Literature DB >> 25006262

Catalytic strategy used by the myosin motor to hydrolyze ATP.

Farooq Ahmad Kiani1, Stefan Fischer2.   

Abstract

Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum-classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO4(2-) state, but in the H2PγO4(-) state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3(-)) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.

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Year:  2014        PMID: 25006262      PMCID: PMC4115568          DOI: 10.1073/pnas.1401862111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  49 in total

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Authors:  A Málnási-Csizmadia; D S Pearson; M Kovács; R J Woolley; M A Geeves; C R Bagshaw
Journal:  Biochemistry       Date:  2001-10-23       Impact factor: 3.162

Review 2.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

3.  ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism.

Authors:  Courtney L Parke; Edward J Wojcik; Sunyoung Kim; David K Worthylake
Journal:  J Biol Chem       Date:  2009-12-15       Impact factor: 5.157

4.  Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis.

Authors:  Petra Imhof; Stefan Fischer; Jeremy C Smith
Journal:  Biochemistry       Date:  2009-09-29       Impact factor: 3.162

5.  Structural mechanism of the recovery stroke in the myosin molecular motor.

Authors:  Stefan Fischer; Björn Windshügel; Daniel Horak; Kenneth C Holmes; Jeremy C Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-29       Impact factor: 11.205

6.  Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis.

Authors:  S J Admiraal; D Herschlag
Journal:  Chem Biol       Date:  1995-11

7.  Oxygen exchange in the gamma-phosphoryl group of protein-bound ATP during Mg2+-dependent adenosine triphosphatase activity of myosin.

Authors:  C R Bagshaw; D R Trentham; R G Wolcott; P D Boyer
Journal:  Proc Natl Acad Sci U S A       Date:  1975-07       Impact factor: 11.205

8.  Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations.

Authors:  Bella L Grigorenko; Alexander V Nemukhin; Maria S Shadrina; Igor A Topol; Stanley K Burt
Journal:  Proteins       Date:  2007-02-01

9.  Three-dimensional structure of myosin subfragment-1: a molecular motor.

Authors:  I Rayment; W R Rypniewski; K Schmidt-Bäse; R Smith; D R Tomchick; M M Benning; D A Winkelmann; G Wesenberg; H M Holden
Journal:  Science       Date:  1993-07-02       Impact factor: 47.728

10.  Functional transitions in myosin: role of highly conserved Gly and Glu residues in the active site.

Authors:  H Onishi; M F Morales; S Kojima; K Katoh; K Fujiwara
Journal:  Biochemistry       Date:  1997-04-01       Impact factor: 3.162

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  12 in total

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

Authors:  Anthony P Baldo; Jil C Tardiff; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2020-11-02       Impact factor: 2.991

2.  Inorganic Polyphosphates As Storage for and Generator of Metabolic Energy in the Extracellular Matrix.

Authors:  Werner E G Müller; Heinz C Schröder; Xiaohong Wang
Journal:  Chem Rev       Date:  2019-11-18       Impact factor: 60.622

3.  Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.

Authors:  Xiya Lu; Victor Ovchinnikov; Darren Demapan; Daniel Roston; Qiang Cui
Journal:  Biochemistry       Date:  2017-03-01       Impact factor: 3.162

4.  miR-29c&b2 encourage extramedullary infiltration resulting in the poor prognosis of acute myeloid leukemia.

Authors:  Yanyu Wei; Wei Lu; Yehua Yu; Yuanmei Zhai; Hezhou Guo; Shaoxin Yang; Chong Zhao; Yanjie Zhang; Jiali Liu; Yuhui Liu; Jian Fei; Jun Shi
Journal:  Oncogene       Date:  2021-04-22       Impact factor: 9.867

5.  Effects of protonation on the hydrolysis of triphosphate in vacuum and the implications for catalysis by nucleotide hydrolyzing enzymes.

Authors:  Farooq Ahmad Kiani; Stefan Fischer
Journal:  BMC Biochem       Date:  2016-06-29       Impact factor: 4.059

Review 6.  Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes.

Authors:  Yi Jin; Robert W Molt; G Michael Blackburn
Journal:  Top Curr Chem (Cham)       Date:  2017-03-15

7.  The GTPase hGBP1 converts GTP to GMP in two steps via proton shuttle mechanisms.

Authors:  Ravi Tripathi; Rachel Glaves; Dominik Marx
Journal:  Chem Sci       Date:  2016-08-22       Impact factor: 9.825

8.  Investigation of the Recovery Stroke and ATP Hydrolysis and Changes Caused Due to the Cardiomyopathic Point Mutations in Human Cardiac β Myosin.

Authors:  Ananya Chakraborti; Anthony P Baldo; Jil C Tardiff; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2021-06-09       Impact factor: 3.466

9.  Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin.

Authors:  Suliman Adam; Ana-Nicoleta Bondar
Journal:  PLoS One       Date:  2018-08-07       Impact factor: 3.240

10.  Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method.

Authors:  Yan Zhou; Pedro Ojeda-May; Mulpuri Nagaraju; Bryant Kim; Jingzhi Pu
Journal:  Molecules       Date:  2018-10-16       Impact factor: 4.411

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