Folding domain B of protein A on a dynamically partitioned free energy landscape.

ABSTRACT: The B domain of staphylococcal protein A (BdpA) is a small helical protein that has been studied intensively in kinetics experiments and detailed computer simulations that include explicit water. The simulations indicate that BdpA needs to reorganize in crossing the transition barrier to facilitate folding its C-terminal helix (H3) onto the nucleus formed from helices H1 and H2. This process suggests frustration between two partially ordered forms of the protein, but recent varphi value measurements indicate that the transition structure is relatively constant over a broad range of temperatures. Here we develop a simplistic model to investigate the folding transition in which properties of the free energy landscape can be quantitatively compared with experimental data. The model is a conti

SUBMITTER: Nelson ED 

PROVIDER: S-EPMC2234171 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature