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Biochemistry (Moscow)

, Volume 78, Issue 4, pp 403–411 | Cite as

Study of structural dynamics of ligand-activated membrane receptors by means of principal component analysis

  • G. V. NovikovEmail author
  • V. S. Sivozhelezov
  • K. V. Shaitan
Article

Abstract

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 

Abbreviations

β-1AR

β-1-adrenergic receptor

β-2AR

β-2-adrenergic receptor

GPCR

G-protein coupled receptors

PCA

principal component analysis

PC1

the first principal component

PDB

Protein Data Bank

RMSD

root-meansquare deviation

7TM receptors

seven transmembrane domain receptors

TMD

transmembrane domain

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Copyright information

© Pleiades Publishing, Ltd. 2013

Authors and Affiliations

  • G. V. Novikov
    • 1
    Email author
  • V. S. Sivozhelezov
    • 1
  • K. V. Shaitan
    • 2
  1. 1.Institute of Cell BiophysicsRussian Academy of SciencesPushchino, Moscow RegionRussia
  2. 2.Faculty of BiologyLomonosov Moscow State UniversityMoscowRussia

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