Multiscale Computational Models to Investigate the Role of Phase Separation in Biology

Project Summary The formation of biomolecular condensates through phase separation is emerging as an important mechanism for cellular organization and function. The frequent observation of these condensates at sites of DNA damage, during stress response, and as a precursor to pathological aggregates in vivo has generated significant interest in their potential roles in cellular function. However, the relationship between protein sequence and formation, microstructural organization, and dynamics of biomolecular condensates is only beginning to be probed. Our belief is that a synergistic combination of computer modeling integrated with experimental techniques such as NMR, microscopy, and microrheology, to name a few, can provide the best path toward uncovering the underlying relationship between amino acid sequence and phase separation. Our strategy to elucidate the molecular origins of phase separation in biology involves utilizing innovative models and methods developed by us in close collaboration with leading experimentalists to reconstitute biologically relevant phase separation systems in silico, thereby translating our extensive knowledge of the molecular determinants of phase separation of proteins, to biologically relevant processes. Our proposed future work aims to develop and utilize multiscale computational methods from the atomic to the mesoscale level to build a molecular mechanistic framework for the predictive modeling of phase separation in essential biological processes. Our efforts will focus on two biological problems of significant interest. The first part of the project will focus on the phase separation of RNA binding proteins and their role in DNA damage repair and transcriptional condensates formed by fusion oncoproteins. The second part of the project will aim to provide a detailed molecular picture of phase separated protein assemblies in chromatin organization as it pertains to the co-phase separation of heterochromatin protein 1 (HP1) family with other chromatin-associated proteins and satellite RNA in constitutive heterochromatin formation, HP1 proteins in gene expression and cancer drug resistance, and the role of phase separation of polyhomeotic protein (PhP) in chromatin regulation. These approaches will generate detailed molecular-level information on the assembly of many components into heterochromatin assemblies and provide the background knowledge needed to better understand its regulation and disease relevance.