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化学进展 2012, Vol. Issue (9): 1674-1682 前一篇   后一篇

所属专题： 计算化学

• 综述与评论 •

计算肽学

任彦荣1, 田菲菲2, 周鹏*3   

  1. 1. 重庆第二师范学院 生物与化学工程系 重庆 400067;
    2. 西南交通大学 生命科学与工程学院 成都 610031;
    3. 电子科技大学 神经信息教育部重点实验室 生物信息中心 成都 610054
  • 收稿日期:2012-04-01 修回日期:2012-05-01 出版日期:2012-09-24 发布日期:2012-09-27
  • 通讯作者: 周鹏 E-mail:p_zhou@uestc.edu.cn
  • 基金资助:

    国家高技术发展计划(863)项目(No.2006AA02Z31)、国家自然科学基金项目(No.31200993)和重庆市教育委员会资助项目(No. KJ101507)资助

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Computational Peptidology

Ren Yanrong1, Tian Feifei2, Zhou Peng3   

  1. 1. Department of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, China;
    2. School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China;
    3. Center of Bioinformatics, Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
  • Received:2012-04-01 Revised:2012-05-01 Online:2012-09-24 Published:2012-09-27
肽作为重要的生理活性物质一直受到相关领域的广泛关注。近年来,由于肽在细胞信号转导中所扮演的中心角色以及作为生物药物靶向蛋白质相互作用网络等特殊性质的发现,再次唤起了人们对肽的浓厚兴趣。与之相伴的是,肽的理论和计算研究工作快速增长,并取得了长足进展。本文以“计算肽学”为主题系统概括了该领域的研究范畴和研究特点,并分别从肽的数据库构建、功能活性预测、分子对接、动力学模拟、结构数据分析、分子设计修饰以及系统生物学行为等几方面分类介绍了计算肽学的主要研究方向和当前发展状况。重点在于探讨采用计算化学和生物信息学方法剖析肽与蛋白质识别和相互作用的分子机制和理化基础,进而为肽类药物设计提供理论指导。此外,本文还提出了计算肽学在肽类纳米材料及生物表面活性剂等领域的潜在应用前景。
关键词： 计算肽学, 蛋白质/肽相互作用, 分子模拟, 药物设计
Peptide is traditionally recognized as an important kind of biologically active substance, which involves in various physiological processes associated with the growth and development of organism. In recent years, however, since it was found that peptide plays a central role in cell signaling and could be exploited as therapeutic drugs targeting protein-protein interaction networks, researchers have redirected their interest to peptide-related topics. In particular, rapidly increasing efforts have been addressed on the use of computational and theoretical methods to investigate the physicochemical properties and biological implications underlying peptide recognition and interaction with protein. Here, we engage the theme “computational peptidology” to cover the field where the methods, strategies and protocols of computational chemistry and bioinformatics are employed to study peptides and peptide mimics. A systematic discussion is also addressed on the database configuration, function inference, molecular docking, dynamics simulation, structure analysis, design and modification, and systems biology of peptides. Through this perspective, we lay our emphasis on protein-peptide recognition and binding which are the basis of peptide-mediated protein interactions and peptidic drug discovery. We also rise the potential applications of computational peptidology in exploring and designing new peptide-based nanomaterials and biological surfactants. Contents 1 Introduction
2 The branches of computational peptidology
2.1 Peptide database
2.2 Peptide function prediction
2.3 Peptide docking
2.4 Peptide dynamics simulation
2.5 Peptide structure analysis
2.6 Peptide design and modification
2.7 Peptide systems biology
3 Conclusions and outlook
Key words: computational peptidology, protein-peptide interaction, molecular modeling, drug design

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摘要

计算肽学