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Biophys J. 2013 Oct 15;105(8):1882-92. doi: 10.1016/j.bpj.2013.09.003.

Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations.

Author information

1
Department of Physics, University at Buffalo, Buffalo, New York. Electronic address: wjzheng@buffalo.edu.

Abstract

Tropomyosin (Tm) is a coiled-coil protein that binds to filamentous actin (F-actin) and regulates its interactions with actin-binding proteins like myosin by moving between three positions on F-actin (the blocked, closed, and open positions). To elucidate the molecular details of Tm flexibility in relation to its binding to F-actin, we conducted extensive molecular dynamics simulations for both Tm alone and Tm-F-actin complex in the presence of explicit solvent (total simulation time >400 ns). Based on the simulations, we systematically analyzed the local flexibility of the Tm coiled coil using multiple parameters. We found a good correlation between the regions with high local flexibility and a number of destabilizing regions in Tm, including six clusters of core alanines. Despite the stabilization by F-actin binding, the distribution of local flexibility in Tm is largely unchanged in the absence and presence of F-actin. Our simulations showed variable fluctuations of individual Tm periods from the closed position toward the open position. In addition, we performed Tm-F-actin binding calculations based on the simulation trajectories, which support the importance of Tm flexibility to Tm-F-actin binding. We identified key residues of Tm involved in its dynamic interactions with F-actin, many of which have been found in recent mutational studies to be functionally important, and the rest of which will make promising targets for future mutational experiments.

PMID:
24138864
PMCID:
PMC3797582
DOI:
10.1016/j.bpj.2013.09.003
[Indexed for MEDLINE]
Free PMC Article

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