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Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking

Abstract

The mitochondrial adenosine diphosphate/adenosine triphosphate (ADP/ATP) carrier—AAC—was crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). The protein consists of a six-transmembrane helix bundle that defines the nucleotide translocation pathway, which is closed towards the matrix side due to sharp kinks in the odd-numbered helices. In this paper, we describe the interaction between the matrix side of the AAC transporter and the ATP4− molecule using carrier structures obtained through classical molecular dynamics simulation (MD) and a protein–ligand docking procedure. Fifteen structures were extracted from a previously published MD trajectory through clustering analysis, and 50 docking runs were carried out for each carrier conformation, for a total of 750 runs (“MD docking”). The results were compared to those from 750 docking runs performed on the X-ray structure (“X docking”). The docking procedure indicated the presence of a single interaction site in the X-ray structure that was conserved in the structures extracted from the MD trajectory. MD docking showed the presence of a second binding site that was not found in the X docking. The interaction strategy between the AAC transporter and the ATP4− molecule was analyzed by investigating the composition and 3D arrangement of the interaction pockets, together with the orientations of the substrate inside them. A relationship between sequence repeats and the ATP4− binding sites in the AAC carrier structure is proposed.

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Acknowledgments

The authors would like to thank the CASPUR Interuniversity Consortium for the Application of Supercomputing for Universities and Research (Rome, Italy) for the use of the parallel computer MATRIX.

Author information

Correspondence to Mattia Falconi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig. S1
figure7

Computational setup. 3D snapshot of the molecular dynamics simulation, representing the protein as a black-colored surface immersed in a lipid bilayer shown as a gray-colored surface. This orientation of the MD simulation system clearly explains the location and the geometry of the region (shown as a black box) in which molecular docking on the matrix side has been carried out. (JPEG 41 kb)

Fig. S2
figure8

GTP4− docking. Docking of 750 GTP4− molecules on one representative MD structure. The protein (dark gray ribbon) is viewed from the matrix side. The GTP4− molecules are shown in stick representation and are colored by atom type. (JPEG 416 kb)

Fig. S3
figure9

Binding site details. Close-up view of the interactions between the ATP4− molecule and A the X-docking site, B MD-docking site I, and C MD-docking site II, located on the matrix face of the ADP/ATP carrier, which is represented by a mesh surface. Red and blue stick models indicate the positive and negative charges, respectively. Magenta, yellow, and green show Gln, Gly, and Met residues. The ATP molecule is represented as a gray stick model. (JPEG 48 kb)

Fig. S4
figure10

AAC multiple alignment. ClustalW multiple alignment of 33 sequences of the ADP/ATP mitochondrial carrier (isoforms 1 and 2) taken from different species. (JPEG 159 kb)

Movie of docked molecules. Short movie representing the ADP/ATP carrier–ATP4− complexes chosen from the MD docking. Red and blue spots on the molecular surface indicate positive and negative charges, respectively. Magenta, yellow, and green spots show Gln, Gly, and Met residues. (MP4 612 kb)

High-resolution image file (TIFF 8491 kb)

High-resolution image file (TIFF 1670 kb)

High-resolution image file (TIFF 12523 kb)

High-resolution image file (TIFF 10801 kb)

Movie M1

Movie of docked molecules. Short movie representing the ADP/ATP carrier–ATP4− complexes chosen from the MD docking. Red and blue spots on the molecular surface indicate positive and negative charges, respectively. Magenta, yellow, and green spots show Gln, Gly, and Met residues. (MP4 612 kb)

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Di Marino, D., Oteri, F., Morozzo della Rocca, B. et al. Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking. J Mol Model 18, 2377–2386 (2012) doi:10.1007/s00894-011-1255-5

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Keyword

  • Mitochondrial ADP/ATP carrier
  • Molecular dynamics
  • Cluster analysis
  • Protein–ligand docking
  • ATP–carrier interaction
  • ATP binding sites