利用量子力学方法研究组氨酸环的质子化。

IF 2.6 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-08-01 Epub Date: 2024-07-25 DOI:10.1107/S2059798324006314

Nigel W Moriarty, Jonathan Moussa, Paul D Adams

{"title":"利用量子力学方法研究组氨酸环的质子化。","authors":"Nigel W Moriarty, Jonathan Moussa, Paul D Adams","doi":"10.1107/S2059798324006314","DOIUrl":null,"url":null,"abstract":"Histidine can be protonated on either or both of the two N atoms of the imidazole moiety. Each of the three possible forms occurs as a result of the stereochemical environment of the histidine side chain. In an atomic model, comparing the possible protonation states in situ, looking at possible hydrogen bonding and metal coordination, it is possible to predict which is most likely to be correct. A more direct method is described that uses quantum-mechanical methods to calculate, also in situ, the minimum geometry and energy for comparison, and therefore to more accurately identify the most likely protonation state.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"639-646"},"PeriodicalIF":2.6000,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301759/pdf/","citationCount":"0","resultStr":"{\"title\":\"Protonation of histidine rings using quantum-mechanical methods.\",\"authors\":\"Nigel W Moriarty, Jonathan Moussa, Paul D Adams\",\"doi\":\"10.1107/S2059798324006314\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Histidine can be protonated on either or both of the two N atoms of the imidazole moiety. Each of the three possible forms occurs as a result of the stereochemical environment of the histidine side chain. In an atomic model, comparing the possible protonation states in situ, looking at possible hydrogen bonding and metal coordination, it is possible to predict which is most likely to be correct. A more direct method is described that uses quantum-mechanical methods to calculate, also in situ, the minimum geometry and energy for comparison, and therefore to more accurately identify the most likely protonation state.\",\"PeriodicalId\":7116,\"journal\":{\"name\":\"Acta Crystallographica. Section D, Structural Biology\",\"volume\":\" \",\"pages\":\"639-646\"},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2024-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301759/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Acta Crystallographica. Section D, Structural Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1107/S2059798324006314\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/7/25 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Acta Crystallographica. Section D, Structural Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1107/S2059798324006314","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/7/25 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

摘要

组氨酸可以在咪唑分子的两个 N 原子中的一个或两个上质子化。组氨酸侧链的立体化学环境决定了组氨酸的三种可能形式。在原子模型中，通过比较可能的原位质子化状态，考察可能的氢键和金属配位，可以预测出哪一种最有可能是正确的。本文介绍了一种更直接的方法，即利用量子力学方法计算（也是在原位）最小几何形状和能量，以便进行比较，从而更准确地确定最可能的质子化状态。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

Protonation of histidine rings using quantum-mechanical methods.

Histidine can be protonated on either or both of the two N atoms of the imidazole moiety. Each of the three possible forms occurs as a result of the stereochemical environment of the histidine side chain. In an atomic model, comparing the possible protonation states in situ, looking at possible hydrogen bonding and metal coordination, it is possible to predict which is most likely to be correct. A more direct method is described that uses quantum-mechanical methods to calculate, also in situ, the minimum geometry and energy for comparison, and therefore to more accurately identify the most likely protonation state.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Acta Crystallographica. Section D, Structural Biology BIOCHEMICAL RESEARCH METHODSBIOCHEMISTRY &-BIOCHEMISTRY & MOLECULAR BIOLOGY

CiteScore

4.50

自引率

13.60%

发文量

216

期刊介绍： Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.