Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain.

ABSTRACT: The folding thermodynamics of the src-SH3 protein domain were characterized under refolding conditions through biased fully atomic molecular dynamics simulations with explicit solvent. The calculated free energy surfaces along several reaction coordinates revealed two barriers. The first, larger barrier was identified as the transition state barrier for folding, associated with the formation of the first hydrophobic sheet of the protein. phi values calculated from structures residing at the transition state barrier agree well with experimental phi values. The microscopic information obtained from our simulations allowed us to unambiguously assign intermediate phi values as the result of multiple folding pathways. The second, smaller barrier occurs later in the folding process and is associ

SUBMITTER: Guo W 

PROVIDER: S-EPMC1303065 | biostudies-literature | 2003 Jul

REPOSITORIES: biostudies-literature