Hydropathy Conformational Letter and its Substitution Matrix HP-CLESUM: an Application to Protein Structural Alignment

TL;DR

This paper introduces a novel joint alphabet combining amino acid hydropathy and conformational letters, along with a substitution matrix, to improve protein structural alignment accuracy.

Contribution

It develops a hydropathy conformational letter (hp-CL) and a corresponding substitution matrix, enhancing protein structure comparison methods.

Findings

Optimized amino acid reduction improves information content.

The hp-CL matrix outperforms traditional systems in alignment accuracy.

Embedding hp-CL in alignment algorithms enhances performance on benchmark datasets.

Abstract

Motivation: Protein sequence world is discrete as 20 amino acids (AA) while its structure world is continuous, though can be discretized into structural alphabets (SA). In order to reveal the relationship between sequence and structure, it is interesting to consider both AA and SA in a joint space. However, such space has too many parameters, so the reduction of AA is necessary to bring down the parameter numbers. Result: We've developed a simple but effective approach called entropic clustering based on selecting the best mutual information between a given reduction of AAs and SAs. The optimized reduction of AA into two groups leads to hydrophobic and hydrophilic. Combined with our SA, namely conformational letter (CL) of 17 alphabets, we get a joint alphabet called hydropathy conformational letter (hp-CL). A joint substitution matrix with (17*2)*(17*2) indices is derived from FSSP. Moreover, we check the three coding systems, say AA, CL and hp-CL against a large database consisting proteins from family to fold, with their performance on the TopK accuracy of both similar fragment pair (SFP) and the neighbor of aligned fragment pair (AFP). The TopK selection is according to the score calculated by the coding system's substitution matrix. Finally, embedding hp-CL in a pairwise alignment algorithm, say CLeFAPS, to replace the original CL, will get an improvement on the HOMSTRAD benchmark.