Allosteric sites can be identified based on the residue-residue interaction energy difference
文献类型：期刊论文
| 作者 | Ma, Xiaomin1; Qi, Yifei1; Lai, Luhua1,2,3 |
| 刊名 | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
 |
| 出版日期 | 2015-08-01 |
| 卷号 | 83期号:8页码:1375-1384 |
| 关键词 | allosteric site identification MM GBSA energy decomposition residue-residue interaction energy CAVITY |
| 英文摘要 | Allosteric drugs act at a distance to regulate protein functions. They have several advantages over conventional orthosteric drugs, including diverse regulation types and fewer side effects. However, the rational design of allosteric ligands remains a challenge, especially when it comes to the identification allosteric binding sites. As the binding of allosteric ligands may induce changes in the pattern of residue-residue interactions, we calculated the residue-residue interaction energies within the allosteric site based on the molecular mechanics generalized Born surface area energy decomposition scheme. Using a dataset of 17 allosteric proteins with structural data for both the apo and the ligand-bound state available, we used conformational ensembles generated by molecular dynamics simulations to compute the differences in the residue-residue interaction energies in known allosteric sites from both states. For all the known sites, distinct interaction energy differences (>25%) were observed. We then used CAVITY, a binding site detection program to identify novel putative allosteric sites in the same proteins. This yielded a total of 31 druggable binding sites, of which 21 exhibited >25% difference in residue interaction energies, and were hence predicted as novel allosteric sites. Three of the predicted allosteric sites were supported by recent experimental studies. All the predicted sites may serve as novel allosteric sites for allosteric ligand design. Our study provides a computational method for identifying novel allosteric sites for allosteric drug design. Proteins 2015; 83:1375-1384. (c) 2014 Wiley Periodicals, Inc. |
| 收录类别 | SCI |
| 语种 | 英语 |
| 公开日期 | 2015-10-27 |
| 源URL | [http://ir.iccas.ac.cn/handle/121111/27868]  |
| 专题 | 化学研究所_分子动态与稳态结构实验室 |
| 作者单位 | 1.Peking Univ, Ctr Quantitat Biol, Beijing 100871, Peoples R China 2.Peking Univ, Coll Chem & Mol Engn, State Key Lab Struct Chem Unstable & Stable Speci, BNLMS, Beijing 100871, Peoples R China 3.Peking Univ, Coll Chem & Mol Engn, Peking Tsinghua Ctr Life Sci, Beijing 100871, Peoples R China |
| 推荐引用方式 GB/T 7714 | Ma, Xiaomin,Qi, Yifei,Lai, Luhua. Allosteric sites can be identified based on the residue-residue interaction energy difference[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2015,83(8):1375-1384. |
| APA | Ma, Xiaomin,Qi, Yifei,&Lai, Luhua.(2015).Allosteric sites can be identified based on the residue-residue interaction energy difference.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,83(8),1375-1384. |
| MLA | Ma, Xiaomin,et al."Allosteric sites can be identified based on the residue-residue interaction energy difference".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 83.8(2015):1375-1384. |
入库方式： OAI收割
来源：化学研究所
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