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Lipid-Loving ANTs: Molecular Simulations of CardiolipinInteractions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes

View Article: PubMed Central - PubMed

ABSTRACT

The exchange of ADPand ATP across the inner mitochondrial membraneis a fundamental cellular process. This exchange is facilitated bythe adenine nucleotide translocase, the structure and function ofwhich are critically dependent on the signature phospholipid of mitochondria,cardiolipin (CL). Here we employ multiscale molecular dynamics simulationsto investigate CL interactions within a membrane environment. Usingsimulations at both coarse-grained and atomistic resolutions, we identifythree CL binding sites on the translocase, in agreement with thoseseen in crystal structures and inferred from nuclear magnetic resonancemeasurements. Characterization of the free energy landscape for laterallipid interaction via potential of mean force calculations demonstratesthe strength of interaction compared to those of binding sites onother mitochondrial membrane proteins, as well as their selectivityfor CL over other phospholipids. Extending the analysis to other membersof the family, yeast Aac2p and mouse uncoupling protein 2, suggestsa degree of conservation. Simulation of large patches of a model mitochondrialmembrane containing multiple copies of the translocase shows thatCL interactions persist in the presence of protein–proteininteractions and suggests CL may mediate interactions between translocases.This study provides a key example of how computational microscopymay be used to shed light on regulatory lipid–protein interactions.

No MeSH data available.


Potentials of mean force for binding of the lipid to ANT1.(A)View onto the base of ANT1 illustrating the reaction coordinates usedin free energy calculations. ANT1 is colored according to its three-foldrepeat topology, with the position of each binding site indicatedby the time-averaged probability density isosurfaces for CL phosphates(magenta). The arrows indicate the approximate 1D reaction coordinatesalong which the PMF was calculated. (B) PMF profiles for interactionsof CL (magenta) and PC (black) with each of the three binding sites,and a control non-CL binding region. For site I, a PMF profile wasalso calculated for a further anionic lipid species, PS (green). Thestandard deviations estimated from bootstrapping40 are shown as the shaded area behind each curve.
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fig5: Potentials of mean force for binding of the lipid to ANT1.(A)View onto the base of ANT1 illustrating the reaction coordinates usedin free energy calculations. ANT1 is colored according to its three-foldrepeat topology, with the position of each binding site indicatedby the time-averaged probability density isosurfaces for CL phosphates(magenta). The arrows indicate the approximate 1D reaction coordinatesalong which the PMF was calculated. (B) PMF profiles for interactionsof CL (magenta) and PC (black) with each of the three binding sites,and a control non-CL binding region. For site I, a PMF profile wasalso calculated for a further anionic lipid species, PS (green). Thestandard deviations estimated from bootstrapping40 are shown as the shaded area behind each curve.

Mentions: To assess the strength andselectivity of CL interactions, we calculated a potential of meanforce (PMF) for the CL–ANT1 interaction via CG simulation andumbrella sampling. The PMF (or free energy profile) between two speciesdescribes the change in free energy along a particular reaction coordinateand is calculated from the probability distribution of the two speciesalong that coordinate.51 This approachhas recently been used to define the binding of CL to mitochondrialrespiratory chain complexes III and IV22,52 and to characterizelipid interactions of the epidermal growth factor receptor (EGFR)transmembrane domain.14 For each of thethree sites, a steered MD simulation was conducted in which a forcewas applied to pull the CL molecule out of its binding site into thebulk membrane along a 1D reaction coordinate (r)perpendicular to the protein surface in the plane of the bilayer (Figure 5A). The free energyprofile along this coordinate was then calculated via umbrella sampling,with r defined as the distance between the centerof mass of three conserved prolines within ANT1 and the β-glycerolmoiety of CL.


Lipid-Loving ANTs: Molecular Simulations of CardiolipinInteractions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes
Potentials of mean force for binding of the lipid to ANT1.(A)View onto the base of ANT1 illustrating the reaction coordinates usedin free energy calculations. ANT1 is colored according to its three-foldrepeat topology, with the position of each binding site indicatedby the time-averaged probability density isosurfaces for CL phosphates(magenta). The arrows indicate the approximate 1D reaction coordinatesalong which the PMF was calculated. (B) PMF profiles for interactionsof CL (magenta) and PC (black) with each of the three binding sites,and a control non-CL binding region. For site I, a PMF profile wasalso calculated for a further anionic lipid species, PS (green). Thestandard deviations estimated from bootstrapping40 are shown as the shaded area behind each curve.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5120876&req=5

fig5: Potentials of mean force for binding of the lipid to ANT1.(A)View onto the base of ANT1 illustrating the reaction coordinates usedin free energy calculations. ANT1 is colored according to its three-foldrepeat topology, with the position of each binding site indicatedby the time-averaged probability density isosurfaces for CL phosphates(magenta). The arrows indicate the approximate 1D reaction coordinatesalong which the PMF was calculated. (B) PMF profiles for interactionsof CL (magenta) and PC (black) with each of the three binding sites,and a control non-CL binding region. For site I, a PMF profile wasalso calculated for a further anionic lipid species, PS (green). Thestandard deviations estimated from bootstrapping40 are shown as the shaded area behind each curve.
Mentions: To assess the strength andselectivity of CL interactions, we calculated a potential of meanforce (PMF) for the CL–ANT1 interaction via CG simulation andumbrella sampling. The PMF (or free energy profile) between two speciesdescribes the change in free energy along a particular reaction coordinateand is calculated from the probability distribution of the two speciesalong that coordinate.51 This approachhas recently been used to define the binding of CL to mitochondrialrespiratory chain complexes III and IV22,52 and to characterizelipid interactions of the epidermal growth factor receptor (EGFR)transmembrane domain.14 For each of thethree sites, a steered MD simulation was conducted in which a forcewas applied to pull the CL molecule out of its binding site into thebulk membrane along a 1D reaction coordinate (r)perpendicular to the protein surface in the plane of the bilayer (Figure 5A). The free energyprofile along this coordinate was then calculated via umbrella sampling,with r defined as the distance between the centerof mass of three conserved prolines within ANT1 and the β-glycerolmoiety of CL.

View Article: PubMed Central - PubMed

ABSTRACT

The exchange of ADPand ATP across the inner mitochondrial membraneis a fundamental cellular process. This exchange is facilitated bythe adenine nucleotide translocase, the structure and function ofwhich are critically dependent on the signature phospholipid of mitochondria,cardiolipin (CL). Here we employ multiscale molecular dynamics simulationsto investigate CL interactions within a membrane environment. Usingsimulations at both coarse-grained and atomistic resolutions, we identifythree CL binding sites on the translocase, in agreement with thoseseen in crystal structures and inferred from nuclear magnetic resonancemeasurements. Characterization of the free energy landscape for laterallipid interaction via potential of mean force calculations demonstratesthe strength of interaction compared to those of binding sites onother mitochondrial membrane proteins, as well as their selectivityfor CL over other phospholipids. Extending the analysis to other membersof the family, yeast Aac2p and mouse uncoupling protein 2, suggestsa degree of conservation. Simulation of large patches of a model mitochondrialmembrane containing multiple copies of the translocase shows thatCL interactions persist in the presence of protein–proteininteractions and suggests CL may mediate interactions between translocases.This study provides a key example of how computational microscopymay be used to shed light on regulatory lipid–protein interactions.

No MeSH data available.