[1]顾万君,周童,马建民,等.不同折叠类型蛋白中基于密码子的二级结构偏向性分析[J].东南大学学报(自然科学版),2004,34(1):72-77.[doi:10.3969/j.issn.1001-0505.2004.01.017]
 Gu Wanjun,Zhou Tong,Ma Jianmin,et al.Codon-based amino acid propensities for secondary structural units in proteins with different folding types[J].Journal of Southeast University (Natural Science Edition),2004,34(1):72-77.[doi:10.3969/j.issn.1001-0505.2004.01.017]
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不同折叠类型蛋白中基于密码子的二级结构偏向性分析()
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《东南大学学报(自然科学版)》[ISSN:1001-0505/CN:32-1178/N]

卷:
34
期数:
2004年第1期
页码:
72-77
栏目:
生物医学工程
出版日期:
2004-01-20

文章信息/Info

Title:
Codon-based amino acid propensities for secondary structural units in proteins with different folding types
作者:
顾万君 周童 马建民 孙啸 陆祖宏
东南大学吴健雄实验室, 南京 210096
Author(s):
Gu Wanjun Zhou Tong Ma Jianmin Sun Xiao Lu Zuhong
Chien-Shiung Wu Laboratory, Southeast University, Nanjing 210096, China
关键词:
同义密码子使用 氨基酸二级结构偏向性 蛋白质二级结构预测 蛋白质折叠类型 蛋白设计
Keywords:
synonymous codon usage secondary structural propensity of amino acid protein secondary structure prediction protein folding type protein design
分类号:
Q52
DOI:
10.3969/j.issn.1001-0505.2004.01.017
摘要:
在传统的Chou-Fasman蛋白质二级结构预测方法的基础上引入同义密码子使用的信息,计算了200个蛋白(49种全α结构蛋白,69种全β结构蛋白,38种α+β结构蛋白,44种α/β结构蛋白)中不同密码子对应的氨基酸形成不同二级结构(α:螺旋,β:折叠,C:卷曲)的偏向性参数.通过对这些密码子对应氨基酸二级结构偏向性的分析,得到了氨基酸二级结构偏向性分析中所忽略的同义密码子的蛋白结构信息.这些新的信息量对于指导蛋白质设计以及提高蛋白质二级结构预测的准确率有着一定的作用.
Abstract:
We have integrated synonymous codon usage information into the amino acid propensities for different protein secondary structural units, which are traditionally used in protein secondary structure prediction method. Codon-based amino acid propensities for different protein secondary structural units in proteins with different folding types have been derived from 200 genes coding for proteins with different folding types(49 all alpha proteins, 69 all beta proteins, 38 alpha+beta proteins and 44 alpha/beta proteins). Protein secondary structure information, which is contained not only in amino acid sequences but also in mRNA sequences, is proposed in these synonymous codon specific amino acid propensity parameters. Detailed analysis shows that codon-based amino acid propensities are not all the same among different synonymous codons, while they are also different in different protein classes with different folding types. These codon-based amino acid propensities we proposed here are helpful to in vitro protein design and to improve the accuracy of protein secondary structure prediction.

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备注/Memo

备注/Memo:
基金项目: 国家自然科学基金资助项目(60121101).
作者简介: 顾万君(1977—),男,博士生,wanjungu@seu.edu.cn; 陆祖宏(联系人),男,博士,教授,博士生导师,zhlu@seu.edu.cn.
更新日期/Last Update: 2004-01-20