Computational Studies of Mechanical Signal Transduction in Proteins

Cellular signaling is a system of complex interplay of communications that guides cellular processes and coordinates cell behavior. In this dissertation, united by three main themes, investigations of mechanisms of mechanical signal transduction in proteins are presented. The first theme focuses on chemical to mechanical signal transduction. Using molecular dynamics simulations, aspects of thin filament calcium-induced regulation are investigated. The calcium-dependent behavior of skeletal troponin, and key conformational events subsequent to calcium expulsion from troponin C regulatory sites are described. Dynamics of cardiac troponin C, and details of residue coordination leading to calcium binding in the regulatory site are elucidated. These findings are incorporated into a model integrating the calcium dependent behavior of troponin to its ability to interact with actin and regulate muscle contraction. The second theme focuses on steered molecular dynamics (SMD) investigations of force induced mechanical unfolding of slipknot proteins. Unfolding of slipknot AFV3-109 occurs via either two-state, or three-state process involving the formation of a stable intermediate state. The results demonstrate a mechanical unfolding pathway bifurcation and potential gearbox mechanism with non similar responses to pulling force that may enable differential mechanical signal transduction. The third theme focuses on two aspects of mechanical proteins stabilization to mechanical unfolding - the solvent environment effect and neighboring beta strands effect. The solvent environment plays an integral role in cellular processes. SMD unfolding of I27 and solvent substitution were combined to reveal that solvent environment modulates the force resistance of I27. During unfolding, solvent molecules interact with I27's force bearing patch, in solvent molecule geometry-dependent mode multiplicity. Protein topology and pulling geometry play important roles in determining protein mechanical stability. The critical importance of neighboring beta strands stabilization effect is explored. The proteins Top7 and barstar have similar force-bearing topology but different mechanical stability. SMD simulations of barstar reveal that barstar unfolds by beta strand peeling whereas Top7, which has two additional beta strands in its force bearing patch unfolds via substructure-sliding. This neighboring beta strands stabilization effect may be a general mechanism in protein mechanics and de-novo design guideline for mechanically stable proteins with novel topology.