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Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank

文献类型：期刊论文

作者Zhang, Qian2; Xu, Zhijian1; Shi, Jiye3; Zhu, Weiliang1
刊名JOURNAL OF CHEMICAL INFORMATION AND MODELING
出版日期2017-07
卷号57期号:7页码:1529-1534
ISSN号1549-9596
DOI10.1021/acs.jcim.7b00235
文献子类Article
英文摘要Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R-F) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 angstrom resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.
WOS关键词SCORING FUNCTION ; LIGAND INTERACTIONS ; MOLECULAR DESIGN ; SIDE-CHAINS ; GLUTAMATE ; DESENSITIZATION ; RECOGNITION ; DISCOVERY ; BINDING ; TARGET
资助项目National Key R&D Program of China[2017YFB0202600] ; National Key R&D Program of China[2016YFA0502800] ; National Natural Science Foundation of China[81273435] ; Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund[U1501501]
WOS研究方向Pharmacology & Pharmacy ; Chemistry ; Computer Science
语种英语
WOS记录号WOS:000406435500003
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.183/handle/2S10ELR8/272582]  
专题药物发现与设计中心
通讯作者Xu, Zhijian; Zhu, Weiliang
作者单位1.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, CAS Key Lab Receptor Res, Shanghai 201203, Peoples R China;
2.East China Normal Univ, Dept Comp Sci & Technol, Shanghai 200241, Peoples R China;
3.UCB Biopharma SPRL, Chemin Foriest, B-1420 Braine Lalleud, Belgium
推荐引用方式
GB/T 7714		 Zhang, Qian,Xu, Zhijian,Shi, Jiye,et al. Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2017,57(7):1529-1534.
APA Zhang, Qian,Xu, Zhijian,Shi, Jiye,&Zhu, Weiliang.(2017).Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.JOURNAL OF CHEMICAL INFORMATION AND MODELING,57(7),1529-1534.
MLA Zhang, Qian,et al."Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank".JOURNAL OF CHEMICAL INFORMATION AND MODELING 57.7(2017):1529-1534.

入库方式： OAI收割

来源：上海药物研究所

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