Towards a mechanistic view of protein motion

Proteins are the fundamental building blocks of all biological systems. To perform their function, proteins generally undergo self-motions that result in changes in their three-dimensional shape. In order to understand the function of a protein and thus to be able to infer how to therapeutically regulate its function, it is necessary to have detailed knowledge of the feasible self-motions of the protein. Such knowledge cannot be obtained by existing experimental methods. In this paper, we present preliminary evidence that accurate and computationally efficient simulation of the self-motions of a protein may be achieved by partitioning the simulation based on the type of self-motions. In support of this view, we present a method and accompanying simulation results that the large-scale motions of a protein can be simulated based entirely on kinematic considerations. The proposed method leverages insights from kinematics and operational space control from robotics. We believe the proposed method to be a first step towards a general, accurate, and efficient method for the simulation of protein motion.