Investigation of the conformational dynamics of the adenosine A2A receptor by means of molecular dynamics simulation

In this work structural behavior of apo form of the adenosine A2A receptor in the implicit membrane-mimicking environment was investigated by means of molecular dynamics (MD) technique. For better interpretation of the obtained data they were analyzed using principal components analysis. The princip...

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Bibliographic Details
Published inBiofizika Vol. 58; no. 4; p. 618
Main Authors Novikov, G V, Sivozhelezov, V S, Shaĭtan, K V
Format Journal Article
LanguageRussian
Published Russia (Federation) 01.07.2013
Subjects
Carbon Tetrachloride - chemistry
Humans
Molecular Dynamics Simulation
Principal Component Analysis
Protein Structure, Secondary
Protein Structure, Tertiary
Receptor, Adenosine A2A - chemistry
Rhodopsin - chemistry
Structural Homology, Protein
Thermodynamics
Water - chemistry
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Summary:In this work structural behavior of apo form of the adenosine A2A receptor in the implicit membrane-mimicking environment was investigated by means of molecular dynamics (MD) technique. For better interpretation of the obtained data they were analyzed using principal components analysis. The principal components analysis technique was applied to both MD snapshots as well as X-ray structures of the adenosine receptor. As the result the charts were obtained which reflected an interconnection interdependence between dynamic behavior of the receptor observed on the MD trajectories as well as experimental dataset of investigated protein. The calculated MD trajectories allow to observe represent pronounced structural dynamics of the A2A receptor especially in the intracellular part loop connecting TM 5 and 6 of that protein. This observation generally corresponds to the dynamic behavior of the investigated protein seen on the experimental dataset. Therefore the pattern of the intramolecular motions might be following directly from the spatial architecture (fold) of the receptor under study.
ISSN:0006-3029