Energy profiles in detection of protein structure modifications

Abstract

Protein structure has a big impact on the protein's activity in the living cells. Conformational modifications as an effect of biochemical reactions or environmental influences cause changes in the conformational energy distributions. Therefore, observations of the energy characteristics allow to detect structural changes of selected proteins. Moreover, having entire sets of energy characteristics it is possible to compare given protein structure to other structures or search for similar structures in the set. In the paper, we present the method of similarity searching based on energy profiles. This method can be employed to detect protein structure modifications. In the method, we use distance matrices to find the alignment between two proteins on the energy level. Energy profiles are received in the computational process based on the molecular mechanics theory. Afterwards, these profiles can be stored in the special purpose database and used by the search engine. In the solution, additional protein features are extracted and stored. They may be used in the searching process in the preselection phase. At the end of the paper, we give some examples of the system usage regarding our recent research on protein kinases and their activity.