Coupling of lever arm swing and biased Brownian motion in actomyosin.

An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement.

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing.

Ab initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an ab initio structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short- and long-range structural restraint information from a fragment library.

A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction.

De novo prediction of protein structures, the prediction of structures from amino acid sequences which are not similar to those of hitherto resolved structures, has been one of the major challenges in molecular biophysics. In this paper, we develop a new method of de novo prediction, which combines the fragment assembly method and the simulation of physical folding process: structures which have consistently assembled fragments are dynamically searched by Langevin molecular dynamics of conformational change. The benchmarking test shows that the prediction is improved when the candidate structures are cross-checked by an empirically derived score function.