D. Eric Walters and Ronald S. Kaplan
We have made extensive use of molecular modeling both to interpret experimental data and to design new experiments in our studies of the yeast mitochondrial citrate transport protein (D.E. Walters and R.S. Kaplan, "Homology modeled structure of the yeast mitochondrial citrate transport protein," Biophys. J. 87, 907-911, 2004). The figure above shows a backbone trace of our homology-modeled CTP (red) superimposed on the X-ray crystal structure of the mitochondrial ADP/ATP carrier (green; Pebay-Peyroula et al., Nature 426, 39-44, 2003; PDB structure 1OKC). Note that the structural similarity (and the sequence similarity) is best along the 6 transmembrane helical segments. The cytoplasmic and mitochondrial loops (which are believed to play an important role in transporter specificity) have less structural similarity and less homology with the ADP/ATP carrier. The figures above show a solvent-accessible surface representation of our homology-modeled CTP structure, viewed from outside the mitochondrial inner membrane, looking into the transport pathway (left), and from the side, in the plane of the mitochondrial inner membrane (right). Transmembrane helices III and IV have been colored on the basis of our experimentally measured reactivity of single-Cys mutants toward methanethiosulfonate reagents. Red indicates residues which are highly reactive (water-accessible) and thus are likely to be part of the transport pathway. Blue indicates residues which show little or no reactivity (not water-accessible) and thus are likely to be buried in the bilayer or in the protein. The following section uses the Jmol java applet. Be sure your browser is java-enabled. Be patient--it may take several seconds for the structure to load! After it loads, you can drag the structure to rotate it or shift-drag to zoom. If you have a 2-button or 3-button mouse, the right-button may give you more display options.
Homology-modeled structure of the yeast mitochondrial CTP transporter (Walters & Kaplan, Biophys. J. 87, 907-911, 2004). Structure is shown as spacefilling atoms, with positively charged aminoacids in blue and negatively charged aminoacids in red.
The mitochondrial citrate transport protein: Evidence for a steric interaction between glutamine 182 and leucine 120 and its relationship to the substrate translocation pathway and identification of other mechanistically essential residues. C. Ma, S. Remani, R. Kotaria, J.A. Mayor, D.E. Walters, and R.S. Kaplan. Biochim. Biophys. Acta 1757, 1271-1276, 2006.
The yeast mitochondrial citrate transport protein: Characterization of transmembrane domain III residue involvement in substrate translocation. C. Ma, R. Kotaria, J.A. Mayor, S. Remani, D.E. Walters and R.S. Kaplan, J. Biol. Chem. 280, 2331-2340, 2005.
The mitochondrial citrate transport protein: Probing the secondary structure of transmembrane domain III, identification of residues that likely comprise a portion o f the citrate transport pathway, and development of a model for the putative TMDIII-TMDIII' interface. C. Ma, R. Kotaria, J.A. Mayor, L.R. Eriks, A.M. Dean, D.E. Walters, and R.S. Kaplan, J. Biol. Chem., 279, 1533-1540, 2004.
Homology modeled structure of the yeast mitochondrial citrate transport protein. D.E. Walters and R.S. Kaplan, Biophys. J. 87, 907-911, 2004.
The Yeast Mitochondrial Citrate Transport Protein: Probing the Roles of Cysteines, Argq181 and Arg189 in Transproter Function. Y. Xu, D.A. Kakhniashvili, D.A. Gremse, D.O. Wood, J.A. Mayor, D.E. Walters, and R.S. Kaplan, J. Biol. Chem., 275, 7117-7124, 2000.
The Yeast Mitochondrial Citrate Transport Protein: Probing the Secondary Structure of Transmembrane Domain IV and Identification of Residues that Likely Comprise a Portion of the Citrate Translocation Pathway. R.S. Kaplan, J.A. Mayor, D. Brauer, R. Kotaria, D.E. Walters, and A.M. Dean, J. Biol. Chem., 275, 12009-12016, 2000.
The Yeast Mitochondrial Citrate Transport Protein: Determination of Secondary Structure and Solvent Accessibility of Transmembrane Domain IV Using Site-directed Spin Labeling. R.S. Kaplan, J.A. Mayor, R. Kotaria, D.E. Walters, and H.S. Mchaourab, Biochemistry, 39, 9157-9163, 2000.
Models of the Transmembrane Domains of the Yeast Mitochondrial Citrate Transport Protein. D.E. Walters and R.S. Kaplan, J. Molecular Modeling, 6, 587-594, 2000.
Oligomeric State of Wild-type and Cysteine-less Yeast Mitochondrial Citrate Transport Proteins. Kotaria, R., Mayor, J.A., Walters, D.E., and Kaplan, R.S. J. Bioenerg. Biomembr. 6, 543-549, 1999.
If you have comments or questions, please contact Eric Walters or Ronald Kaplan.