[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 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.
G V
GV
Novikov
V S
VS
Sivozhelezov
K V
KV
Shaĭtan
D002251:Carbon Tetrachloride / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D043705:Receptor, Adenosine A2A / Q000737:chemistry*; D012243:Rhodopsin / Q000737:chemistry*; D040681:Structural Homology, Protein; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D043705:Receptor, Adenosine A2A; D014867:Water; D012243:Rhodopsin; D002251:Carbon Tetrachloride