Molecular codes in motion Simulations of specificity, stability, and structural adaptation in protein-DNA complexes

Molecular Codes in Motion: Simulations of Specificity, Stability, and Adaptation in Protein-DNA Complexes examines protein-DNA interactions with a focus on the Histone-like Nucleoid Structuring protein (H-NS), an architectural protein that regulates bacterial chromatin organization and gene expression. Using molecular dynamics (MD), steered MD, and metadynamics simulations, the dissertation demonstrates that H-NS preferentially binds AT-rich DNA, inducing sequence-dependent structural changes such as minor groove widening, local undertwisting, and DNA bending. Experimental validation using fluorescence spectroscopy and circular dichroism confirms that H-NS binds ApT-rich DNA more tightly than GpC-rich sequences, and induces local A-like DNA conformations. A key contribution is the development of a computational framework to model protein-DNA dissociation and estimate free energy differences using contact maps and Jarzynski’s equality. This thesis also introduces MDNA, a Python software tool for constructing and analysing DNA structures using a rigid base model, which enables detailed geometric and topological analysis and modification of nucleic acid assemblies. By integrating simulation and experiment, the dissertation advances our understanding of sequence-specific DNA recognition, structural adaptation, and chromatin regulation, with broader implications for bacterial gene control and computational modelling of protein-DNA interactions.