用于分析蛋白质-糖蛋白相互作用的计算工具箱。

IF 2.2 4区 化学 Q2 CHEMISTRY, ORGANIC
Beilstein Journal of Organic Chemistry Pub Date : 2024-08-22 eCollection Date: 2024-01-01 DOI:10.3762/bjoc.20.180
Ferran Nieto-Fabregat, Maria Pia Lenza, Angela Marseglia, Cristina Di Carluccio, Antonio Molinaro, Alba Silipo, Roberta Marchetti
{"title":"用于分析蛋白质-糖蛋白相互作用的计算工具箱。","authors":"Ferran Nieto-Fabregat, Maria Pia Lenza, Angela Marseglia, Cristina Di Carluccio, Antonio Molinaro, Alba Silipo, Roberta Marchetti","doi":"10.3762/bjoc.20.180","DOIUrl":null,"url":null,"abstract":"<p><p>Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"2084-2107"},"PeriodicalIF":2.2000,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346309/pdf/","citationCount":"0","resultStr":"{\"title\":\"Computational toolbox for the analysis of protein-glycan interactions.\",\"authors\":\"Ferran Nieto-Fabregat, Maria Pia Lenza, Angela Marseglia, Cristina Di Carluccio, Antonio Molinaro, Alba Silipo, Roberta Marchetti\",\"doi\":\"10.3762/bjoc.20.180\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.</p>\",\"PeriodicalId\":8756,\"journal\":{\"name\":\"Beilstein Journal of Organic Chemistry\",\"volume\":\"20 \",\"pages\":\"2084-2107\"},\"PeriodicalIF\":2.2000,\"publicationDate\":\"2024-08-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346309/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Beilstein Journal of Organic Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.3762/bjoc.20.180\",\"RegionNum\":4,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, ORGANIC\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Beilstein Journal of Organic Chemistry","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.3762/bjoc.20.180","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"CHEMISTRY, ORGANIC","Score":null,"Total":0}
引用次数: 0

摘要

从细胞识别到免疫反应调节,蛋白质与聚糖的相互作用在众多生物过程中发挥着关键作用。了解这些相互作用的复杂细节对于破译各种生理和病理状况的分子机制至关重要。计算技术已经成为一种强大的工具,可以帮助绘制、构建和可视化复杂的生物分子,并深入了解它们在原子和分子水平上的动态行为。本综述概述了用于研究生物分子系统(尤其是自由状态和与蛋白质复合状态的聚糖)的主要计算工具,同时还介绍了全原子分子动力学模拟的原理、方法和应用。在这里,我们重点介绍了通常用于准备蛋白质和聚糖输入文件以执行分子动力学模拟和分析相应结果的程序。所介绍的计算工具箱是研究蛋白质-聚糖相互作用的研究人员的宝贵资源,它结合了先进的计算方法,可用于构建、可视化和预测蛋白质/聚糖结构,建立蛋白质配体复合物模型,以及分析 MD 结果。此外,还报告了一些案例研究,以突出计算工具在研究蛋白质-聚糖系统中的重要性,揭示这些工具有能力为特定分子相互作用的结合动力学、能量学和结构决定因素提供有价值的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Computational toolbox for the analysis of protein-glycan interactions.

Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.

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
CiteScore
4.90
自引率
3.70%
发文量
167
审稿时长
1.4 months
期刊介绍: The Beilstein Journal of Organic Chemistry is an international, peer-reviewed, Open Access journal. It provides a unique platform for rapid publication without any charges (free for author and reader) – Platinum Open Access. The content is freely accessible 365 days a year to any user worldwide. Articles are available online immediately upon publication and are publicly archived in all major repositories. In addition, it provides a platform for publishing thematic issues (theme-based collections of articles) on topical issues in organic chemistry. The journal publishes high quality research and reviews in all areas of organic chemistry, including organic synthesis, organic reactions, natural product chemistry, structural investigations, supramolecular chemistry and chemical biology.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信