A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM sigma pi molecular dynamics simulations

doi:10.1080/08927022.2017.1350660

	A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM sigma pi molecular dynamics simulations
	Yu, Ling 2; Yang, Zhong-Zhi 1; Zhang, Chao 1; Zhao, Dong-Xia 1; Wang, Qian 1; Li, Guo-Hui 3
刊名	MOLECULAR SIMULATION
	2017
卷号	43 期号:13-16 页码:1045-1055
关键词	Molecular Dynamics Flexible Recognition Polarisation Signal Water-bridge Binding Free Energy
ISSN号	0892-7022
DOI	10.1080/08927022.2017.1350660
文献子类	Article
英文摘要	How the receptor and ligand recognise each other is a challenging subject in explaining the mechanism of recognition at the molecular level. As a starting point, here, a synthesised RS receptor and its RGD ligand were investigated as a proper model to simulate their recognition process in terms of ABEEM sigma pi/MM polarisable force field. It is found that a switch of forming up a salt bridge in the ligand triggers the recognition of the receptor and ligand. Through the salt-bridge switch that undergoes several cycles from on-state with parallel hydrogen bonds to off-state with bifurcated hydrogen bonds, the active site of ligand can flex easily to interact with the active site of the receptor. In addition, the water molecules form a decisive bridge connecting the active sites of the bound system. The salt-bridge switch and water-mediated movement are cooperative as the important factors for the receptor-ligand recognition. In addition, the properties, such as binding free energy, conformational flexibility and solvent accessible surface area have been calculated to provide adequate evidence for the whole recognition process. According to the simulation, a detailed mechanism was derived involving diffusion, a switch triggered cooperative water-mediated movement, and conformational folding, for the flexible recognition.
WOS关键词	ELECTRONEGATIVITY EQUALIZATION METHOD ; ARG-GLY-ASP ; INTEGRIN ALPHA(V)BETA(3) ANTAGONISTS ; PANCREATIC TRYPSIN-INHIBITOR ; PROTEIN-PROTEIN RECOGNITION ; 7-SITE FLUCTUATING CHARGE ; WATER POTENTIAL FUNCTION ; CRYSTAL-STRUCTURE ; FORCE-FIELD ; CELL ATTACHMENT
WOS研究方向	Chemistry ; Physics
语种	英语
出版者	TAYLOR & FRANCIS LTD
WOS记录号	WOS:000416672600011
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/169246]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
通讯作者	Yang, Zhong-Zhi; Zhao, Dong-Xia
作者单位	1.Liaoning Normal Univ, Sch Chem & Chem Engn, Dalian, Peoples R China 2.Liaoning Panjin Fine Chem Ind Pk Adm Comm, Panjin, Peoples R China 3.Chinese Acad Sci, Dalian Inst Chem Phys, Dalian, Peoples R China
推荐引用方式 GB/T 7714	Yu, Ling,Yang, Zhong-Zhi,Zhang, Chao,et al. A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM sigma pi molecular dynamics simulations[J]. MOLECULAR SIMULATION,2017,43(13-16):1045-1055.
APA	Yu, Ling,Yang, Zhong-Zhi,Zhang, Chao,Zhao, Dong-Xia,Wang, Qian,&Li, Guo-Hui.(2017).A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM sigma pi molecular dynamics simulations.MOLECULAR SIMULATION,43(13-16),1045-1055.
MLA	Yu, Ling,et al."A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM sigma pi molecular dynamics simulations".MOLECULAR SIMULATION 43.13-16(2017):1045-1055.