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Molecular modeling studies on CNG channel from bovine retinal rod: A structural model of the cyclic nucleotide‐binding domain
Author(s) -
Punta Marco,
Cavalli Andrea,
Torre Vincent,
Carloni Paolo
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10324
Subject(s) - homomeric , chemistry , cyclic nucleotide binding domain , activator (genetics) , cyclic nucleotide , cyclic nucleotide gated ion channel , biophysics , helix (gastropod) , molecular model , molecular dynamics , nucleotide , biochemistry , biology , gene , protein subunit , snail , computational chemistry , ecology
A dimeric model of the cyclic nucleotide‐binding domain of the all‐α 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). Proteins 2003;52:332–338. © 2003 Wiley‐Liss, Inc.