Alignment of protein structure energy patterns represented as sequences of Fuzzy Numbers

Abstract

The comparative analysis of structural and energy features of proteins can be a key to understand how proteins work and interact to each other in cellular reactions. Potential energy, which is a function of atomic positions in a protein structure, can be used to describe molecule's abilities to interact with other biological molecules. Potential energy characteristics are supportive in searching similar, biologically important molecular regions that have similar functions in different organisms or organs. In the paper, we present the similarity searching method, which base on the alignment of energy patterns. In the alignment phase energy patterns are represented as sequences of fuzzy numbers. This increases the fault-tolerance of the alignment and ensures the approximate character of the method. The alignment of fuzzy sequences is one of the main steps in the new FN-EAST method (Fuzzy Numbers -Energy Alignment Search Tool). The FN-EAST allows to seek similar structural regions represented as energy patterns. The new alignment incorporated in the similarity searching eliminates some weaknesses of the FN-EAST predecessors.

eProS – A Bioinformatics Knowledgebase, Toolbox and Database for Characterizing Protein Function

“…Recent studies have demonstrated that sequences of energy values, referred to as energy profiles, obtained from protein structures using fine and coarse-grained energy models can be used to characterize protein functionality and structural features [10,11,7,9]. Mrozek et al had introduced a dynamic programming approach for generating energy profile alignments [10,11].…”

“…Mrozek et al had introduced a dynamic programming approach for generating energy profile alignments [10,11]. Furthermore, they had shown that energy profile alignment analyses can be employed to investigate the changes of conformational energy distributions that can be caused by structural rearrangements as results of f.e.…”

“…To implement an automated energy profile generation pipeline for large-scale analyses thus becomes challenging. However, such analyses can be of interest in structural biology, as entire protein folds and families can be investigated in the focus of characterizing and understanding the energetic features that determine protein structure, stability and function [10,11,7,9].…”

eProS—a database and toolbox for investigating protein sequence–structure–function relationships through energy profiles

“…They have shown that pairwise comparisons and detected energy profile similarities can lead to the identification of proteins assigned to the same protein families. Additionally, conformational modifications as a result of enzymatic reactions or, in general, protein–environment interactions can be inspected (7,10,11). These studies substantiate the possible fields of application of energy profile-based methods.…”

“…Because of the semi-automatic computation and error-prone nature often implicated by all-atom-based models, generating data sets on a large scale, for example, comparable with the Protein Data Bank (PDB) (12), becomes difficult. This holds especially if physics-based approaches are used as proposed by Kozielski and colleagues (7,10,11). …”