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Computational Research in Molecular Chemistry
Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation.Ma, Y., S. You, M. Regnier, J.A. McCammonProc. Natl. Acad. Sci. USA in press.    
Muscle contraction is performed by arrays of contractile proteins in the sarcomere. Serious heart diseases, such as cardiomyopathy, can often be results of mutations in myosin and actin. Direct characterization of how small changes in the myosin-actin complex impact its force production remains challenging. Molecular dynamics (MD) simulations, although capable of studying protein structurefunction relationships, are limited owing to the slow timescale of the myosin cycle as well as a lack of various intermediate structures for the actomyosin complex. Here, employing comparative modeling and enhanced sampling MD simulations, we show how the human cardiac myosin generates force during the mechanochemical cycle. Initial conformational ensembles for different myosin-actin states are learned from multiple structural templates with Rosetta. This enables us to efficiently sample the energy landscape of the system using Gaussian accelerated MD. Key myosin loop residues, whose substitutions are related to cardiomyopathy, are identified to form stable or metastable interactions with the actin surface. We find that the actin-binding cleft closure is allosterically coupled to the myosin core transitions and ATP-hydrolysis product release from the active site. Furthermore, a gate between switch I and switch II is suggested to control phosphate release at the pre-powerstroke state. Our approach demonstrates the ability to link sequence and structural information to motor functions.
Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learningMiao, Y., C.A. Chang, W. Zhu, J.A. McCammonFront. Molec. Biosci. In press (2023).    
PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period.
Philpott, J.M., A.M. Freeberg, J. Park, K. Lee, C.G. Ricci, S.R. Hunt, R. Narasimamurthy, D.H. Segal, R. Robles, Y. Cai, S. Tripathi, J.A. McCammon, D.M. Virshup, J.C. Chiu, C. Lee, C.L. Partch.
Molecular Cell, in press (2023).
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