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Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations
[Image: see text] The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling betwe...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9336149/ https://www.ncbi.nlm.nih.gov/pubmed/35912346 http://dx.doi.org/10.1021/acscentsci.1c01599 |
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author | Shekhar, Mrinal Gupta, Chitrak Suzuki, Kano Chan, Chun Kit Murata, Takeshi Singharoy, Abhishek |
author_facet | Shekhar, Mrinal Gupta, Chitrak Suzuki, Kano Chan, Chun Kit Murata, Takeshi Singharoy, Abhishek |
author_sort | Shekhar, Mrinal |
collection | PubMed |
description | [Image: see text] The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V(1)-type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using X-ray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P(i)) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V(1)-ATPase to be the rate-limiting step of motor action. |
format | Online Article Text |
id | pubmed-9336149 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-93361492022-07-30 Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations Shekhar, Mrinal Gupta, Chitrak Suzuki, Kano Chan, Chun Kit Murata, Takeshi Singharoy, Abhishek ACS Cent Sci [Image: see text] The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V(1)-type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using X-ray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P(i)) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V(1)-ATPase to be the rate-limiting step of motor action. American Chemical Society 2022-06-14 2022-07-27 /pmc/articles/PMC9336149/ /pubmed/35912346 http://dx.doi.org/10.1021/acscentsci.1c01599 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Shekhar, Mrinal Gupta, Chitrak Suzuki, Kano Chan, Chun Kit Murata, Takeshi Singharoy, Abhishek Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations |
title | Revealing a Hidden Intermediate of Rotatory Catalysis
with X-ray Crystallography and Molecular Simulations |
title_full | Revealing a Hidden Intermediate of Rotatory Catalysis
with X-ray Crystallography and Molecular Simulations |
title_fullStr | Revealing a Hidden Intermediate of Rotatory Catalysis
with X-ray Crystallography and Molecular Simulations |
title_full_unstemmed | Revealing a Hidden Intermediate of Rotatory Catalysis
with X-ray Crystallography and Molecular Simulations |
title_short | Revealing a Hidden Intermediate of Rotatory Catalysis
with X-ray Crystallography and Molecular Simulations |
title_sort | revealing a hidden intermediate of rotatory catalysis
with x-ray crystallography and molecular simulations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9336149/ https://www.ncbi.nlm.nih.gov/pubmed/35912346 http://dx.doi.org/10.1021/acscentsci.1c01599 |
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