Distributions Of Palindromes And Their Influences On Protein Folding Rate

Palindromes which contain the information of sequences and structures,are a kind of rotational symmetry structure.They widely exist in the genome sequences eukaryotes and prokaryotes,and also play a crucial role in these genes.Some studies have shown that many diseases are closely related with the palindromes,such as male sterility,leukemia,nerve fibroma,hypertrophic osteoarthropathy and so on.These diseases are caused by the variations of palindromes.So far the characteristics and functions of palindromes yet and further research need to be prospected in the future.For palindromes of some species,the characteristics of palindrome frequency as well as palindrome abundance and palindrome density have been studied in this work.Besides,the protein folding is one of the most important research subjects in molecular biology.Among them,the protein folding rate has become a hot area in recent years.At present,the researches on protein folding rate are mostly based on the protein structures,environment and amino acid sequences etc.Besides,the fact that mRNA sequences may also have the factors which can influence the protein folding rates has been shown in other studies.It has been noticed that in the point of sequence,palindromes reflect the characteristics of RNA hereditary language,and in the point of structure,palindromes are the basic units of constituting RNA structures.If the protein folding rate is also affected by mRNA,it could be shown in palindromes.Inspired by this idea,the influences of various parameters of palindromes on the protein folding rates have been analyzed.Specific content is as follows:1.The information of RNA from all the coronavirus was collected in the NCBI,and the palindromes in the each sequence were calculated,characteristic quantity such as palindrome frequency,palindrome abundance and palindrome density was analyzed.The result indicated the value of palindrome abundance decreased with palindrome length increasing,more short palindromes,and less long palindromes.And some special long palindromes in individual viruses may influence the structure or function of the virus has been founded.2.Based on the related literatures and a few small database of protein folding rates,the proteins that contained the information of protein folding rates were collected.According to the database of PDB ? EMBL and NCBI's cross-reference,the corresponding mRNA information was found.Palindrome frequency and palindrome density of palindromes in the each mRNA were calculated,and a large protein database including palindromes' parameters was set up.3.The influence of palindrome frequency on the protein folding rates was analyzed,and the result indicated the protein folding rates showed negative correlation with the palindrome frequency for all proteins.And palindrome frequency of palindromes which length is four has significant correlation with its corresponding protein folding rates.For different secondary structure protein,palindrome frequency of mixed-class proteins showed better correlation with the corresponding protein folding rates.According to different classification of fold type,the correlation between palindrome frequency and multi-state protein folding rates was founded stronger.The palindrome frequency reflects the complexity of mRNA sequence,and this complexity affects the extension speed of the peptide chain,and then affects the protein folding rates.4.The influence of palindrome density on the protein folding rates was analyzed.The results showed that the protein folding rates correlated negatively with the palindrome density for all proteins.For different sort of proteins(secondary structure class and folding class),the correlation between palindrome density and the protein folding rate had huge differences.As further analysis shown,what plays a crucial role on theprotein folding rate is the repeated used bases group in palindromes,which reflects the mRNA sequence variability,and this variability can affect the extension speed of the peptide chain.So palindrome density becomes an important factor influencing the protein folding rate.