The Q-Cycle Mechanism of the bc1 Complex: A Biologist's Perspective on Atomistic Studies.
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| Title: | The Q-Cycle Mechanism of the bc |
|---|---|
| Authors: | Crofts, Antony R.1,2 crofts@illinois.edu, Rose, Stuart W.2, Burton, Rodney L.1, Desai, Amit V.3, Kenis, Paul J. A.3, Dikanov, Sergei A.4 |
| Source: | Journal of Physical Chemistry B. Apr2017, Vol. 121 Issue 15, p3701-3717. 17p. |
| Subjects: | Ubiquinones, Molecular dynamics, Rhodobacter, Reactive oxygen species, Semiquinone |
| Abstract: | The Q-cycle mechanism of the bc1 complex is now well enough understood to allow application of advanced computational approaches to the study of atomistic processes. In addition to the main features of the mechanism, these include control and gating of the bifurcated reaction at the Qo-site, through which generation of damaging reactive oxygen species is minimized. We report a new molecular dynamics model of the Rhodobacter sphaeroides bc1 complex implemented in a native membrane, and constructed so as to eliminate blemishes apparent in earlier Rhodobacter models. Unconstrained MD simulations after equilibration with ubiquinol and ubiquinone respectively at Qo- and Qi-sites show that substrate binding configurations at both sites are different in important details from earlier models. We also demonstrate a new Qo-site intermediate, formed in the sub-ms time range, in which semiquinone remains complexed with the reduced iron sulfur protein. We discuss this, and a spring-loaded mechanism for modulating interactions of the iron sulfur protein with occupants of the Qo-site, in the context of control and gating roles. Such atomistic features of the mechanism can usefully be explored through simulation, but we stress the importance of constraints from physical chemistry and biology, both in setting up a simulation and in interpreting results. [ABSTRACT FROM AUTHOR] |
| Copyright of Journal of Physical Chemistry B is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 122618324 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: The Q-Cycle Mechanism of the bc<subscript>1</subscript> Complex: A Biologist's Perspective on Atomistic Studies. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Crofts%2C+Antony+R%2E%22">Crofts, Antony R.</searchLink><relatesTo>1,2</relatesTo><i> crofts@illinois.edu</i><br /><searchLink fieldCode="AR" term="%22Rose%2C+Stuart+W%2E%22">Rose, Stuart W.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Burton%2C+Rodney+L%2E%22">Burton, Rodney L.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Desai%2C+Amit+V%2E%22">Desai, Amit V.</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Kenis%2C+Paul+J%2E+A%2E%22">Kenis, Paul J. A.</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Dikanov%2C+Sergei+A%2E%22">Dikanov, Sergei A.</searchLink><relatesTo>4</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Journal+of+Physical+Chemistry+B%22">Journal of Physical Chemistry B</searchLink>. Apr2017, Vol. 121 Issue 15, p3701-3717. 17p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Ubiquinones%22">Ubiquinones</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Rhodobacter%22">Rhodobacter</searchLink><br /><searchLink fieldCode="DE" term="%22Reactive+oxygen+species%22">Reactive oxygen species</searchLink><br /><searchLink fieldCode="DE" term="%22Semiquinone%22">Semiquinone</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: The Q-cycle mechanism of the bc1 complex is now well enough understood to allow application of advanced computational approaches to the study of atomistic processes. In addition to the main features of the mechanism, these include control and gating of the bifurcated reaction at the Qo-site, through which generation of damaging reactive oxygen species is minimized. We report a new molecular dynamics model of the Rhodobacter sphaeroides bc1 complex implemented in a native membrane, and constructed so as to eliminate blemishes apparent in earlier Rhodobacter models. Unconstrained MD simulations after equilibration with ubiquinol and ubiquinone respectively at Qo- and Qi-sites show that substrate binding configurations at both sites are different in important details from earlier models. We also demonstrate a new Qo-site intermediate, formed in the sub-ms time range, in which semiquinone remains complexed with the reduced iron sulfur protein. We discuss this, and a spring-loaded mechanism for modulating interactions of the iron sulfur protein with occupants of the Qo-site, in the context of control and gating roles. Such atomistic features of the mechanism can usefully be explored through simulation, but we stress the importance of constraints from physical chemistry and biology, both in setting up a simulation and in interpreting results. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Journal of Physical Chemistry B is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1021/acs.jpcb.6b10524 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 17 StartPage: 3701 Subjects: – SubjectFull: Ubiquinones Type: general – SubjectFull: Molecular dynamics Type: general – SubjectFull: Rhodobacter Type: general – SubjectFull: Reactive oxygen species Type: general – SubjectFull: Semiquinone Type: general Titles: – TitleFull: The Q-Cycle Mechanism of the bc1 Complex: A Biologist's Perspective on Atomistic Studies. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Crofts, Antony R. – PersonEntity: Name: NameFull: Rose, Stuart W. – PersonEntity: Name: NameFull: Burton, Rodney L. – PersonEntity: Name: NameFull: Desai, Amit V. – PersonEntity: Name: NameFull: Kenis, Paul J. A. – PersonEntity: Name: NameFull: Dikanov, Sergei A. IsPartOfRelationships: – BibEntity: Dates: – D: 20 M: 04 Text: Apr2017 Type: published Y: 2017 Identifiers: – Type: issn-print Value: 15206106 Numbering: – Type: volume Value: 121 – Type: issue Value: 15 Titles: – TitleFull: Journal of Physical Chemistry B Type: main |
| ResultId | 1 |
