Absolute comparison of simulated and experimental protein-folding dynamics
10.1038/nature01160
Crossref journal-article
Springer Science and Business Media LLC
Nature (297)
Bibliography

Snow, C. D., Nguyen, H., Pande, V. S., & Gruebele, M. (2002). Absolute comparison of simulated and experimental protein-folding dynamics. Nature, 420(6911), 102–106.

Authors 4
  1. Christopher D. Snow (first)
  2. Houbi Nguyen (additional)
  3. Vijay S. Pande (additional)
  4. Martin Gruebele (additional)
References 29 Referenced 571
  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) (10.1021/ar9700825) / Acc. Chem. Res. by WA Eaton (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) (10.1073/pnas.250473497) / Proc. Natl Acad. Sci. USA by U Mayor (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) (10.1126/science.282.5389.740) / Science by Y Duan (1998)
  4. Wolynes, P. G., Onuchic, J. N. & Thirumalai, D. Navigating the folding routes. Science 267, 1619–1620 (1995) (10.1126/science.7886447) / Science by PG Wolynes (1995)
  5. Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10–19 (1997) (10.1038/nsb0197-10) / Nature Struct. Biol. by KA Dill (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) (10.1146/annurev.physchem.52.1.499) / Annu. Rev. Phys. Chem. by J Shea (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) (10.1021/jp994157t) / J. Phys. Chem. B by P Ferrara (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) (10.1006/jmbi.1998.1885) / J. Mol. Biol. by X Daura (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) (10.1073/pnas.190324897) / Proc. Natl Acad. Sci. USA by P Ferrara (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) (10.1006/jmbi.2001.5033) / J. Mol. Biol. by B Zagrovic (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) (10.1016/0022-2836(92)90561-W) / J. Mol. Biol. by AR Fersht (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) (10.1073/pnas.97.13.7220) / Proc. Natl Acad. Sci. USA by LJ Lapidus (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) (10.1073/pnas.96.17.9597) / Proc. Natl Acad. Sci. USA by O Bieri (1999)
  14. Shirts, M. & Pande, V. S. Screen savers of the world unite. Science 290, 1903–1904 (2000) (10.1126/science.290.5498.1903) / Science by M Shirts (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) (10.1016/S1359-0278(98)00015-7) / Folding Des. by M Struthers (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) (10.1126/science.271.5247.342) / Science by MD Struthers (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) (10.1016/S1011-1344(00)00002-6) / J. Photochem. Photobiol. Biol. by J Ervin (2000)
  18. Chandler, D. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J. Chem. Phys. 68, 2959–2970 (1978) (10.1063/1.436049) / J. Chem. Phys. by D Chandler (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) (10.1073/pnas.94.8.3709) / Proc. Natl Acad. Sci. USA by R Gilmanshin (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) (10.1073/pnas.93.12.5759) / Proc. Natl Acad. Sci. USA by RM Ballew (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) (10.1006/jmbi.1998.1645) / J. Mol. Biol. by KW Plaxco (1998)
  22. Moore, S. & Stein, W. Amino acid determination, methods and techniques. J. Biol. Chem. 192, 663–670 (1951) (10.1016/S0021-9258(19)77791-6) / J. Biol. Chem. by S Moore (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) (10.1002/jcc.540080710) / J. Comput. Chem. by JW Ponder (1987)
  24. Fletcher, R. & Powell, M. J. D. A rapidly convergent descent method for minimization. Comput. J. 6, 163–168 (1963) (10.1093/comjnl/6.2.163) / Comput. J. by R Fletcher (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) (10.1006/jmbi.1994.1366) / J. Mol. Biol. by P Koehl (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) (10.1021/jp961992r) / J. Phys. Chem. A by D Qiu (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) (10.1021/ja00214a001) / J. Am. Chem. Soc. by WL Jorgensen (1988)
  28. Andersen, H. C. Rattle: a ‘velocity’ version of the shake algorithm for molecular dynamics calculations. J. Comput. Phys. 52, 24–34 (1983) (10.1016/0021-9991(83)90014-1) / J. Comput. Phys. by HC Andersen (1983)
  29. Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983) (10.1002/bip.360221211) / Biopolymers by W Kabsch (1983)
Dates
Type When
Created 22 years, 10 months ago (Nov. 6, 2002, 7:46 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 2:10 p.m.)
Indexed 1 month ago (Aug. 6, 2025, 8:58 a.m.)
Issued 22 years, 10 months ago (Oct. 20, 2002)
Published 22 years, 10 months ago (Oct. 20, 2002)
Published Online 22 years, 10 months ago (Oct. 20, 2002)
Published Print 22 years, 10 months ago (Nov. 1, 2002)
Funders 0

None

@article{Snow_2002, title={Absolute comparison of simulated and experimental protein-folding dynamics}, volume={420}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature01160}, DOI={10.1038/nature01160}, number={6911}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Snow, Christopher D. and Nguyen, Houbi and Pande, Vijay S. and Gruebele, Martin}, year={2002}, month=oct, pages={102–106} }