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

Wenjun Zheng, Bipasha Barua, Sarah E. Hitchcock-Degregori

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1882-1892
Number of pages11
JournalBiophysical Journal
Volume105
Issue number8
DOIs
StatePublished - Oct 15 2013

All Science Journal Classification (ASJC) codes

  • Biophysics

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