title: Inherent dynamics of head domain correlates with ATP-recognition of P2X4 receptors: insights gained from molecular simulations.
abstract: P2X receptors are ATP-gated ion channels involved in many physiological functions, and determination of ATP-recognition (AR) of P2X receptors will promote the development of new therapeutic agents for pain, inflammation, bladder dysfunction and osteoporosis. Recent crystal structures of the zebrafish P2X4 (zfP2X4) receptor reveal a large ATP-binding pocket (ABP) located at the subunit interface of zfP2X4 receptors, which is occupied by a conspicuous cluster of basic residues to recognize triphosphate moiety of ATP. Using the engineered affinity labeling and molecular modeling, at least three sites (S1, S2 and S3) within ABP have been identified that are able to recognize the adenine ring of ATP, implying the existence of at least three distinct AR modes in ABP. The open crystal structure of zfP2X4 confirms one of three AR modes (named AR1), in which the adenine ring of ATP is buried into site S1 while the triphosphate moiety interacts with clustered basic residues. Why architecture of ABP favors AR1 not the other two AR modes still remains unexplored. Here, we examine the potential role of inherent dynamics of head domain, a domain involved in ABP formation, in AR determinant of P2X4 receptors. In silico docking and binding free energy calculation revealed comparable characters of three distinct AR modes. Inherent dynamics of head domain, especially the downward motion favors the preference of ABP for AR1 rather than AR2 and AR3. Along with the downward motion of head domain, the closing movement of loop139-146 and loop169-183, and structural rearrangements of K70, K72, R298 and R143 enabled ABP to discriminate AR1 from other AR modes. Our observations suggest the essential role of head domain dynamics in determining AR of P2X4 receptors, allowing evaluation of new strategies aimed at developing specific blockers/allosteric modulators by preventing the dynamics of head domain associated with both AR and channel activation of P2X4 receptors.
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Li-Dong
authors.initials: LD
authors.lastname: Huang
authors.affiliation: Putuo District Center Hospital, Shanghai University of Chinese Traditional Medicine, Shanghai, China.
authors.forename: Ying-Zhe
authors.initials: YZ
authors.lastname: Fan
authors.affiliation: College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Tian
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Wen-Shan
authors.initials: WS
authors.lastname: Zhao
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Putuo District Center Hospital, Shanghai University of Chinese Traditional Medicine, Shanghai, China.
authors.forename: Wen-Chao
authors.initials: WC
authors.lastname: Zhou
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Xiao-Yang
authors.initials: XY
authors.lastname: Cheng
authors.affiliation: Jiangsu Province Institute of Traditional Chinese Medicine, Nanjing, Jiangsu, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Cao
authors.affiliation: College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.
authors.forename: Xiang-Yang
authors.initials: XY
authors.lastname: Lu
authors.affiliation: Department of Pharmacology and Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Yu
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism*; D000494:Allosteric Regulation; D000818:Animals; D001665:Binding Sites; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009068:Movement; D017434:Protein Structure, Tertiary; D058848:Receptors, Purinergic P2X4 / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D058848:Receptors, Purinergic P2X4; D029961:Zebrafish Proteins; D000255:Adenosine Triphosphate