ArticleProceedings of the National Academy of Sciences of the United States of America2007
Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 78 citations in OpenAlex.
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- Systematic QM/MM Study for PredictingJournal of chemical theory and computation · 2024Article
- Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Simulation toolkits at the molecular scale for trans-scale thermal signaling.Computational and structural biotechnology journal · 2023Review
- ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter.Molecules (Basel, Switzerland) · 2020Review
- Exhaustion of Skeletal Muscle Fibers Within Seconds: Incorporating Phosphate Kinetics Into a Hill-Type Model.Frontiers in physiology · 2020Article
- Modeling DNA Unwinding by AddAB Helicase-Nuclease and Modulation by Chi Sequences: Comparison with AdnAB and RecBCD.Cellular and molecular bioengineering · 2019Article
- Thiacalix[4]arenes Remove the Inhibitory Effects of Zn Cations on the Myosin ATPase Activity.Nanoscale research letters · 2018Article
- Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations.PLoS computational biology · 2018Article
- Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations.Methods in enzymology · 2018Article
- Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics.Journal of chemical theory and computation · 2017Article
- Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.Biochemistry · 2017Article
- The GTPase hGBP1 converts GTP to GMP in two stepsChemical science · 2017Article
- Review: Ras GTPases and myosin: Qualitative conservation and quantitative diversification in signal and energy transduction.Biopolymers · 2016Review
- Effects of protonation on the hydrolysis of triphosphate in vacuum and the implications for catalysis by nucleotide hydrolyzing enzymes.BMC biochemistry · 2016Article
- Kinesin Motor Enzymology: Chemistry, Structure, and Physics of Nanoscale Molecular Machines.Biophysical reviews · 2015Article
- Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study.PloS one · 2015Article
- Catalytic strategy used by the myosin motor to hydrolyze ATP.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Lytic water dynamics reveal evolutionarily conserved mechanisms of ATP hydrolysis by TIP49 AAA+ ATPases.Structure (London, England : 1993) · 2014Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
The intrinsic chemical reaction of adenosine triphosphate (ATP) hydrolysis catalyzed by myosin is modeled by using a combined quantum mechanics and molecular mechanics (QM/MM) methodology that achieves a near ab initio representation of the entire model. Starting with coordinates derived from the heavy atoms of the crystal structure (Protein Data Bank ID code 1VOM) in which myosin is bound to the ATP analog ADP.VO(4)(-), a minimum-energy path is found for the transformation ATP + H(2)O --> ADP + P(i) that is characterized by two distinct events: (i) a low activation-energy cleavage of the P(gamma) O(betagamma) bond and separation of the gamma-phosphate from ADP and (ii) the formation of the inorganic phosphate as a consequence of proton transfers mediated by two water molecules and assisted by the Glu-459-Arg-238 salt bridge of the protein. The minimum-energy model of the enzyme-substrate complex features a stable hydrogen-bonding network in which the lytic water is positioned favorably for a nucleophilic attack of the ATP gamma-phosphate and for the transfer of a proton to stably bound second water. In addition, the P(gamma) O(betagamma) bond has become significantly longer than in the unbound state of the ATP and thus is predisposed to cleavage. The modeled transformation is viewed as the part of the overall hydrolysis reaction occurring in the closed enzyme pocket after ATP is bound tightly to myosin and before conformational changes preceding release of inorganic phosphate.
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