Conformational changes accompanying with the binding of protein and ligand
Liu, ZJ; Jiang, L; Li, WZ; Han, YZ; Lai, LH
AbstractThe binding of protein with its ligand can be generalized into two major modes: direct binding with surface loops or binding associated with hinge movement. Two different strategies were developed to study the conformational variation in the binding process. For directive loop binding, a combinatorial conformational library for the backbone structure of the loop was built up, which includes all possible sub - stable conformations of the loop during the binding procedure. The library of conformations was subject to screening by rigid docking. The Streptavidin complex was used as an example to explore the possibility to build the combinatorial conformational library of loop backbone. For hinge binding movement, step - by - step docking method has been proposed and applied to HIV - 1 protease and inhibitor system. The results show that both methods can simulate the conformational variation of proteins in the binding process successfully. The proposed methods for studying the binding process of protein and ligand will be helpful for protein and drug design.
KeywordProtein Ligand Docking Loop Hinge Binding Movement Induced Fit Effect Sub - Stable States Hypothesis
Indexed BySCI
WOS IDWOS:000088279100008
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Document Type期刊论文
Corresponding AuthorLiu, ZJ
AffiliationPeking Univ, Inst Phys Chem, Coll Chem & Mol Engn, State Key Lab Struct Chem Unstable & Stable Speci, Beijing 100871, Peoples R China
Recommended Citation
GB/T 7714
Liu, ZJ,Jiang, L,Li, WZ,et al. Conformational changes accompanying with the binding of protein and ligand[J]. ACTA CHIMICA SINICA,2000,58(7):772-776.
APA Liu, ZJ,Jiang, L,Li, WZ,Han, YZ,&Lai, LH.(2000).Conformational changes accompanying with the binding of protein and ligand.ACTA CHIMICA SINICA,58(7),772-776.
MLA Liu, ZJ,et al."Conformational changes accompanying with the binding of protein and ligand".ACTA CHIMICA SINICA 58.7(2000):772-776.
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