Cellular Crowded Environments

Inside cells, proteins, RNA, and other biomolecules reach concentrations of 200-400 mg/mL, occupying roughly 20–40% of the cellular volume. The intracellular environment is therefore highly crowded, and this macromolecular crowding strongly influences the structure, dynamics, and function of biomolecules. At the same time, this environment is itself created by biomolecules within the cell, raising a fundamental question: how do biomolecules collectively generate and function within such crowded environments?

Recent studies have also revealed that intrinsically disordered proteins and RNA can form biomolecular condensates through liquid–liquid phase separation. These condensates act as dynamic platforms for cellular processes such as signal transduction, while in some cases serving as precursors to disease-related aggregates.

To date, we have been actively simulating crowded environments containing a large number of different proteins; moving forward, we aim to elucidate systems involving nucleic acids such as DNA and RNA along with proteins, as well as the interactions between cell membranes and droplets. We also hope to gain new insights into the molecular mechanisms of biological phenomena directly involving droplets, such as signal transduction and transcription.

Computational Study of Intracellular Environments

• Protein Hydration and Stability
• Protein Ligand Binding
• All-atom MD Simulations of Bacterial Cytoplasm
• Regulating of Biomolecular Droplets