A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling.

ABSTRACT: Recently, a series of closely related theoretical constructs termed the "topomer search model" (TSM) has been proposed for the folding mechanism of small, single-domain proteins. A basic assumption of the proposed scenarios is that the rate-limiting step in folding is an essentially unbiased, diffusive search for a conformational state called the native topomer defined by an overall native-like topological pattern. Successes in correlating TSM-predicted folding rates with that of real proteins have been interpreted as experimental support for the model. To better delineate the physics entailed, key TSM concepts are examined here using extensive Langevin dynamics simulations of continuum C(alpha) chain models. The theoretical native topomers of four experimentally well-studied two-state pro

SUBMITTER: Wallin S 

PROVIDER: S-EPMC2253387 | biostudies-literature | 2005 Jun

REPOSITORIES: biostudies-literature