Randomness in the Primary Structure of Protein: Methods and Implications

Abstract

It is no doubt that the evolutionary process is affected by chance, but the question is to what extent the chance plays its role. The random analysis can throw light on the underlying reasoning for the primary structure of proteins. With the use of random principles, we have explored three approaches to analyse protein primary structure, i.e. the randomness in the construction of amino-acid sequences, in the follow-up amino acid, and in the distribution of amino acid/amino acids. As the results, (i) we can evaluate the impact of chance on the composition of aminoacid sequences by comparing the measured probability/frequency with the predicted probability/ frequency; (ii) we can evaluate the impact of chance on the follow-up amino acid by comparing the Markov transition probability with the predicted conditional probability; and (iii) we can evaluate the effect of chance on the distribution of amino acids by comparing the real distribution probability with the theoretical distribution probability. These approaches can be used to quantitatively analyse the primary structure of intra-protein as well as inter-proteins, thus we can get more insights into the mechanisms of protein construction, mutation, and evolutionary process. Also, these approaches may have some potential use for development of new drugs.