Conformational variability in proteins bound to single-stranded DNA: a new benchmark for new docking perspectives

TL;DR

This paper introduces a new benchmark based on protein-ssDNA structures from the PDB to evaluate conformational changes and improve docking methods for ssDNA-protein interactions.

Contribution

It creates the first comprehensive benchmark for protein-ssDNA conformational variability, facilitating the development of better docking algorithms.

Findings

Identified 91 bound-unbound protein structure groups

Analyzed conformational changes induced by ssDNA binding

Performed docking experiments with ATTRACT software

Abstract

We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included in the benchmark. For the 91 sequence-identity groups identified as bound-unbound structures of the same protein, we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions, and compared it to the supposedly binding-induced modifications. To illustrate a use case of this benchmark, we performed docking experiments using ATTRACT docking software. This benchmark is, to our knowledge, the first one made to peruse available structures of ssDNA-protein interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.