| 引用本文: | 于志芬,李瑞芳,黄俏.枯草芽孢杆菌同义密码子使用偏性对蛋白质折叠速率的影响[J].生物信息学,2014,12(4):. |
| YU Zhifen,LI Ruifang,HUANG Qiao.Influence of synonymous codon usage bias on protein folding rate of bacillus subtillis[J].Chinese Journal of Bioinformatics,2014,12(4):. |
|
| 摘要: |
| 目前，有关同义密码子使用偏性对蛋白质折叠的影响研究中，样本蛋白均来源于不同的物种。考虑到同义密码子使用偏性的物种差异性，选取枯草杆菌的核蛋白为研究对象。首先，将每条核蛋白按二级结构截取为α螺旋片段、β折叠片段和无规卷曲（α－β混合）片段，并计算其蛋白质折叠速率。然后，整理每个片段相应的核酸序列信息，计算其同义密码子使用度。在此基础上，分析枯草芽孢杆菌核蛋白的同义密码子使用偏性与蛋白质折叠速率的相关性。发现对于不同二级结构的肽链片段，都有部分密码子的使用偏性与其对应的肽链折叠速率显著相关。进一步分析发现，与肽链片段折叠速率显著相关的密码子绝大部分为枯草杆菌全序列或核蛋白序列的每一组同义密码子中使用度最高的密码子。结果表明，在蛋白质的折叠过程中，枯草芽孢杆菌的同义密码子使用偏性起着重要作用。 |
| 关键词: 枯草芽孢杆菌 同义密码子 蛋白质折叠速率 使用偏性 |
| DOI：10.3969/j.issn.1672-5565.2014-04.20140410 |
| 分类号: |
| 基金项目:内蒙古自治区自然科学基金(2012MS0115)；内蒙古自治区研究生教育创新计划(S20141013523)；内蒙古师范大学研究生科研创新基金( CXJJS14061)资助。 |
|
| Influence of synonymous codon usage bias on protein folding rate of bacillus subtillis |
|
YU Zhifen, LI Ruifang, HUANG Qiao
|
|
College of Physics and Electronic Information,Inner Mongolia Normal University, Hohhot 010022, China
|
| Abstract: |
| In the current study about the influence of synonymous codon usage bias on protein folding rate, the proteins are always derived from different species.In this article, considering the species differences of synonymous codon bias, the nucleoproteins of bacillus subtillis was selected as the samples.First, each of the nucleoprotein was cut into α-helices, β-strands and mixed-class segments according to their secondary structure.Then, the information of its corresponding mRNA sequence of each peptide segment was found, the synonymous codon usage bias and the protein folding rate of corresponding peptide segments were calculated.On this basis, the correlation between synonymous codon usage bias and the corresponding peptide folding rate of bacillus subtillis were analyzed. It was found that some of codon usage bias were significantly correlated with the protein folding rate of the peptide segments for different secondary structures.Further analysis found, most of codons significant correlated with peptide folding rate are the high RSCU value of bacillus subtillis complete sequences and ribosomal sequences.The results showed that the synonymous codon usage bias of bacillus subtillis plays an important role in protein folding. |
| Key words: Bacillus subtillis Synonymous codon Protein folding rate Using bias |
