Investigating Genome Organization and Regulation with Coarse-Grained Molecular Simulations


Among the multiscale hierarchy of computational simulations of the biomolecular systems, coarse-grained (CG) molecular dynamics (MD) simulations are used to study long-time behaviors of large systems. Here we present our recent developments of CG models for protein-DNA interactions and applications to genomic systems. We designed hydrogen-bond-based models for both sequence-specific and nonspecific protein-DNA interactions. With these renovations, we investigated the dynamics of the target search process of transcription factors on the highly rugged landscapes and the different scenarios of genome compaction assisted by eucaryotic histone and prokaryotic histone-like protein. On top of these, we explored the binding of pioneer transcription factors to nucleosomal DNA.

Okayama, Japan

Okayama 2018 BSJ meeting talk