Molecular modeling studies on CNG channel from bovine retinal rod: a structural model of the cyclic nucleotide-binding domain.
A dimeric model of the cyclic nucleotide-binding domain of the all-alpha homomeric cyclic nucleotide-gated channel from bovine retinal rod is constructed. The model, based on the structure of the fairly homologous catabolite gene activator protein (Weber and Steitz, J Mol Biol 1987;198:311-326), is obtained by use of comparative modeling and molecular dynamics simulations. Our model provides a structural basis for the experimentally measured difference in activity between cAMP and cGMP, as well as the different solvent accessibilities of GLY597 in the complex with cGMP, with cAMP and in the protein in free state. In addition, it provides support for the rearrangement of the domain C helix on ligand binding and releasing proposed by Matulef et al. (Neuron 1999;24:443-452).
Punta
Marco
M
International School for Advanced Studies, Trieste, Italy.
Cavalli
Andrea
A
Torre
Vincent
V
Carloni
Paolo
P
D000818:Animals; D001665:Binding Sites / Q000235:genetics; D002417:Cattle; D003198:Computer Simulation; D000242:Cyclic AMP / Q000737:chemistry / Q000378:metabolism; D006152:Cyclic GMP / Q000737:chemistry / Q000378:metabolism; D054815:Cyclic Nucleotide-Gated Cation Channels; D019281:Dimerization; D007473:Ion Channels / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017948:Retinal Rod Photoreceptor Cells / Q000378:metabolism*; D016415:Sequence Alignment
D054815:Cyclic Nucleotide-Gated Cation Channels; D007473:Ion Channels; D000242:Cyclic AMP; D006152:Cyclic GMP