ArticleJournal of molecular modeling2005
Molecular dynamics simulations of bovine rhodopsin: influence of protonation states and different membrane-mimicking environments.
Article in Journal of molecular modeling, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- Molecular modeling, quantum polarized ligand docking and structure-based 3D-QSAR analysis of the imidazole series as dual AT(1) and ET(A) receptor antagonists.Acta pharmacologica Sinica · 2013Article
- Molecular modeling and computational simulation of the photosystem-II reaction center to address isoproturon resistance in Phalaris minor.Journal of molecular modeling · 2012Article
- Beyond modeling: all-atom olfactory receptor model simulations.Frontiers in genetics · 2012Article
- Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site.Journal of biomedicine & biotechnology · 2012Article
- Structural basis for μ-opioid receptor binding and activation.Structure (London, England : 1993) · 2011Article
- Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation.The Journal of biological chemistry · 2010Article
- Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin.Journal of molecular modeling · 2009Article
- Atomistic insights into rhodopsin activation from a dynamic model.Journal of the American Chemical Society · 2008Article
- Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors.Expert opinion on drug discovery · 2008Article
- Generation of a homology model of the human histamine H(3) receptor for ligand docking and pharmacophore-based screening.Journal of computer-aided molecular design · 2007Article
- How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations.Proteins · 2007Article
- Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer.Journal of computer-aided molecular designArticle
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Authors and funding
3 authors.
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Abstract
G-protein coupled receptors (GPCRs) are a protein family of outstanding pharmaceutical interest. GPCR homology models, based on the crystal structure of bovine rhodopsin, have been shown to be valuable tools in the drug-design process. The initial model is often refined by molecular dynamics (MD) simulations, a procedure that has been recently discussed controversially. We therefore analyzed MD simulations of bovine rhodopsin in order to identify contacts that could serve as constraints in the simulation of homology models. Additionally, the effect of an N-terminal truncation, the nature of the membrane mimic, the influence of varying protonation states of buried residues and the importance of internal water molecules was analyzed. All simulations were carried out using the program-package GROMACS. While N-terminal truncation negatively influenced the overall protein stability, a stable simulation was possible in both solvent environments. As regards the protonation state of titratable sites, the experimental data could be reproduced by the program UHBD (University of Houston Brownian Dynamics), suggesting its application for studying homology models of GPCRs. A high flexibility was observed for internal water molecules at some sites. Finally, interhelical hydrogen-bonding interactions could be derived, which can now serve as constraints in the simulations of GPCR homology models.
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