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Absolute comparison of simulated and experimental protein-folding dynamics


Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as α-helices and β-hairpins can form in 0.1–10 µs (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds2. The longest folding simulation to date is a single 1-µs simulation of the villin headpiece3; however, such single runs may miss many features of the folding process as it is a heterogeneous reaction involving an ensemble of transition states4,5. Here, we have used a distributed computing implementation to produce tens of thousands of 5–20-ns trajectories (700 µs) to simulate mutants of the designed mini-protein BBA5. The fast relaxation dynamics these predict were compared with the results of laser temperature-jump experiments. Our computational predictions are in excellent agreement with the experimentally determined mean folding times and equilibrium constants. The rapid folding of BBA5 is due to the swift formation of secondary structure. The convergence of experimentally and computationally accessible timescales will allow the comparison of absolute quantities characterizing in vitro and in silico (computed) protein folding6.

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Figure 1: Folding results.
Figure 2: BBA5 double mutant thermodynamics and kinetics.
Figure 3: Folded population growth.


  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)

    CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  4. Wolynes, P. G., Onuchic, J. N. & Thirumalai, D. Navigating the folding routes. Science 267, 1619–1620 (1995)

    ADS  CAS  Article  Google Scholar 

  5. Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10–19 (1997)

    CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  9. Ferrara, P. & Caflisch, A. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl Acad. Sci. USA 97, 10780–10785 (2000)

    ADS  CAS  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  14. Shirts, M. & Pande, V. S. Screen savers of the world unite. Science 290, 1903–1904 (2000)

    CAS  Article  Google Scholar 

  15. Struthers, M., Ottesen, J. J. & Imperiali, B. Design and NMR analyses of compact, independently folded BBA motifs. Folding Des. 3, 95–103 (1998)

    CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  17. Ervin, J., Sabelko, J. & Gruebele, M. Submicrosecond real-time fluorescence detection: application to protein folding. J. Photochem. Photobiol. Biol. 54, 1–15 (2000)

    CAS  Article  Google Scholar 

  18. Chandler, D. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J. Chem. Phys. 68, 2959–2970 (1978)

    ADS  CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  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)

    ADS  CAS  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  22. Moore, S. & Stein, W. Amino acid determination, methods and techniques. J. Biol. Chem. 192, 663–670 (1951)

    CAS  PubMed  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  24. Fletcher, R. & Powell, M. J. D. A rapidly convergent descent method for minimization. Comput. J. 6, 163–168 (1963)

    MathSciNet  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  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)

    CAS  Article  Google Scholar 

  28. Andersen, H. C. Rattle: a ‘velocity’ version of the shake algorithm for molecular dynamics calculations. J. Comput. Phys. 52, 24–34 (1983)

    ADS  CAS  Article  Google Scholar 

  29. Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983)

    CAS  Article  Google Scholar 

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We thank the Folding@Home volunteers whose processor power made this work possible; the members of the Pande, Levitt and Gruebele laboratories for discussion; J. Ottesen for the BBA5 coordinates; B. Imperiali for NMR data; the UIUC Laboratory for Fluorescence Dynamics; and the Suslick group for equipment use. C.S. was supported by a pre-doctoral Howard Hughes Medical Institute fellowship. V.P. and the Folding@Home project were supported by the National Institutes of Health (NIH), American Chemical Society-Petroleum Research Fund, National Science Foundation Materials Research Science & Engineering Centers, Center on Polymer Interfaces and Macromolecular Assemblies seed funds, and a gift from Intel. H.N. was supported by an NIH biophysics training grant. H.N. and M.G. were also funded by the NIH.

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Correspondence to Vijay S. Pande or Martin Gruebele.

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Snow, C., Nguyen, H., Pande, V. et al. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420, 102–106 (2002).

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