Molecular rewiring and compensatory mechanisms sustain DNA recognition in mutant ZTA transcription factor: insights from molecular dynamics simulations

Abstract

Protein-DNA complexes are stabilized by various interactions forming an interaction network between the protein and DNA molecules. Any change in the system - whether through mutations in the protein or DNA, external factors, or protein conformational transitions -- can alter this interaction network, thereby affecting structural and functional aspects. Employing all-atom classical molecular dynamics, we investigated how the interaction network in the ZTA TF-DNA is rewired when key arginine residues in ZTA are mutated to oppositely charged glutamic acids. Using the MMPBSA technique, we calculated per-residue binding energies for all systems and correlated binding affinity with structural features. Our detailed mechanistic study shows that when key arginine residues are mutated, new interactions are formed either around the mutation site and/or in other ZTA monomer. Through load-sharing, the system attempts to counter-balance the interaction load, leading to reorganization of the interaction network. As the number of mutations increases from single-to-double site, the system is able to partially maintain its structural stability. However, with multi-site mutations, even after reorganization of the interaction network, system cannot sustain its structural stability and therefore becomes destabilized. Despite the structural symmetry of the ZTA TF, we observed asymmetric monomer contributions upon mutation. Overall, our rigorous mechanistic studies provide deeper insights into the mechanism of interaction network reorganization in ZTA-DNA system. These comprehensive insights may be useful for tuning binding affinity and structural adaptability under adverse conditions. Since ZTA is a key factor in the Epstein-Barr virus (EBV), this study will be central to understanding DNA recognition and developing drug therapeutics targeting viral transcription factors in EBV.