Contact and impact in the multibody dynamics of motor protein locomotion

This paper presents the development of a rigid multibody dynamics approach to modeling, simulation, and analysis of motor proteins. A key element of this new model is that it retains the mass properties, in contrast to many commonly used models that do not. The mass properties are usually omitted because their inclusion yields a model with multiple time scales whose simulation requires a significant amount of time. However, the proposed model can be numerically integrated in a reasonable amount of time. Thus this approach represents a new method for treating multiple scale models. In addition, retaining the mass properties allows a detailed study of contact and impact between the protein and substrate, which is critical for protein processivity. The new model also provides insights into the characteristics of the protein and its environment, specifically, the effective damping experienced by the protein moving through its fluid environment may be quite small yielding under or critically damped motion. This conclusion runs contrary to the widely accepted notion that the protein's motion is strictly over damped. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of Myosin V.