Viral Nucleosome-Like Particles Exhibit Dynamic Flexibility and Reduced Thermodynamic Stability

Abstract

DNA packaging imposes fundamental physical constraints on genomes across the tree of life. However, most of our mechanistic understanding of these processes comes from the eukaryotic nucleosome, where highly basic histones, along with their flexible tails, coordinate DNA compaction and gene accessibility. Large DNA viruses challenge this paradigm by assembling nucleosome-like particles with a divergent histone architecture. These viral assemblies lack canonical histone tails, contain covalently fused domains linked by structured connectors, and exhibit altered surface electrostatics, features that collectively impose unique biophysical properties on viral chromatin. Here, we use multi-microsecond all-atom molecular dynamics simulations to dissect how histone fusion, tail loss, and connector architecture reshape the structural and thermo-dynamic behavior of the Melbournevirus nucleosome, a model system for studying viral chromatin organization. We find that viral systems exhibit elevated DNA unwrapping, weaker and more transient histone-DNA contacts, and localized flexibility at connector regions. Conformational adaptation at histone junctions partially offsets these effects, with structural shifts tuned to local DNA geometry during wrapping transitions. By capturing how nucleosome dynamics shift across time and sequence, our study reveals how conserved biophysical principles of chromatin architecture are reconfigured across life to meet distinct evolutionary demands.