TY - JOUR
T1 - Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations
AU - Zheng, Wenjun
AU - Barua, Bipasha
AU - Hitchcock-Degregori, Sarah E.
N1 - Funding Information:
By performing total 440-ns MD/aMD simulations of explicitly solvated Tm in the absence or presence of F-actin, we successfully captured key dynamic features of Tm observed by x-ray crystallography studies but not by previous, less extensive and/or implicit-solvent-based MD simulations ( 25–28,63 ) and normal mode analysis ( 63 ). Our finding of good correlation between key destabilizing regions of Tm (including six Ala clusters) and regions with high local flexibility has given strong support to the proposal that these regions are involved in the Tm flexibility that is critical for Tm function. Thanks to the enhanced conformational sampling by aMD, we observed variable fluctuations of Tm from the closed position toward the open position on the F-actin surface and uncovered new potential interactions between Tm and F-actin that will make good targets for future mutational studies. This study validates the MD-based approach to the investigation of Tm flexibility and the dynamic interactions between Tm and F-actin. In the future, we will use this approach to investigate how specific Tm mutations perturb Tm dynamics and its interactions with F-actin, and to perform mutational and binding experiments to test the computational predictions. We thank Dr. Lehman for sharing the EM-based model of Tm - F-actin complex. The simulations were conducted using the supercomputing cluster of the Center for Computational Research at the University at Buffalo and the Biowulf cluster at the National Institutes of Health. This study was supported by an American Heart Association grant (0835292N) and a National Science Foundation grant (0952736) to W.Z. and a National Institutes of Health grant (GM093065) to S.E.H.D.
PY - 2013/10/15
Y1 - 2013/10/15
N2 - 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.
AB - 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.
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U2 - 10.1016/j.bpj.2013.09.003
DO - 10.1016/j.bpj.2013.09.003
M3 - Article
C2 - 24138864
AN - SCOPUS:84886022133
VL - 105
SP - 1882
EP - 1892
JO - Biophysical Journal
JF - Biophysical Journal
SN - 0006-3495
IS - 8
ER -