Kinetic definition of protein folding transition state ensembles and reaction coordinates.

ABSTRACT: Using distributed molecular dynamics simulations we located four distinct folding transitions for a 39-residue betabetaalphabeta protein fold. To characterize the nature of each room temperature transition, we calculated the probability of transmission for 500 points along each free energy barrier. We introduced a method for determining transition states by employing the transmission probability, Ptrans, and determined which conformations were transition state ensemble members (Ptrans approximately 0.5). The transmission probability may be used to characterize the barrier in several ways. For example, we ran simulations at 82 degrees C, determined the change in Ptrans with temperature for all 2,000 conformations, and quantified Hammond behavior directly using Ptrans correlation. Additional

SUBMITTER: Snow CD 

PROVIDER: S-EPMC1479057 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature