Comprehensive in silico characterization of Arabidopsis thaliana RecQl helicases through structure prediction and molecular dynamics simulations

Abstract

Helicases are ubiquitous enzymes with specific functions that contribute to almost all nucleic acid metabolic processes. The RecQ helicase family is essential for integrity in all organisms through DNA replication, repair, and recombination. This study investigated five RecQ-like helicases in Arabidopsis thaliana (AtRecQl) that exhibit diverse structural and physiochemical attributes and functions. Cis-regulatory element analysis identified stress, hormone, cell cycle, and development-responsive modules involved in various events in plant growth and development. Gene ontology analysis revealed that the five AtRecQl were associated with various cellular components, molecular functions, and biological processes. Protein-protein interaction analysis also implicated some in various abiotic stress processes. Structural analysis and molecular dynamics (MD) simulations were performed to examine conformational stability through root means square deviation and radius of gyration, showing stable AtRecQl protein structures. Free energy landscape analysis validated thermodynamically stable structures throughout the MD simulation. Principle component analysis and probability density functions from MD simulations provided satisfactory structural variational data for the complexes and limited coordinate movements. These insights might greatly benefit future studies.