Detection of hidden periodicity in protein sequences and its correlation with structure and function of proteins

摘要

This paper is directed to advance the mathematical methods of to reveal the hidden periodicity in biomolecular symbolic sequences and to apply them to particular questions of structure-function relationships in proteins. The abilities to predict thestructure and function of a protein based on its primary structure have ever been in the center of attention in bioinformatic research, and their importance is vastly increasing in the postgenomic era. Here we state that at least some of domainlevel structures have latent periodicities in their primary structure. They can be described using the periodic position-weight matrix, also called profile matrix, and then easily detected the way similar to common profile searches, using the novel notion of cyclic alignment. The results we obtained show that this is the case for many NAD-binding domains of oxidoreductases, and the period is close to 24 in that case. We noted that this periodicity may be involved by specific structure of NAD-binding site, knownfor the alternation of alpha helices and anti-parallel beta layers in it.