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Biophys J, December 1999, p. 2942-2952, Vol. 77, No. 6
-Hairpin Assembly:
Insights from Various Simulation Techniques
*Department of Chemistry, University of Warsaw, 02-093 Warsaw, Poland, and #Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 USA
Small peptides that might have some features of globular
proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on
the Metropolis sampling scheme, and Entropy Sampling Monte Carlo
(ESMC), were applied in a study of a high-resolution lattice model of
the C-terminal fragment of the B1 domain of protein G. The results
provide a detailed description of folding dynamics and thermodynamics
and agree with recent experimental findings (Munoz et al., 1997.
Nature. 390:196-197). In particular, it was found that
the folding is cooperative and has features of an all-or-none transition. Hairpin assembly is usually initiated by turn formation; however, hydrophobic collapse, followed by the system rearrangement, was also observed. The denatured state exhibits a substantial amount of
fluctuating helical conformations, despite the strong 
-type
secondary structure propensities encoded in the sequence.
Biophys J, December 1999, p. 2942-2952, Vol. 77, No. 6
© 1999 by the Biophysical Society 0006-3495/99/12/2942/11 $2.00
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