A unique approach for protein secondary structure comparison under TOPS representation

To unravel the intricate connection between protein function and protein structure, it is imperative to comprehensively evaluate protein secondary structure similarity from various perspectives. While numerous techniques have been suggested for comparing protein secondary structure elements (SSE), there continues to be a substantial need for finding alternative ways of comparing the same. In this paper, Topology of Protein Structure (TOPS) representations of protein secondary structures are considered to offer a new alignment-free method for evaluating similarities/dissimilarities of protein secondary structures. Initially, a two-dimensional numerical representation of the SSE is created, associating each point with a mass reflecting its frequency of occurrence. Then the means of coordinate values are determined by averaging weighted sums, and these mean values are subsequently used to calculate moments-of-inertia. Next, a four-component descriptor is generated out of the eigenvalues of the matrix and the mean values of the represented coordinates. Thereafter, Manhattan distance measure is used to obtain the distance matrix. This is finally applied to obtain the phylogenetic trees under the use of NJ method. SSE considered in the proposed method comprises 36-elements from the Chew-Kedem database giving five different taxa: globin, alpha-beta, tim-barrel, beta, and alpha. Phylogenetic trees were created for these SSE through the application of various methods: Clustal-Omega, LZ-Complexity, SED, TOPS + and TOC, to facilitate comparative analysis. Phylogenetic tree of the proposed method outperformed results of the previous methods when applied to the same SSE. Therefore, the method effectively constructs phylogenetic tree for analyzing protein secondary structure comparison.