The significance of molecular mechanics property to protein evolution

In the study of protein homology, multiple physical systems that correspond to different proteins must be jointly considered, such that the similarity of homologs can be explained in an aspect of the physics. Compared with the investigations that focus on the character of certain protein, the research object changes from one physical system to a set of systems. For this enlarged object, the importance of different physical quantities is still unclear. In an aspect of hydrophobic interaction, we rank the significance of different physical quantities here, according to their contribution to the conservation of family representative biological properties in protein evolution. Molecular mechanics property is suggested to be the governing factor responsible for protein homology.