Mehri Javid, Ahmad Reza Shahverdi, Atiyeh Ghasemi, Ali Akbar Moosavi-Movahedi, Azadeh Ebrahim-Habibi, Zargham Sepehrizadeh
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Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in <i>silico</i> modeling and the informed design of next-generation enzybiotic treatments.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 3","pages":"522 - 543"},"PeriodicalIF":1.9000,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Decoding the Structure–Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics\",\"authors\":\"Mehri Javid, Ahmad Reza Shahverdi, Atiyeh Ghasemi, Ali Akbar Moosavi-Movahedi, Azadeh Ebrahim-Habibi, Zargham Sepehrizadeh\",\"doi\":\"10.1007/s10930-024-10195-z\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. 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Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in <i>silico</i> modeling and the informed design of next-generation enzybiotic treatments.</p></div>\",\"PeriodicalId\":793,\"journal\":{\"name\":\"The Protein Journal\",\"volume\":\"43 3\",\"pages\":\"522 - 543\"},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2024-04-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"The Protein Journal\",\"FirstCategoryId\":\"2\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s10930-024-10195-z\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"The Protein Journal","FirstCategoryId":"2","ListUrlMain":"https://link.springer.com/article/10.1007/s10930-024-10195-z","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
噬菌体内溶素是治疗耐多药革兰氏阴性细菌感染的传统抗生素的潜在替代品。然而,人们对它们的结构-功能关系知之甚少,这阻碍了它们的优化和应用。在这项研究中,我们重点研究了来自大肠杆菌 O157:H7 噬菌体 PhaxI 的模块化溶菌素 Gp127 的 C 端酪氨酸酶结构域的个体功能。该结构域具有酶活性,而 N 端结构域则与细菌细胞壁结合。通过蛋白质建模、对接实验和分子动力学模拟,我们研究了分离出的 C 端结构域的活性、稳定性以及与配体的相互作用。我们还利用实验数据评估了它的表达、溶解性、毒性和溶解活性。我们的结果表明,在单独测试时,C-末端结构域表现出很高的活性和毒性,它在不同宿主中的表达受到调控,以防止自毁。此外,我们还通过酶标仪和标准化检测验证了纯化的重折叠蛋白的壁垒分解活性。这些发现质疑了 N 端结合域在安排活性位点和调整肽聚糖裂解关键残基间隙方面的必要性。我们的研究揭示了μramidase内溶酶的三维结构和功能,从而丰富了现有的知识库,并为精确的硅学建模和下一代酵素治疗的知情设计奠定了基础。
Decoding the Structure–Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics
Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. However, their structure–function relationships are poorly understood, hindering their optimization and application. In this study, we focused on the individual functionality of the C-terminal muramidase domain of Gp127, a modular endolysin from E. coli O157:H7 bacteriophage PhaxI. This domain is responsible for the enzymatic activity, whereas the N-terminal domain binds to the bacterial cell wall. Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in silico modeling and the informed design of next-generation enzybiotic treatments.
期刊介绍:
The Protein Journal (formerly the Journal of Protein Chemistry) publishes original research work on all aspects of proteins and peptides. These include studies concerned with covalent or three-dimensional structure determination (X-ray, NMR, cryoEM, EPR/ESR, optical methods, etc.), computational aspects of protein structure and function, protein folding and misfolding, assembly, genetics, evolution, proteomics, molecular biology, protein engineering, protein nanotechnology, protein purification and analysis and peptide synthesis, as well as the elucidation and interpretation of the molecular bases of biological activities of proteins and peptides. We accept original research papers, reviews, mini-reviews, hypotheses, opinion papers, and letters to the editor.