The mechanical modeling of proteins
The principal objective of this dissertation is to develop and apply coarse-grained models for mechanical characterization of proteins, in particular strong proteins. This work may be regarded as the initial stage of the broader efforts toward the mechanical characterization of proteins. In this dissertation, we proposed a simple topological model of a cross-linked chain model. The purpose of this model is to identify the optimal cross-links topologies with respect to the strength and/or toughness. The model predicts that strong proteins possess the so-called “parallel strands” cross-links. This simple topological model of a cross-linked chain was extended to understand the role of kinetic effects on the mechanical characterization of a protein. That is, we identified the optimal topology in terms of strength and/or toughness with respect to the loading rate. This extended model indicates us why the terminal parallel strands exhibits such remarkable strength and toughness in atomic force microscopy experiments. Furthermore, we developed a coarse-grained model consistent with the molecular dynamics. In this modeling, we are not concerned with strong protein per se. One may regard this approach as the homogenization of molecular dynamics. This approach is based on the relationship between stiffness matrix and correlation matrix, which can be calculated in molecular dynamics simulations. With this model, we demonstrate that the dominant deformation mode of retinol binding is twist and bending. Moreover, the stiffness matrix of a coarse-grained model is dictated by the contact map. This means that the equivalent mass-spring system for a protein can be constructed based on the topology of contacts.