Structure modeling of the chemokine receptor CCR5: implications for ligand binding and selectivity.
The G-protein coupled receptor CCR5 is the main co-receptor for macrophage-tropic HIV-1 strains. I have built a structural model of the chemokine receptor CCR5 and used it to explain the binding and selectivity of the antagonist TAK779. Models of the extracellular (EC) domains of CCR5 have been constructed and used to rationalize current biological data on the binding of HIV-1 and chemokines. Residues spanning the transmembrane region of CCR5 have been modeled after rhodopsin, and their functional significance examined using the evolutionary trace method. The receptor cavity shares six residues with CC-chemokine receptors CCR1 through CCR4, while seven residues are unique to CCR5. The contribution of these residues to ligand binding and selectivity is tested by molecular docking simulations of TAK779 to CCR1, CCR2, and CCR5. TAK779 binds to CCR5 in the cavity formed by helices 1, 2, 3, and 7 with additional interactions with helices 5 and 6. TAK779 did not dock to either CCR1 or CCR2. The results are consistent with current site-directed mutagenesis data and with the observed selectivity of TAK779 for CCR5 over CCR1 and CCR2. The specific residues responsible for the observed selectivity are identified. The four EC regions of CCR5 have been modeled using constrained simulated annealing simulations. Applied dihedral angle constraints are representative of the secondary structure propensities of these regions. Tertiary interactions, in the form of distance constraints, are generated from available epitope mapping data. Analysis of the 250 simulated structures provides new insights to the design of experiments aimed at determining residue-residue contacts across the EC domains and for mapping CC-chemokines on the surface of the EC domains.
Paterlini
M Germana
MG
Department of Medicinal Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455, USA. germana@certusoft.com
D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D065100:CCR5 Receptor Antagonists; D003198:Computer Simulation; D005110:Extracellular Space; D006801:Humans; D008024:Ligands; D008565:Membrane Proteins / Q000737:chemistry; D051379:Mice; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D000644:Quaternary Ammonium Compounds / Q000737:chemistry; D019713:Receptors, CCR5 / Q000737:chemistry*; D019707:Receptors, Chemokine / Q000737:chemistry; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein; D013329:Structure-Activity Relationship
D000577:Amides; D000596:Amino Acids; D065100:CCR5 Receptor Antagonists; D008024:Ligands; D008565:Membrane Proteins; D010446:Peptide Fragments; D000644:Quaternary Ammonium Compounds; D019713:Receptors, CCR5; D019707:Receptors, Chemokine; C119369:TAK 779