Classification of rhodopsin structures by modern methods of structural bioinformatics

Abstract

We report a classification of the crystallographic structures of bovine and squid rhodopsins corresponding to different stages of their photocycles. Using the resource Protein (Structure) Comparison, Knowledge, Similarity, and Information server (ProCKSI, http://www.procksi.net/), selected spatial structures were compared on the basis of classification schemes (dendrograms). To compare the spatial structures of transmembrane proteins, optimal consensus was developed from methods implemented in ProCKSI. Structures were also clustered using principal component analysis, resulting in good agreement with the classification based on the ProCKSI consensus method. Analysis of the results revealed the basic movements of individual transmembrane domains of these proteins that we were able to relate to different stages of the photoactivation of rhodopsin. A combination of methods identified in this study can be used as an up-to-date analytical tool to study the conformational dynamics of membrane receptors.