Bioinformatic investigation of Nipah virus surface protein mutations: Molecular docking with Ephrin B2 receptor, molecular dynamics simulation, and structural impact analysis

IF 1.9 4区 医学 Q4 IMMUNOLOGY Microbiology and Immunology Pub Date : 2023-10-09 DOI:10.1111/1348-0421.13098
Emre Aktaş, İrem Saygılı, Elif Kahveci, Zeynep Tekbıyık, Nehir Özdemir Özgentürk
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Abstract

The SARS‐CoV‐2 outbreak resulted in significant challenges and loss of life. The Nipah virus, known for its high infectivity and severity, was designated an emergency concern by the World Health Organization. To understand its mutations, the Nipah virus proteins were analyzed extensively, with a focus on the essential G and F proteins responsible for viral entry into host cells. Our bioinformatics analysis unveiled multiple mutations, including simultaneous mutations within a single sequence. Notably, the G273S mutation in the F protein was identified as a potential cause of structural damage, which carries significant implications for vaccine development. Comparing the docking scores of G and F proteins with the Ephrin B2 receptor, it was found that the Y228H mutation in the G protein and the D252G mutation in the F protein likely affect virus entry into host cells. Moreover, our investigation into stability and deformability highlighted the impact of the Y228H mutation in the G protein complex. Molecular dynamics simulations revealed increased flexibility and conformational changes in the G protein complex with the Y228H mutation compared with the known complex. Furthermore, evaluating the root mean square deviation variation demonstrated greater dynamic behavior in the G protein complex and the Ephrin B2 receptor complex. This comprehensive study provides valuable insights into Nipah virus mutations, their significance for vaccine development, and the importance of understanding protein complex behavior in drug discovery. The identified mutations, especially G273S and Y228H, hold crucial implications for future research and potential interventions against the Nipah virus.
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尼帕病毒表面蛋白突变的生物信息学研究:与Ephrin B2受体的分子对接、分子动力学模拟和结构影响分析。
严重急性呼吸系统综合征冠状病毒2型的爆发带来了重大挑战和生命损失。尼帕病毒以其高传染性和严重性而闻名,被世界卫生组织指定为紧急关注对象。为了了解其突变,对尼帕病毒蛋白进行了广泛分析,重点是负责病毒进入宿主细胞的必需G和F蛋白。我们的生物信息学分析揭示了多个突变,包括单个序列中的同时突变。值得注意的是,F蛋白中的G273S突变被确定为结构损伤的潜在原因,这对疫苗开发具有重要意义。比较G和F蛋白与Ephrin B2受体的对接得分,发现G蛋白中的Y228H突变和F蛋白中的D252G突变可能影响病毒进入宿主细胞。此外,我们对稳定性和可变形性的研究强调了G蛋白复合体中Y228H突变的影响。分子动力学模拟显示,与已知的复合物相比,具有Y228H突变的G蛋白复合物的灵活性和构象变化增加。此外,评估均方根偏差变化表明G蛋白复合物和Ephrin B2受体复合物具有更大的动态行为。这项全面的研究为尼帕病毒突变、其对疫苗开发的意义以及了解蛋白质复合物行为在药物发现中的重要性提供了有价值的见解。已确定的突变,特别是G273S和Y228H,对未来的研究和针对尼帕病毒的潜在干预措施具有重要意义。
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来源期刊
Microbiology and Immunology
Microbiology and Immunology 医学-免疫学
CiteScore
5.20
自引率
3.80%
发文量
78
审稿时长
1 months
期刊介绍: Microbiology and Immunology is published in association with Japanese Society for Bacteriology, Japanese Society for Virology, and Japanese Society for Host Defense Research. It is peer-reviewed publication that provides insight into the study of microbes and the host immune, biological and physiological responses. Fields covered by Microbiology and Immunology include:Bacteriology|Virology|Immunology|pathogenic infections in human, animals and plants|pathogenicity and virulence factors such as microbial toxins and cell-surface components|factors involved in host defense, inflammation, development of vaccines|antimicrobial agents and drug resistance of microbes|genomics and proteomics.
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