Recently the structure of rhodopsin was determined from the X-ray diffraction data extending to the resolution of 2.8 A. We have studied the effects of amino acids and of water using A density functional based tight-binding code. A model retinal binding pocket was employed containing 27 residues within 4.5 A distance from the retinal molecule and water molecules. Our results show that one water molecule hydrogen bonded to Glu113 plays an important role in stabilizing the protonated state of the Schi base. We also discuss the structure of 11-cis-retinal PSB, which is highly twisted in the protein pocket. The C11-C12 and C12-C13 bonds are twisted in negative and positive directions respectively, which is confirmed by circular dichroism experiments.
Journal: TechConnect Briefs
Volume: 2, Technical Proceedings of the 2002 International Conference on Computational Nanoscience and Nanotechnology
Published: April 22, 2002
Pages: 77 - 80
Industry sectors: Energy & Sustainability | Medical & Biotech
Topicss: Biofuels & Bioproducts, Sustainable Materials