Li Rui-Fang, Li Hong
School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
Protein Pept Lett. 2010 Jul;17(7):881-8. doi: 10.2174/092986610791306652.
Taking all the proteins of four virus genomes as samples, the segments of alpha-helix and beta-strand in proteins of the four viruses were obtained. Linear regression analyses between the average polarities and the folding rates of peptide chains were performed for alpha-helices and beta-strands respectively. The results indicated that the folding rates show significant positive linear correlation for alpha-helices and negative linear correlation for beta-strands with the average polarities. Based on the corresponding protein coding sequences of these amino acid segments, the influences of GC content of palindromes and palindrome densities in protein coding segments on the relations between the folding rates and the average polarities were studied. Results showed that the folding rates correlated positively with the GC content of palindromes and the palindrome density, and protein coding sequences do carry the information which can influence the folding rates of peptide chains or protein structures. Our analysis indicated that this kind of effects mostly comes from the information palindrome structure itself or from the synonymous codon usage, but not from the translation information from codons to amino acids.
以四种病毒基因组的所有蛋白质为样本，获得了这四种病毒蛋白质中的α螺旋和β链片段。分别对α螺旋和β链的肽链平均极性与折叠速率进行线性回归分析。结果表明，α螺旋的折叠速率与平均极性呈显著正线性相关，β链的折叠速率与平均极性呈负线性相关。基于这些氨基酸片段的相应蛋白质编码序列，研究了蛋白质编码片段中回文序列的GC含量和回文密度对折叠速率与平均极性之间关系的影响。结果表明，折叠速率与回文序列的GC含量和回文密度呈正相关，并且蛋白质编码序列确实携带了能够影响肽链折叠速率或蛋白质结构的信息。我们的分析表明，这种影响主要来自回文结构本身的信息或同义密码子的使用，而不是来自密码子到氨基酸的翻译信息。
