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

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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.


ANT1 and CL. (A) Topology and structure of bovine ANT1 coloredto indicate the internal three-fold repeat symmetry. The structureshown corresponds to the cytoplasm-facing state of ANT1 (Protein DataBank entry 1OKC).8 (B) Coarse-grained (CG) representationof ANT1 embedded in a lipid bilayer. (C) Atomistic and CG models ofCL.
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fig1: ANT1 and CL. (A) Topology and structure of bovine ANT1 coloredto indicate the internal three-fold repeat symmetry. The structureshown corresponds to the cytoplasm-facing state of ANT1 (Protein DataBank entry 1OKC).8 (B) Coarse-grained (CG) representationof ANT1 embedded in a lipid bilayer. (C) Atomistic and CG models ofCL.

Mentions: To date, atomic-resolutionstructures of bovine and yeast formsof ANT have been determined in a cytoplasm-facing state.8,9 A nuclear magnetic resonance (NMR) structure has been determinedfor another MC family member, uncoupling protein 2 (UCP2).10 These translocase structures revealed a foldin which six transmembrane helices (H1–H6) form a bundle arounda central substrate binding cavity, abutted on the matrix side bythree amphipathic helices (MH1–MH3) arranged around the outerrim of the helix bundle (Figure 1). There is an internal pseudo-3-fold symmetry, seenalso in the UCP2 structure, which sequence comparisons suggest tobe conserved across the MC family. The presence of CL was essentialfor reconstitution and crystallization of ANT, and CL molecules havebeen resolved in all crystal forms of the translocase, bound betweenthe short matrix helices. This agrees with earlier 31PNMR measurements that indicated tight binding of CL molecules to bovineheart translocase.11 Although CL moleculeswere not resolved in the structure of UCP2, the presence of this lipidwas essential to obtain interpretable spectra.10


Lipid-Loving ANTs: Molecular Simulations of CardiolipinInteractions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes
ANT1 and CL. (A) Topology and structure of bovine ANT1 coloredto indicate the internal three-fold repeat symmetry. The structureshown corresponds to the cytoplasm-facing state of ANT1 (Protein DataBank entry 1OKC).8 (B) Coarse-grained (CG) representationof ANT1 embedded in a lipid bilayer. (C) Atomistic and CG models ofCL.
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Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC5120876&req=5

fig1: ANT1 and CL. (A) Topology and structure of bovine ANT1 coloredto indicate the internal three-fold repeat symmetry. The structureshown corresponds to the cytoplasm-facing state of ANT1 (Protein DataBank entry 1OKC).8 (B) Coarse-grained (CG) representationof ANT1 embedded in a lipid bilayer. (C) Atomistic and CG models ofCL.
Mentions: To date, atomic-resolutionstructures of bovine and yeast formsof ANT have been determined in a cytoplasm-facing state.8,9 A nuclear magnetic resonance (NMR) structure has been determinedfor another MC family member, uncoupling protein 2 (UCP2).10 These translocase structures revealed a foldin which six transmembrane helices (H1–H6) form a bundle arounda central substrate binding cavity, abutted on the matrix side bythree amphipathic helices (MH1–MH3) arranged around the outerrim of the helix bundle (Figure 1). There is an internal pseudo-3-fold symmetry, seenalso in the UCP2 structure, which sequence comparisons suggest tobe conserved across the MC family. The presence of CL was essentialfor reconstitution and crystallization of ANT, and CL molecules havebeen resolved in all crystal forms of the translocase, bound betweenthe short matrix helices. This agrees with earlier 31PNMR measurements that indicated tight binding of CL molecules to bovineheart translocase.11 Although CL moleculeswere not resolved in the structure of UCP2, the presence of this lipidwas essential to obtain interpretable spectra.10

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.