Study on the Influences of Palindromes in Protein Coding Sequences on the Folding Rates of Peptide Chains

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 indicates that this kind of effect mostly comes from the information of palindrome structure itself or from the synonymous codon usage, but not from the translation information from codons to amino acids.