Force Distribution in Proteins from Molecular Dynamics Simulations

摘要

Mechanical force is routinely applied to proteins in force probing experiments and simulations to observe a protein's response to external stress. A yet unanswered question is how force propagates through proteins. How do perturbations like an external force flow through protein scaffolds and how is this related to protein stability and function? We elucidate force distribution in the titin 127 domain by monitoring alterations in forces between pairs of atoms in the folded state upon pulling the protein with a constant force. We find forces to be a more direct measure for internal strain than the only minor changes in atomic coordinates. We observe that the externally applied force is anisotropically distributed throughout the protein scaffold highlighting three prominent regions that contribute most of the protein's mechanical resistance. The functional relevance of the force distribution network is highlighted by additional mutant simulations. The method can easily be extended to other types of perturbation including allosteric signals, such as ligand binding, phosphorylation, or a change in protonation state.