Search

Finding any regularity in the sequences of proteins and determining their correlation with structural features are of great interest for an understanding of molecular biology. We statistically analyzed the relative frequencies of all 400 possible dipeptides in a data set containing randomly selected proteins of different defined structural classes including all-alpha, all-beta, alpha + beta and alpha/beta families. We found that the distribution of dipeptides is not the same for different structural classes, and some of them are significantly far from a random distribution. A tendency of a given amino acid to localize in the first or second position of a dipeptide depending on the structural class of protein was also found. Interestingly, some amino acids may be substituted for each other in the first or second positions of specific dipeptides in each structural class. This finding apparently contrasts with the routine expectation from the viewpoint of amino acid properties, as classically understood. [ABSTRACT FROM AUTHOR]

Previous researches have shown that relevant words to the main topic of a given text have a long-range correlation in their spatial distribution, while common words are randomly distributed. Inspired by the features of human-written texts, in the present study, we have used non-extensive statistical mechanics for ranking dipeptides in proteomes of prokaryotes and eukaryotes. The ranking is performed based on the correlation between the words' spatial distributions. It is found that some representative dipeptides have higher values of the non-extensivity parameter, and the majority of dipeptides are randomly distributed in their respective proteomes. Interestingly, the number of random-distributed dipeptides in evolutionary higher organisms is greater than those in prokaryotes. It concluded that reduction in the number of clustered dipeptides; provide a more effective energy optimization to overcome energetic challenges in more complex organisms. Also the reduction of the dipeptides clustering in the proteome of eukaryotes could be effectively compensated by higher clustering of CG dinucleotide at the genome level, that are used to control and optimize the gene expression. • In linguistics, keywords of a given text are clustered. • Cystein has the highest clustering level in proteomes. • Number of clustered dipeptides in eukaryotes is lower than those in prokaryotes. • Increasing the information entropy leads to energy optimization in eukaryotes. [ABSTRACT FROM AUTHOR]