ArticleProceedings of the National Academy of Sciences of the United States of America2010
Atomically detailed simulation of the recovery stroke in myosin by Milestoning.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 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
- Binding pocket dynamics along the recovery stroke of human β-cardiac myosin.PLoS computational biology · 2023Article
- Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- 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
- Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.The Journal of chemical physics · 2017Article
- Highly selective inhibition of myosin motors provides the basis of potential therapeutic application.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Perspective: Computer simulations of long time dynamics.The Journal of chemical physics · 2016Article
- Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.PLoS computational biology · 2015Article
- Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition.The journal of physical chemistry. B · 2015Article
- Exact milestoning.The Journal of chemical physics · 2015Article
- Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.Journal of the American Chemical Society · 2015Article
- Bridging scales through multiscale modeling: a case study on protein kinase A.Frontiers in physiology · 2015Review
- Serpin latency transition at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.The Journal of chemical physics · 2014Article
- Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain.Biophysical journal · 2013Article
- Milestoning simulation reveals mechanism of helix-breaking.Biophysical journal · 2013Article
- Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations.Topics in current chemistry · 2013Review
- The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein.Proteins · 2012Article
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Authors and funding
2 authors.
Funding
Abstract
Myosin II is a molecular motor that converts chemical to mechanical energy and enables muscle operations. After a power stroke, a recovery transition completes the cycle and returns the molecular motor to its prestroke state. Atomically detailed simulations in the framework of the Milestoning theory are used to calculate kinetics and mechanisms of the recovery stroke. Milestoning divides the process into transitions between hyper-surfaces (Milestones) along a reaction coordinate. Decorrelation of dynamics between sequential Milestones is assumed, which speeds up the atomically detailed simulations by a factor of millions. Two hundred trajectories of myosin with explicit water solvation are used to sample transitions between sequential pairs of Milestones. Collective motions of hundreds of atoms are described at atomic resolution and at the millisecond time scale. The experimentally measured transition time of about a millisecond is in good agreement with the computed time. The simulations support a sequential mechanism. In the first step the P-loop and switch 2 close on the ATP and in the second step the mechanical relaxation is induced via the relay and the SH1 helices. We propose that the entropy of switch 2 helps to drive the power stroke. Secondary structure elements are progressing through a small number of discrete states in a network of activated transitions and are assisted by side chain flips between rotameric states. The few-state sequential mechanism is likely to enhance the efficiency of the relaxation reducing the probability of off-pathway intermediates.
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