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Bovine Rhodopsin (bovine + rhodopsin)
Selected AbstractsExploring the binding site of the human muscarinic M3 receptor: Homology modeling and docking studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2007Liliana Ostopovici Abstract The human muscarinic M3 receptor (hM3) and its interactions with selective agonists and antagonists were investigated by means of combined homology and docking approach. Also, two pharmacophoric models for the hM3 agonist and antagonist binding sites were proposed. The three-dimensional (3D) structure of hM3 receptor was modeled based on the high-resolution X-ray structure of bovine rhodopsin from the Protein Data Bank (PDB). To validate the reliability of the model obtained, the main chain torsion angles phi (,) and psi (,) were examined in a Ramachandran plot, and all omega angles were measured for peptidic bond planarity. The characteristics of the active site, the position, and the orientation of ligands in situ, as well as the binding modes of the representative agonists and antagonists, were analyzed by applying a molecular docking technique using the AutoDock 3.0.5 program. Specific interactions responsible for recognition of the hM3 receptor, like ionic bond formed between protonated amine of the ligands and the Asp3.6 side chain were identified. Structure,reactivity relationships have been explained by analyzing the 3D structure of the hM3 model and the ligand conformations resulted from molecular docking simulation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Quantum Mechanical/Molecular Mechanical Studies on Spectral Tuning Mechanisms of Visual Pigments and Other Photoactive Proteins,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Ahmet Altun The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants. [source] Rhodopsin Regeneration is Accelerated via Noncovalent 11- cis Retinal,Opsin Complex,A Role of Retinal Binding Pocket of Opsin,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Hiroyuki Matsumoto The regeneration of bovine rhodopsin from its apoprotein opsin and the prosthetic group 11- cis retinal involves the formation of a retinylidene Schiff base with the , -amino group of the active lysine residue of opsin. The pH dependence of a Schiff base formation in solution follows a typical bell-shaped profile because of the pH dependence of the formation and the following dehydration of a 1-aminoethanol intermediate. Unexpectedly, however, we find that the formation of rhodopsin from 11- cis retinal and opsin does not depend on pH over a wide pH range. These results are interpreted by the Matsumoto and Yoshizawa (Nature258 [1975] 523) model of rhodopsin regeneration in which the 11- cis retinal chromophore binds first to opsin through the , -ionone ring, followed by the slow formation of the retinylidene Schiff base in a restricted space. We find the second-order rate constant of the rhodopsin formation is 6100 ± 300 mol,1 s,1 at 25°C over the pH range 5,10. The second-order rate constant is much greater than that of a model Schiff base in solution by a factor of more than 107. A previous report by Pajares and Rando (J Biol Chem264 [1989] 6804) suggests that the lysyl ,-NH2 group of opsin is protonated when the , -ionone ring binding site is unoccupied. The acceleration of the Schiff base formation in rhodopsin is explained by stabilization of the deprotonated form of the lysyl ,-NH2 group which might be induced when the , -ionone ring binding site is occupied through the noncovalent binding of 11- cis retinal to opsin at the initial stage of rhodopsin regeneration, followed by the proximity and orientation effect rendered by the formation of noncovalent 11- cis retinal,opsin complex. [source] An improved tripod amphiphile for membrane protein solubilizationPROTEIN SCIENCE, Issue 12 2000Seungju M. Yu Abstract Intrinsic membrane proteins represent a large fraction of the proteins produced by living organisms and perform many crucial functions. Structural and functional characterization of membrane proteins generally requires that they be extracted from the native lipid bilayer and solubilized with a small synthetic amphiphile, for example, a detergent. We describe the development of a small molecule with a distinctive amphiphilic architecture, a "tripod amphiphile," that solubilizes both bacteriorhodopsin (BR) and bovine rhodopsin (Rho). The polar portion of this amphiphile contains an amide and an amine-oxide; small variations in this polar segment are found to have profound effects on protein solubilization properties. The optimal tripod amphiphile extracts both BR and Rho from the native membrane environments and maintains each protein in a monomeric native-like form for several weeks after delipidation. Tripod amphiphiles are designed to display greater conformational rigidity than conventional detergents, with the long-range goal of promoting membrane protein crystallization. The results reported here represent an important step toward that ultimate goal. [source] | ||||||||||