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Underestimated Noncovalent Interactions in Protein Data Bank

文献类型：期刊论文

作者Xu, Zhijian1; Zhang, Qian2; Shi, Jiye1; Zhu, Weiliang1,3
刊名JOURNAL OF CHEMICAL INFORMATION AND MODELING
出版日期2019-08-01
卷号59期号:8页码:3389-3399
ISSN号1549-9596
DOI10.1021/acs.jcim.9b00258
通讯作者Xu, Zhijian(zjxu@simm.ac.cn) ; Zhu, Weiliang(wlzhu@simm.ac.cn)
英文摘要Noncovalent interactions (NCIs) play essential roles in the structure and function of biomacromolecules. There are various NCIs, e.g., hydrogen bonds (HBs), cation-pi and pi-pi interactions, and ionic bonds, among angstrom longer than the HB distance criteria without angle constraints), we demonstrated that HBs in both protein-ligand and protein-protein interfaces are overlooked in which HBs are the most widespread and well-studied. By utilizing the ratio of the observed HBs over pseudo HBs (1.0 structures deposited in PDB. After the QM/MM optimization of 12 protein-ligand complexes, we showed that the overlooked HBs could be recovered. With a systematic search in the PDB, we found that the HB number per residue (N-HB/R) in proteins decreases as structural resolution becomes lower, implying that HBs are overlooked even today, regardless of the type of refinement approach used. Similarly, cation-pi, pi-pi, and ionic interactions were found to be significantly lost, manifesting the universal underestimation of various NCIs. Considering the vital role of NCIs, it is important to recover the NCIs to facilitate drug design, to explore protein-protein interaction, and to study protein structure and function.
WOS关键词CATION-PI INTERACTIONS ; BARRIER HYDROGEN-BOND ; CONFIDENCE-INTERVAL ; CRYSTAL-STRUCTURES ; FORCE-FIELD ; THERMOCHEMISTRY ; ASSEMBLIES ; ENERGIES ; DESIGN ; SERVER
资助项目National Key Research and Development Program of China[2017YFB0202601] ; National Key Research and Development Program of China[2016YFA0502301] ; National Natural Science Foundation of China[31870717] ; Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase)[nsfc2015_447]
WOS研究方向Pharmacology & Pharmacy ; Chemistry ; Computer Science
语种英语
WOS记录号WOS:000483436400005
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.183/handle/2S10ELR8/288838]  
专题中国科学院上海药物研究所
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.Open Studio Druggabil Res Marine Nat Prod, Pilot Natl Lab Marine Sci & Technol Qingdao, Qingdao 266237, Shandong, Peoples R China
推荐引用方式
GB/T 7714		 Xu, Zhijian,Zhang, Qian,Shi, Jiye,et al. Underestimated Noncovalent Interactions in Protein Data Bank[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2019,59(8):3389-3399.
APA Xu, Zhijian,Zhang, Qian,Shi, Jiye,&Zhu, Weiliang.(2019).Underestimated Noncovalent Interactions in Protein Data Bank.JOURNAL OF CHEMICAL INFORMATION AND MODELING,59(8),3389-3399.
MLA Xu, Zhijian,et al."Underestimated Noncovalent Interactions in Protein Data Bank".JOURNAL OF CHEMICAL INFORMATION AND MODELING 59.8(2019):3389-3399.

入库方式： OAI收割

来源：上海药物研究所

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