Aligning Multiple Protein Structures using Biochemical and Biophysical Properties

TL;DR

This paper introduces msTALI, a progressive algorithm for aligning multiple protein structures based on biochemical and biophysical properties, revealing structural and functional similarities.

Contribution

The paper presents a novel alignment algorithm that incorporates biochemical and biophysical properties for multiple protein structure alignment, improving functional residue alignment.

Findings

Successfully aligned kinase family structures and functional residues.

Effectively aligned acyl carrier protein family members, including modeled structures.

Demonstrated the algorithm's utility in revealing structural and functional similarities.

Abstract

Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an algorithm (msTALI) for aligning multiple protein structures using biochemical and biophysical properties, including torsion angles, secondary structure, hydrophobicity, and surface accessibility. The algorithm is a progressive alignment algorithm motivated by popular techniques from multiple sequence alignment. It has demonstrated success in aligning the major structural regions of a set of proteins from the s/r kinase family. The algorithm was also successful at aligning functional residues of these proteins. In addition, the algorithm was also successful in aligning seven members of the acyl carrier protein family, including both experimentally derived as well as computationally modeled structures.