A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM sigma pi molecular dynamics simulations
文献类型：期刊论文
| 作者 | Yu, Ling2; Yang, Zhong-Zhi1; Zhang, Chao1; Zhao, Dong-Xia1; Wang, Qian1; Li, Guo-Hui3 |
| 刊名 | MOLECULAR SIMULATION
 |
| 出版日期 | 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 |
| WOS记录号 | WOS:000416672600011 |
| 出版者 | TAYLOR & FRANCIS LTD |
| 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. |
入库方式： OAI收割
来源：大连化学物理研究所
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