ArticlePLoS computational biology2007
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis.PLoS computational biology · 2024Article
- Unraveling a Force-Generating Allosteric Pathway of Actomyosin Communication Associated with ADP and PInternational journal of molecular sciences · 2020Article
- Structural and Computational Insights into a Blebbistatin-Bound Myosin•ADP Complex with Characteristics of an ADP-Release Conformation along the Two-Step Myosin Power Stoke.International journal of molecular sciences · 2020Article
- Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain.PLoS computational biology · 2020Article
- An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil.PLoS computational biology · 2017Article
- Simulating the dynamics of the mechanochemical cycle of myosin-V.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Allostery Wiring Map for Kinesin Energy Transduction and Its Evolution.The Journal of biological chemistry · 2016Article
- Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity.PLoS computational biology · 2016Article
- A Failure to Communicate: MYOSIN RESIDUES INVOLVED IN HYPERTROPHIC CARDIOMYOPATHY AFFECT INTER-DOMAIN INTERACTION.The Journal of biological chemistry · 2015Article
- Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.Journal of the American Chemical Society · 2015Article
- Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.The Journal of chemical physics · 2014Article
- Electrostatic origin of the unidirectionality of walking myosin V motors.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Allosteric switching of agonist/antagonist activity by a single point mutation in the interluekin-1 receptor antagonist, IL-1Ra.Journal of molecular biology · 2013Article
- Multiple pathways promote dynamical coupling between catalytic domains in Escherichia coli prolyl-tRNA synthetase.Biochemistry · 2013Article
- Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations.Topics in current chemistry · 2013Review
- Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid.Biophysical journal · 2012Article
- Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.The journal of physical chemistry. B · 2012Article
- Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases.PLoS computational biology · 2011Article
- Hysteresis-based mechanism for the directed motility of the Ncd motor.Biophysical journal · 2011Article
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4 authors.
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Abstract
An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural rearrangements. In this work, a systematic attempt is made to tackle this issue for the conventional myosin. By judiciously combining a range of computational techniques with different approximations and strength, which include targeted molecular dynamics, normal mode analysis, and statistical coupling analysis, we are able to identify a set of important residues and propose their relevant function during the recovery stroke of myosin. These analyses also allowed us to make connections with previous experimental and computational studies in a critical manner. The behavior of the widely used reporter residue, Trp501, in the simulations confirms the concern that its fluorescence does not simply reflect the relay loop conformation or active-site open/close but depends subtly on its microenvironment. The findings in the targeted molecular dynamics and a previous minimum energy path analysis of the recovery stroke have been compared and analyzed, which emphasized the difference and complementarity of the two approaches. In conjunction with our previous studies, the current set of investigations suggest that the modulation of structural flexibility at both the local (e.g., active-site) and domain scales with strategically placed "hotspot" residues and phosphate chemistry is likely the general feature for mechanochemical coupling in many molecular motors. The fundamental strategies of examining both collective and local changes and combining physically motivated methods and informatics-driven techniques are expected to be valuable to the study of other molecular motors and allosteric systems in general.
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