Calculation and Visualization of Atomistic Mechanical Stresses in Biomolecules

Abstract

Many biomolecules have machine-like functions, and accordingly are analyzed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We think that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses and their decomposition of the various potential energy terms from molecular dynamics (MD) simulations. We apply the stress analysis to steered MD simulations of a single titin immunoglobulin-like domain (I27) and of a linear chain of six similar titin domains (I65-I70) found in cardiac and skeletal muscle. The post-processing stress analysis elucidates where throughout the protein tensile and compressive stresses load before structural failure occurs and the beta sheets in the domain start to unfold.