson JM, Head-Gordon T. Redesigning the hydrophobic core of a model beta-sheet protein: destabilizing traps through a threading approach. Proteins 1999;37:582-591.
15. Fawzi NL, Chubukov V, Clark LA, Brown S, Head-Gordon T. Influence of denatured and intermediate states of folding on protein aggregation. Protein Sci 2005;14:993-1003.
16. Fawzi N, Okabe Y, Yap E, Head-Gordon T. Determining the critical nucleus and mechanism of fibril elongation of the alzheimer's Aβ1-40 peptide. J Mol Biol 2006;365:535-550.
17. Dobson CM. Principles of protein folding, misfolding and aggregation. Semin Cell Dev Biol 2004;15:3-16.
18. Buchete NV, Straub JE, Thirumalai D. Orientational potentials extracted from protein structures improve native fold recognition. Protein Sci 2004;13:862-874.
19. Das P, Matysiak S, Clementi C. Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. Proc Natl Acad Sci USA 2005;102:10141-10146.
20. Smith AV, Hall CK. Alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model. Proteins 2001;44:344-360.
21. Klimov DK, Betancourt MR, Thirumalai D. Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Folding Design 1998;3:481-496.
22. Klimov DK, Thirumalai D. Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci USA 2000;97:2544-2549.
23. Marcus Y, Ben-Naim A. A study of the structure of water and its dependence on solutes, based on the isotope effects on solvation thermodynamics in water. J Chem Phys 1985;83:4744-4759.
24. Silverstein KAT, Haymet ADJ, Dill KA. A simple model of water and the hydrophobic effect. J Am Chem Soc 1998;120:3166-3175.
25. Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein-G. Science 1991;253:657-661.
26. Wikstrom M, Drakenberg T, Forsen S, Sjobring U, Bjorck L. 3-dimensional solution structure of an immunoglobulin light chain-binding domain of protein-1-comparison with the IgG-binding domains of protein-G. Biochemistry 1994;33:14011-14017.
27. Alexander P, Fahnestock S, Lee T, Orban J, Bryan P. Thermodynamic analysis of the folding of the streptococcal protein-G IgG-binding domains B1 and B2 - why small proteins tend to have high denaturation temperatures. Biochemistry 1992;31:3597-3603.
28. Alexander P, Orban J, Bryan P. Kinetic-analysis of folding and unfolding the 56-amino acid IgG-binding domain of streptococcal protein-G. Biochemistry 1992;31:7243-7248.
29. Krantz BA, Mayne L, Rumbley J, Englander SW, Sosnick TR. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol 2002;324:359-371.
30. McCallister EL, Alm E, Baker D. Critical role of beta-hairpin formation in protein G folding. Nat Struct Biol 2000;7:669-673.
31. Park SH, ONeil KT, Roder H. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core. Biochemistry 1997;36:14277-14283.
32. Park SH, Shastry MCR, Roder H. Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing. Nat Struct Biol 1999;6:943-947.
33. Roder H, Maki K, Cheng H. Early events in protein folding explored by rapid mixing methods. Chem Rev 2006;106:1836-1861.
34. Roder H, Maki K, Cheng H, Shastry MCR. Rapid mixing methods for exploring the kinetics of protein folding. Methods 2004;34:15-27.
35. Scalley ML, Yi Q, Gu HD, McCormack A, Yates JR, Baker D. Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L. Biochemistry 1997;36:3373-3382.
36. 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.
37. Kuszewski J, Clore GM, Gronenborn AM. Fast folding of a prototypic polypeptide - the immunoglobulin binding domain of streptococcal protein-G. Protein Sci 1994;3:1945-1952.
38. Andersen HC. Rattle - a velocity version of the shake algorithm for molecular-dynamics calculations. J Computat Phys 1983;52:24-34.
39. Ferguson DM, Garrett DG. Simulated annealing - optimal histogram methods. Monte Carlo Methods Chem Phys 1999;105:311-336.
40. Ferrenberg AM, Swendsen RH. Optimized Monte-Carlo data-analysis. Phys Rev Lett 1989;63:1195-1198.
41. Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich ES. On the transition coordinate for protein folding. J Chem Phys 1998;108: 334-350.
42. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11:739-747.
43. Feig M, Karanicolas J, Brooks CL. MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 2004;22:377-395.
44. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein-folding - a synthesis. Proteins 1995;21:167-195.
45. Socci ND, Onuchic JN. Folding kinetics of proteinlike heteropolymers. J Chem Phys 1994;101:1519-1528.
46. Marianayagam NJ, Fawzi NL, Head-Gordon T. Protein folding by distributed computing and the denatured state ensemble. Proc Natl Acad Sci USA 2005;102:16684-16689.
47. DeLano WL. The PyMOL Molecular Graphics System. San Carlos, CA: DeLano Scientific; 2002.