Mechanical Model of Hydrogen Bonds in Protein Molecules

The unique properties of protein molecules have motivated researchers exploit them in the design and fabrication of bio-mimetic nano devices to perform a special task. Function of protein molecules is in turn dependent on their 3D structure and their ability to modify their shape for a specific task. To study and manipulate protein molecules we need to have knowledge of mechanical properties of these molecules. In this paper a multiscale model to predict stiffness of helical protein molecules has been developed. Hydrogen bonds as major contributing factor to proteins flexibility, are modeled as elastic springs based on their empirical potential energy. Such mechanical representation of hydrogen bonds enables us to obtain the stiffness ellipsoid of hydrogen bonds which leads to an understanding of the directional stiffness of protein molecules. The model has also been applied to three different protein molecules whose stiffness were reported in the literature. The comparison shows an agreement between the stiffness computed by the proposed model and that obtained through experiments and/or Molecular Dynamics (MD) simulations.

Website:  http://www.arjonline.org/engineering/american-research-journal-of-mechanical-and-automation-engineering/