Paper Citing NAMD - Abstract
Bray, Jenelle K.; Goddard, William A., I.I.I.
The structure of human serotonin 2c G-protein-coupled receptor bound to agonists and antagonists
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 27:66-81, AUG 2008
We used the MembStruk computational procedure to predict the three-dimensional (3D) structure for the serotonin 5-HT2C G-protein-coupled receptor (GPCR). Using this structure, we used the MSCDock computational procedure to predict the 3D structures for bound ligand-protein complexes for agonists such as serotonin and antagonists such as ritanserin, metergoline, and methiothepin. In addition, we predicted the SAR data for a series of psilocybin analogs, both agonists and antagonists. We performed molecular dynamics (MD) on serotonin bound to 5-HT2C and we find the protein and binding site to be stable after 5 ns. We find good agreement with the currently known experimental data and we predict a number of new mutations which could be used to validate further our predicted structures. This agreement between theory and experiment suggests that our 3D structure is sufficiently accurate for use in drug design. We also compare a preliminary prediction for 5-HT2B with our prediction for 5-HT2C and find a difference in TM5 that contributes to different serotonin binding modes in 5-HT2B and 5-HT2C. (C) 2008 Elsevier Inc. All rights reserved.
