Absolute comparison of simulated and experimental protein-folding dynamics

Nature

Volumn 420, Issue 6911, 2002, Pages 102-106

  Snow, Christopher D ^a   Nguyen, Houbi ^b   Pande, Vijay S ^a   Gruebele, Martin ^b  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; LASERS; MOLECULAR DYNAMICS;

MUTANTS;

PROTEINS;

PROTEIN; PROTEIN BBA5; UNCLASSIFIED DRUG; VILLIN;

PROTEIN;

ALPHA HELIX; ARTICLE; EQUILIBRIUM CONSTANT; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SIMULATION; TEMPERATURE;

AMINO ACID SEQUENCE; CIRCULAR DICHROISM; COMPUTER SIMULATION; KINETICS; LASERS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SPECTROMETRY, FLUORESCENCE; TEMPERATURE; THERMODYNAMICS;

APUS APUS; MUS;

EID: 0037038372     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature01160     Document Type: Article

References (29)

1. Eaton, W. A., Muñoz, V., Thompson, P. A., Henry, E. R. & Hofrichter. J. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Acc. Chem. Res. 31, 745-753 (1998).
2. Mayor, U., Johnson, C. M., Daggett, V. & Fersht, A. R. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl Acad. Sci. USA 97, 13518-13522 (2000).
3. Duan, Y. & Kollman, P. A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282, 740-744 (1998).
4. Wolynes, P. G., Onuchic, J. N. & Thirumalai, D. Navigating the folding routes. Science 267, 1619-1620 (1995).
5. Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19 (1997).
6. Shea, J. & Brooks, C. L. From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52, 499-535 (2001).
7. Ferrara, P., Apostolakis, J. & Caflisch, A. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B 104, 5000-5010 (2000).
8. Daura, X., Jaun, B., Seebach, D., Gunsteren, W. F. v. & Mark, A. E. Reversible peptide folding in solution by molecular dynamics simulation. J. Mol. Biol. 280, 925-932 (1998).
9. Ferrara, P. & Caflisch, A. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl Acad. Sci. USA 97, 10780-10785 (2000).
10. Zagrovic, B., Sorin, E. J. & Pande, V.S. β-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313, 151-169 (2001).
11. Fersht, A. R., Matouschek, A. & Serrano, L. The folding of an enzyme I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224, 771-782 (1992).
12. Lapidus, L. J., Eaton, W. A. & Hofrichter, J. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl Acad. Sci. USA 97, 7220-7225 (2000).
13. Bieri, O. et al. The speed limit of protein folding measure by triplet-triplet energy transfer. Proc. Natl Acad. Sci. USA 96, 9597-9601 (1999).
14. Shirts, M. & Pande, V. S. Screen savers of the world unite. Science 290, 1903-1904 (2000).
15. Struthers, M., Ottesen, J. J. & Imperiali, B. Design and NMR analyses of compact, independently folded BBA motifs, Folding Des. 3, 95-103 (1998).
16. Struthers, M. D., Cheng, R. C. & Imperiali, B. Design of a monomeric 23-residue polypeptide with defined tertiary structure. Science 271, 342-345 (1996).
17. Ervin, J., Sabelko, J. & Gruebele, M. Submicrosecond real-time fluorescence detection: Application to protein folding. J. Photochem. Photobiol. Biol. 54, 1-15 (2000).
18. Chandler, D. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J. Chem. Phys. 68, 2959-2970 (1978).
19. Gilmanshin, R., Williams, S., Callender, R. H., Woodruff, W. H. & Dyer, R. B. Fast events in protein folding: Relaxation dynamics of secondary and tertiary structure in native apomyoglobin. Proc. Natl Acad. Sci. USA 94, 3709-3713 (1997).
20. Ballew, R. M., Sabelko, J. & Gruebele, M. Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. USA 93, 5759-5764 (1996).
21. Plaxco, K. W., Simons, K. T. & Baker, D. Contact order transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985-994 (1998).
22. Moore, S. & Stein, W. Amino acid determination, methods and techniques. J. Biol. Chem. 192, 663-670 (1951).
23. Ponder, J. W. & Richards, F. M. An efficient Newton-like method for molecular mechanics energy minimization of large molecules. J. Comput. Chem. 8, 1016-1024 (1987).
24. Fletcher, R. & Powell, M. J. D. A rapidly convergent descent method for minimization. Comput. J. 6, 163-168 (1963).
25. Koehl, P. & Delarue, M. On the use of a self-consistent mean field theory to predict protein side chain conformations and estimate their entropies. J. Mol. Biol. 239, 249-275 (1994).
26. Qiu, D., Shenkin, P. S., Hollinger, F. P. & Still, W. C. The GB/SA Continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. A 101, 3005-3014 (1997).
27. Jorgensen, W. L. & Tirado-Rives, J. The OPLS force field for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 1657-1666 (1988).
28. Andersen, H. C. Rattle: A 'velocity' version of the shake algorithm for molecular dynamics calculations. J. Comput. Phys. 52, 24-34 (1983).
29. Kabsch, W. & Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637 (1983).