Hydrogen Bonds and Kinematic Mobility of Protein Molecules

Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation, and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOFs) with considerable computational implications. On the other hand, real protein molecules appear to exhibit a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of hydrogen bonds during the folding process. In this paper, we explore the pivotal role of hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of hydrogen bonds are reviewed and a new set of geometric criteria is proposed. We show that the new criteria better correlate the number of predicted hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have enormous computational implications in protein folding simulations.