Modelling and predicting the binding mechanics of HIV P1053-0.5P1053-0.5β antibody complex

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Title:	Modelling and predicting the binding mechanics of HIV P1053-0.5P1053-0.5β antibody complex
Authors:	Wang, Yeng-Tseng Su, Zhi-Yuan
Contributors:	資訊管理系
Keywords:	molecular dynamics potential mean force antibody antigen gp120
Date:	2011-02
Issue Date:	2013-09-28 16:25:38 (UTC+8)
Publisher:	Taylor & Francis
Abstract:	Simulating antigen–antibody interactions is crucial in understanding the mechanics of antigen–antibody binding in medical science. In this study, molecular dynamics simulations are performed to analyse the dissociation of the P1053-0.5β antibody complex structure. The two-dimensional free energy profiles of the complex structure are extracted using the weighted histogram analysis method, and the binding pathway is then predicted using a modified form of the MaxFlux-PRM method. The simulation results suggest that 10 amino residues (i.e. Leu11, Val13, Asp34, Arg112, Thr101, Gly127, Val229, Ser231, Ile235 and Arg236) play a key role in relaxing the antibody structure, thereby facilitating the binding of the 0.5β antibody-P1053 peptide system.
Relation:	Molecular Simulation 37(2), pp.164-171
Appears in Collections:	[Dept. of Information Management] Periodical Articles

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