中国在翻译后修饰的生物信息学研究领域的进展与前瞻

doi:10.16288/j.yczz.15-003

遗传 ›› 2015, Vol. 37 ›› Issue (7): 621-634.doi: 10.16288/j.yczz.15-003

中国在翻译后修饰的生物信息学研究领域的进展与前瞻

刘泽先¹, 蔡煜东², 郭雪江³, 李骜⁴, 李婷婷⁵, 邱建丁⁶, 任间⁷, 施绍萍⁸, 宋江宁⁹, 王明会⁴, 谢鹭¹⁰, 薛宇¹, 张子丁¹¹, 赵兴明¹²

1. 华中科技大学生命科学与技术学院生物医学工程系,武汉 430074;
2. 上海大学系统生物技术研究所,上海 200444;
3. 南京医科大学组织胚胎学系,生殖医学国家重点实验室,南京 210029;
4. 中国科学技术大学信息科学与技术学院,合肥 230027;
5. 北京大学医学部基础医学院医学信息学系,北京 100191;
6. 南昌大学化学学院化学系,南昌 330031;
7. 中山大学生命科学学院,生物防治国家重点实验室,广州 510275;
8. 南昌大学理学院数学系,南昌 330031;
9. 中国科学院天津工业生物技术研究所,工业酶国家工程实验室与系统微生物工程重点实验室,天津 300308;
10. 上海科学院,上海生物信息技术研究中心,上海 201203;
11. 中国农业大学生物学院,农业生物技术国家重点实验室,北京 100193;
12. 同济大学电子与信息工程学院计算机系,上海 201804

收稿日期:2014-12-31 修回日期:2015-02-05 出版日期:2015-07-20 发布日期:2015-07-20
通讯作者: 薛宇,博士,教授,研究方向：生物信息学与计算蛋白质组学。E-mail: xueyu@hust.edu.cn
作者简介:刘泽先,博士,研究方向：生物信息学与计算蛋白质组学。E-mail: lzx@hust.edu.cn
基金资助:
国家自然科学基金项目(编号：31471252,31371337,81222006,61471331),国家重点基础研究发展规划(973计划)项目(编号：2011CB910600)和国家高技术研究发展计划(863计划)项目(编号：2012AA020201)资助

Post-translational modification (PTM) bioinformatics in China: progresses and perspectives

Zexian Liu¹, Yudong Cai², Xuejiang Guo³, Ao Li⁴, Tingting Li⁵, Jianding Qiu⁶, Jian Ren⁷, Shaoping Shi⁸, Jiangning Song⁹, Minghui Wang⁴, Lu Xie¹⁰, Yu Xue¹, Ziding Zhang¹¹, Xingming Zhao¹²

1. Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
2. Institute of Systems Biology, Shanghai University, Shanghai 200444, China;
3. State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 210029, China;
4. School of Information Science and Technology, University of Science and Technology of China, Hefei 232207, China;
5. Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China;
6. Department of Chemistry, School of chemistry, Nanchang University, Nanchang 330031, China;
7. State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
8. Department of Mathematics, College of Science, Nanchang University, Nanchang 330031, China;
9. National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
10. Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China;
11. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural Universty, Beijing 100193, China;
12. Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China

Received:2014-12-31 Revised:2015-02-05 Online:2015-07-20 Published:2015-07-20

摘要/Abstract

摘要： 翻译后修饰在调控蛋白质构象变化、活性以及功能方面具有重要作用,并参与了几乎所有细胞通路和过程。蛋白质翻译后修饰的鉴定是阐明细胞内分子机理的基础。相对于劳动密集的、耗费时间的实验工作,利用各种生物信息学方法开展翻译后修饰预测,能够提供准确、简便和快速的研究方案,并产生有价值的信息为进一步实验研究提供参考。文章主要综述了中国生物信息学者在翻译后修饰生物信息学领域所取得的研究进展,包括修饰底物与位点预测的计算方法学设计与完善、在线或本地化工具的设计与维护、修饰相关数据库及数据资源的构建及基于修饰蛋白质组学数据的生物信息学分析。通过比较国内外的同类研究,发现优势和不足,并对未来的研究作出前瞻。

关键词: 翻译后修饰, 共价修饰, 修饰组学, 磷酸化

Abstract: Post-translational modifications (PTMs) are essential for regulating conformational changes, activities and functions of proteins, and are involved in almost all cellular pathways and processes. Identification of protein PTMs is the basis for understanding cellular and molecular mechanisms. In contrast with labor-intensive and time-consuming experiments, the PTM prediction using various bioinformatics approaches can provide accurate, convenient, and efficient strategies and generate valuable information for further experimental consideration. In this review, we summarize the current progresses made by Chineses bioinformaticians in the field of PTM Bioinformatics, including the design and improvement of computational algorithms for predicting PTM substrates and sites, design and maintenance of online and offline tools, establishment of PTM-related databases and resources, and bioinformatics analysis of PTM proteomics data. Through comparing similar studies in China and other countries, we demonstrate both advantages and limitations of current PTM bioinformatics as well as perspectives for future studies in China.

Key words: post-translational modification, covalent modification, PTM proteomics, phosphorylation

刘泽先, 蔡煜东, 郭雪江, 李骜, 李婷婷, 邱建丁, 任间, 施绍萍, 宋江宁, 王明会, 谢鹭, 薛宇, 张子丁, 赵兴明. 中国在翻译后修饰的生物信息学研究领域的进展与前瞻[J]. 遗传, 2015, 37(7): 621-634.

Zexian Liu, Yudong Cai, Xuejiang Guo, Ao Li, Tingting Li, Jianding Qiu, Jian Ren, Shaoping Shi, Jiangning Song, Minghui Wang, Lu Xie, Yu Xue, Ziding Zhang, Xingming Zhao. Post-translational modification (PTM) bioinformatics in China: progresses and perspectives[J]. HEREDITAS(Beijing), 2015, 37(7): 621-634.

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中国在翻译后修饰的生物信息学研究领域的进展与前瞻

Post-translational modification (PTM) bioinformatics in China: progresses and perspectives

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