The actomyosin molecular motor, the motor composed of myosin II and actin filament, is responsible for muscle contraction, converting chemical energy into mechanical work. Although recent single molecule and structural studies have shed new light on the energy-converting mechanism, the physical basis of the molecular-level mechanism remains unclear because of the experimental limitations. To provide a clue to resolve the controversy between the lever-arm mechanism and the Brownian ratchet-like mechanism, we here report an in silico single molecule experiment of an actomyosin motor. When we placed myosin on an actin filament and allowed myosin to move along the filament, we found that myosin exhibits a unidirectional Brownian motion along the filament. This unidirectionality was found to arise from the combination of a nonequilibrium condition realized by coupling to the ATP hydrolysis and a ratchet-like energy landscape inherent in the actin-myosin interaction along the filament, indicating that a Brownian ratchet-like mechanism contributes substantially to the energy conversion of this molecular motor. M olecular machines in living organisms are nanometer-sized small systems working robustly and efficiently in the presence of the severely disturbing thermal noises. Furthermore, in the case of the molecular motors, the energy supplied by the hydrolysis of adenosine triphosphate (ATP), which is to be converted to the mechanical work, is only an order of magnitude larger than the thermal energy at room temperature (∼20k B T), and hence it seems likely that the molecular machines harness the thermal noise, instead of suppressing it as the human-made machines do (1). This distinct feature of the molecular machines should arise from the atomic structures of the constituent proteins, which is reflected in the current focus of interest in the structural aspect of the molecular machines. However, it should be remembered that the structural aspect is not everything but is inseparably linked to the dynamical and energetical aspects. Therefore, a unified description of structure, dynamics, and energetics is the step necessary to understand the molecular-level physical principle of how the molecular machines work.The actomyosin molecular motor, the system composed of myosin II and actin molecules, is responsible for muscle contraction, and is the most extensively studied molecular motor. It has been shown by single molecule experiments (SME) that a single myosin molecule and an actin filament (polymerized actin) constitute the minimal force-generating unit of this motor (2-4) (see Fig. 1A). Although SME has been a powerful approach to study the dynamical aspect of the force-generating unit (2-4), the limitation of the spatiotemporal resolution of SME has inhibited us from developing the full atomistic picture of the force-generating process. On the other hand, since the currently available high-resolution structures of myosin (5-7) are those obtained in the crystalline environment and in the absence of actin, it remains unc...

We present a molecular dynamics study of the R-helix formation in a system consisting of a 15-residue poly(L-alanine) and surrounding water molecules. By applying a relatively high temperature, we observed the R-helix formation several times during a 17-ns run, and reversible helix-coil transitions were also observed. The R-helix formations were usually initiated by the -turn structures. A crank-shaft-like motion of the peptide was included in the folding process. In the formed R-helical domains, substantial 3 10 -helix formations were found especially at the termini, as observed by the NMR study. The folding time scale at room temperature estimated from our simulation was found to lie in the range of 100 ns, which is in accord with the time scale of the T-jump experiments. The total energy of the whole system was lower in the R-helix state than in the random-coil state by 20.4 ( 4.8 kcal/mol, which is consistent with the experimental value obtained by calorimetry. This energy decrease in forming the R-helix was mainly caused by the Coulombic energy and the torsional energy.

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