Collective motions of myosin head derived from backbone molecular dynamics and combination with X‐ray solution scattering data

Collective modes of myosin head, S1, were derived from molecular dynamics trajectories of a simplified protein model, backbone model. Because the model requires only the positions of C_α‐atoms, large proteins are tractable, even when the amino acid sequence and the side‐chain orientations are unknown. The S1 is a large molecule and only the C_α‐atomic positions have been experimentally determined. In the simulation, large flipping motions of the extended α‐helical C‐terminal tail of S1 were found only in the largest and second largest amplitude collective modes, which were approximately perpendicular to each other. A few collective modes other than the first and second largest ones largely deformed the actin binding site of S1. The pair‐distance distribution, obtained from the X‐ray solution scattering, suggests a large conformational change of S1, isolated in solution without binding to actin filament, during the ATP hydrolysis. The modeling of the large conformational change was done with using the collective modes, and showed that the second mode mainly contributed to the large conformational change. The modeling procedure, introduced here, can be easily generalized for various experimental data, and applicable to the collective modes obtained from an all‐atom simulation. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1983–1994, 2001