Preferred microenvironments of halogen bonds and hydrogen bonds revealed using statistics and QM/MM calculation studies
文献类型：期刊论文
| 作者 | Zhou, Liping1,2; Li, Jintian1,2; Shi, Yulong1,2; Wu, Leyun1,2; Zhu, Weiliang1,2 ; Xu, Zhijian1,2
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| 刊名 | PHYSICAL CHEMISTRY CHEMICAL PHYSICS
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| 出版日期 | 2023-07-05 |
| 卷号 | 25期号:26页码:17692-17699 |
| ISSN号 | 1463-9076 |
| DOI | 10.1039/d3cp02096g |
| 通讯作者 | Zhu, Weiliang(wlzhu@simm.ac.cn) ; Xu, Zhijian(zjxu@simm.ac.cn) |
| 英文摘要 | Hydrogen bonds (HBs) and halogen bonds (XBs) are two essential non-covalent interactions for molecular recognition and drug design. As proteins are heterogeneous in structure, the microenvironments of protein structures should have effects on the formation of HBs and XBs with ligands. However, there are no systematic studies reported on this effect to date. For quantitatively describing protein microenvironments, we defined the local hydrophobicities (LHs) and local dielectric constants (LDCs) in this study. With the defined parameters, we conducted an elaborate database survey on the basis of 22 011 ligand-protein structures to explore the microenvironmental preference of HBs (91 966 in total) and XBs (1436 in total). The statistics show that XBs prefer hydrophobic microenvironments compared to HBs. The polar residues like ASP are more likely to form HBs with ligands, while nonpolar residues such as PHE and MET prefer XBs. Both the LHs and LDCs (10.69 & PLUSMN; 4.36 for HBs; 8.86 & PLUSMN; 4.00 for XBs) demonstrate that XBs are prone to hydrophobic microenvironments compared with HBs with significant differences (p < 0.001), indicating that evaluating their strengths in the corresponding environments should be necessary. Quantum Mechanics-Molecular Mechanics (QM/MM) calculations reveal that in comparison with vacuum environments, the interaction energies of HBs and XBs are decreased to varying degrees given different microenvironments. In addition, the strengths of HBs are impaired more than those of XBs when the local dielectric constant's difference between the XB microenvironments and the HB microenvironments is large. |
| WOS关键词 | TOTAL ENERGIES ; LIPOPHILICITY ; PROTEINS ; SYSTEMS ; SC |
| 资助项目 | National Key Ramp;D Program of China[2022YFA1004304] |
| WOS研究方向 | Chemistry ; Physics |
| 语种 | 英语 |
| 出版者 | ROYAL SOC CHEMISTRY |
| WOS记录号 | WOS:001014123700001 |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/306322]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Zhu, Weiliang; Xu, Zhijian |
| 作者单位 | 1.Univ Chinese Acad Sci, Sch Pharm, 19A Yuquan Rd, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhou, Liping,Li, Jintian,Shi, Yulong,et al. Preferred microenvironments of halogen bonds and hydrogen bonds revealed using statistics and QM/MM calculation studies[J]. PHYSICAL CHEMISTRY CHEMICAL PHYSICS,2023,25(26):17692-17699. |
| APA | Zhou, Liping,Li, Jintian,Shi, Yulong,Wu, Leyun,Zhu, Weiliang,&Xu, Zhijian.(2023).Preferred microenvironments of halogen bonds and hydrogen bonds revealed using statistics and QM/MM calculation studies.PHYSICAL CHEMISTRY CHEMICAL PHYSICS,25(26),17692-17699. |
| MLA | Zhou, Liping,et al."Preferred microenvironments of halogen bonds and hydrogen bonds revealed using statistics and QM/MM calculation studies".PHYSICAL CHEMISTRY CHEMICAL PHYSICS 25.26(2023):17692-17699. |
入库方式： OAI收割
来源：上海药物研究所
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