Paper Citing NAMD - Abstract
Pogorelov, T.V.; Luthey-Schulten, Z.
Variations in the fast folding rates of the lambda-repressor: A hybrid molecular dynamics study
BIOPHYSICAL JOURNAL, 87:207-214, JUL 2004
The ability to predict the effects of mutations on protein folding rates and mechanisms would greatly facilitate folding studies. Using a realistic full atom potential coupled with a G(o) over bar -like potential biased to the native state structure, we have investigated the effects of point mutations on the folding rates of a small single domain protein. The hybrid potential provides a detailed level of description of the folding mechanism that we correlate to features of the folding energy landscapes of fast and slow mutants of an 80-residue-long fragment of the lambda-repressor. Our computational reconstruction of the folding events is compared to the recent experimental results of W. Y. Yang and M. Gruebele (see companion article) and T. G. Oas and co-workers on the lambda-repressor, and helps to clarify the differences observed in the folding mechanisms of the various mutants.
