Mechanochemical Function of Myosin II: Investigation into the Recovery Stroke and ATP Hydrolysis

Abstract

Myosin regulates muscle function through a complex cycle of conformational rearrangements coupled with the hydrolysis of adenosine triphosphate (ATP). The recovery stroke reorganizes the myosin active site to hydrolyze ATP and cross bridge with the thin filament to produce muscle contraction. Engineered mutations K84M and R704E in Dictyostelium myosin have been designed to specifically inhibit the recovery stroke and have been shown to indirectly affect the ATPase activity of myosin. We investigated these mutagenic perturbations to the recovery stroke and generated thermodynamically correct and unbiased trajectories for native ATP hydrolysis with computationally enhanced sampling methods. Our methodology was able to resolve experimentally observed changes to kinetic and equilibrium dynamics for the recovery stroke with the correct prediction in the severity of these changes. For ATP hydrolysis, the sequential nature along with the stabilization of a metaphosphate intermediate was observed in agreement with previous studies. However, we observed glutamate 459 being utilized as a proton abstractor to prime the attacking water instead of a lytic water, a phenomenon not well categorized in myosin but has in other ATPases. Both rare event methodologies can be extended to human myosin to investigate isoformic differences from Dictyostelium and scan cardiomyopathic mutations to see differential perturbations to kinetics of other conformational changes in myosin such as the power stroke.

Clinical Effects of Acupuncture for Stroke Patients Recovery

“…Baldo et al reported that acupuncture could regulate vasoactive substances and activate nitric oxide synthase III, and it also inhibits the angiotensin system and platelet adhesion. Inflammatory response after cerebral ischemia is mainly mediated by microglia, astrocytes, and leukocytes, including cytokines (IL-1, IL-6, IL-10, and TNF- α ) [ 22 ]. This inflammatory response induces the activation of gene expression and transcription factors that regulate the ischemic cascade and further aggravates the local inflammatory response.…”

Computational and biophysical determination of pathogenicity of variants of unknown significance in cardiac thin filament

“…In addition, understanding the pathogenic effects on interactions of the CTF with other proteins in the sarcomere (e.g. the thick filament) is under intensive study (49,50). Moreover, we hope to be able to expand this analysis to other regions of the CTF, such as the C-terminus of cTnT, and to extend the length of simulations in the future.…”

“…These distributions and changes are difficult for an individual to assess, but a more automated process, such as deep machine learning, is exactly tailored to such a task and is a topic of ongoing research. In addition, understanding the pathogenic effects on interactions of the CTF with other proteins in the sarcomere (e.g., the thick filament) is under intensive study ( 49 , 50 ). Moreover, we hope to be able to expand this analysis to other regions of the CTF, such as the C-terminus of cTnT, and to extend the length of simulations in the future.…”

Embedding Quantum Statistical Excitations in a Classical Force Field

“…The pioneering QM/MM , method can be used to focus attention on a smaller, predefined, region using quantum mechanics, while treating the rest of the system classically. This technique requires careful consideration of boundary and embedding effects, including interactions between the QM and MM regions, but is a valuable tool for studying free energies, catalysis including ATP hydrolysis, − and photochemistry , integrates the quantum mechanical evaluation of the forces on each atomtypically done using DFTwith the classical dynamical evolution of the system itself.…”