Chemical frustration in the protein folding landscape: grand canonical ensemble simulations of cytochrome c.

ABSTRACT: A grand canonical formalism is developed to combine discrete simulations for chemically distinct species in equilibrium. Each simulation is based on a perturbed funneled landscape. The formalism is illustrated using the alkaline-induced transitions of cytochrome c as observed by FTIR spectroscopy and with various other experimental approaches. The grand canonical simulation method accounts for the acid/base chemistry of deprotonation, the inorganic chemistry of heme ligation and misligation, and the minimally frustrated folding energy landscape, thus elucidating the physics of protein folding involved with an acid/base titration of a protein. The formalism combines simulations for each of the relevant chemical species, varying by protonation and ligation states. In contrast to models based

SUBMITTER: Weinkam P 

PROVIDER: S-EPMC2842011 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature