Folding a protein in a computer: an atomic description of the folding/unfolding of protein A.

ABSTRACT: We study the folding mechanism of a three-helix bundle protein at atomic resolution, including effects of explicit water. Using replica exchange molecular dynamics we perform enough sampling over a wide range of temperatures to obtain the free energy, entropy, and enthalpy surfaces as a function of structural reaction coordinates. Simulations were started from different configurations covering the folded and unfolded states. Because many transitions between all minima at the free energy surface are observed, a quantitative determination of the free energy barriers and the ensemble of configurations associated with them is now possible. The kinetic bottlenecks for folding can be determined from the thermal ensembles of structures on the free energy barriers, provided the kinetically determi

SUBMITTER: Garcia AE 

PROVIDER: S-EPMC283518 | biostudies-literature | 2003 Nov

REPOSITORIES: biostudies-literature