title: Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase.
abstract: The actual conformation switching of proteins in the crowded cellular environment is completely different from that in vitro. Proteins in cytoplasm are continually subject to confinement and/or attraction to other molecules in their surroundings due to the existence of various biological species. To gain insight into the nature of crowded environments, we investigated the effects of confinement and affinity on the conformation switching of adenylate kinase (ADK) in a spherical cavity. It was found that even a small degree of confinement reduces the entropy of the open state and stabilizes the closed state, which leads to increased energy barriers for transition. Furthermore, the analysis of transition temperatures and mean first passage times indicates that the proper affinity can promote the transition of ADK from closed state to open state. This study reveals that the crowded cellular environment plays an important role in the thermodynamics and kinetics of proteins in vivo.
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China.
authors.forename: Min
authors.initials: M
authors.lastname: Li
authors.forename: Weixin
authors.initials: W
authors.lastname: Xu
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.forename: Fei
authors.initials: F
authors.lastname: Xia
mesh_terms: D000263:Adenylate Kinase / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D004735:Energy Transfer; D019277:Entropy; D004789:Enzyme Activation; D004795:Enzyme Stability; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D044366:Transition Temperature
chemical_list: D000263:Adenylate Kinase