The three-dimensional organization of chromatin is shaped by nucleosome interactions and chromatin-associated proteins, yet how different proteins influence chromatin folding and stability remains unclear. Using our high-resolution sequence-specific coarse-grained protein and DNA models in molecular dynamics simulations, we examine how histone H1, heterochromatin protein 1 (HP1α) dimer, and a truncated Polyhomeotic (PHC3) protein affect the stability and folding pathways of a tetra-nucleosome array. These proteins have distinct chromatin-associated functions, but the mechanistic differences in how they modulate nucleosome interactions and chromatin architecture remain poorly understood. Our simulations aim to determine whether these proteins stabilize, disrupt, or reorganize the characteristic α-tetrahedron and β-rhombus conformations observed in chromatin fibers. By comparing their effects on chromatin compaction, flexibility, structural transitions, and molecular interactions we seek to uncover how these proteins differentially regulate chromatin folding.
