Application of complex demodulation on bZIP and bHLH-PAS protein domains

Proteins are built with molecular modular building blocks such as an α-helix, β-sheet, loop region and other structures. This is an economical way of constructing complex molecules. Periodicity analysis of protein sequences has allowed us to obtain meaningful information concerning their structure, function and evolution. In this work, complex demodulation (CDM) is introduced to detect functional regions in protein sequences data. More specifically, we analyzed bZIP and bHLH-PAS protein domains. Complex demodulation provided insightful information about changing amplitudes of periodic components in protein sequences. Furthermore, it was found that the local amplitude minimum or local amplitude maximum of the 3.6-aa periodic component is associated with protein structural or functional information due to the observation that the extrema are mainly located in the boundary area of two structural or functional regions.