GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins

Abstract

Structured tandem repeat proteins (STRPs) are characterized by preserved structural motifs arranged in a modular way. The structural and functional diversity of STRPs makes them particularly important for studying evolution, novel structure and function relationships, and ultimately for designing new synthetic proteins with specific functions. One crucial aspect of their classification is the estimation of geometrical parameters, which can provide better insight into their properties and the relationship between the spatial arrangement of repeated units and protein function. Calculating geometric descriptors for STRPs is challenging because naturally occurring repeats are not perfect and often contain insertions and deletions. Existing tools for predicting structural symmetry work well on simple cases but often fail for most natural proteins. Here we present GeomeTRe, an algorithm that calculates geometrical descriptors such as curvature (yaw), twist (roll), and pitch for a protein structure with known repeat unit positions. The algorithm simulates the movement of consecutive units, identifies rotational axes, and calculates the corresponding Tait-Bryan angles. The parameters of GeomeTRe can enhance STRP annotation and classification by identifying variations in geometric arrangements among different functional groups. The package is fast and suitable for processing large protein structure datasets when repeat region information (e.g., from RepeatsDB) is available. GeomeTRe is available as a Python package; source code and documentation can be found at https://github.com/BioComputingUP/GeomeTRe