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Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study
Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study
The mitochondrial ADP/ATP carrier is a six helix bundle membrane transport protein, which couples the exit of ATP from the mitochondrial matrix to the entry of ADP. Extended (4×20 ns) molecular dynamics simulations of the carrier, in the presence and absence of bound inhibitor (carboxyatractyloside), have been used to explore the conformational dynamics of the protein in a lipid bilayer environment, in the presence and absence of the carboxyatractyloside inhibitor. The dynamic flexibility (measured as conformational drift and fluctuations) of the protein is reduced in the presence of bound inhibitor. Proline residues in transmembrane helices H1, H3 and H5 appear to form dynamic hinges. Fluctuations in inter-helix salt bridges are also observed over the time course of the simulations. Inhibitor-protein and lipid-protein interactions have been characterised in some detail. Overall, the simulations support a transport mechanism in which flexibility about the proline hinges enables a transition between a ‘closed’ and an ‘open’ pore-like state of the carrier protein.
0968-7688
506-517
Johnston, Jennifer M.
2dd3dee4-7339-45cb-ad97-554382d8c0c8
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e
Johnston, Jennifer M.
2dd3dee4-7339-45cb-ad97-554382d8c0c8
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e

Johnston, Jennifer M., Khalid, Syma and Sansom, Mark S.P. (2008) Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study. Molecular Membrane Biology, 25 (6-7), 506-517. (doi:10.1080/09687680802459271). (PMID:18988066)

Record type: Article

Abstract

The mitochondrial ADP/ATP carrier is a six helix bundle membrane transport protein, which couples the exit of ATP from the mitochondrial matrix to the entry of ADP. Extended (4×20 ns) molecular dynamics simulations of the carrier, in the presence and absence of bound inhibitor (carboxyatractyloside), have been used to explore the conformational dynamics of the protein in a lipid bilayer environment, in the presence and absence of the carboxyatractyloside inhibitor. The dynamic flexibility (measured as conformational drift and fluctuations) of the protein is reduced in the presence of bound inhibitor. Proline residues in transmembrane helices H1, H3 and H5 appear to form dynamic hinges. Fluctuations in inter-helix salt bridges are also observed over the time course of the simulations. Inhibitor-protein and lipid-protein interactions have been characterised in some detail. Overall, the simulations support a transport mechanism in which flexibility about the proline hinges enables a transition between a ‘closed’ and an ‘open’ pore-like state of the carrier protein.

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Published date: September 2008

Identifiers

Local EPrints ID: 149571
URI: http://eprints.soton.ac.uk/id/eprint/149571
ISSN: 0968-7688
PURE UUID: 07811428-4832-44cf-aa98-820fbf116ec5
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

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Date deposited: 30 Apr 2010 13:35
Last modified: 20 Jul 2019 00:51

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