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Study of Structural Dynamics of Ligand-Activated Membrane Receptors by Means of Principal Component Analysis

G. V. Novikov1*, V. S. Sivozhelezov1, and K. V. Shaitan2

1Institute of Cell Biophysics, Russian Academy of Sciences, ul. Institutskaya 3, 142290 Pushchino, Moscow Region, Russia; fax: (4967) 330-509; E-mail: gnovikov87@gmail.com

2Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia

* To whom correspondence should be addressed.

Received April 29, 2012; Revision received December 7, 2012
The structural dynamics of three different ligand-activated G-protein coupled receptors (GPCRs) and the photoreactive receptor rhodopsin from mammals were comparatively studied. As a result, diagrams demonstrating the main structural differences between the studied membrane receptors were obtained. These diagrams represent the projection of the crystal structures of rhodopsin photointermediates and ligand-activated receptors onto the plane defined by the principal components. Thus, we were able to associate the activation process of the receptors with large-scale movements of their individual transmembrane (TM) domains. In addition, the dynamics of extracellular loops of ligand-activated receptors responsible for recognition and initial binding of ligands was studied. Based on these results, two parameters of functionally significant structural dynamics of membrane receptors can be thoroughly analyzed simultaneously – movements of individual TM helices and of extracellular loops.
KEY WORDS: dynamics, conformation, membrane proteins, X-ray crystallography, principal component analysis, structural bioinformatics

DOI: 10.1134/S0006297913040093