Membraneless organelles (MLOs) are condensates that compartmentalize and thereby facilitate specific biological functions. Multivalent interactions between RNA and protein components elicit phase separation to form MLOs. Many MLOs are multiple-layered, and the physiological properties of each layer contribute to MLO functions. MLOs sequestrate specific factors to promote/suppress the biological reaction in which they are involved. MLOs are also known to associate with specific chromosomal loci to place genes in the appropriate sub-nuclear environment for regulating their expression. Reflecting the physiological importance of MLOs, aberrant morphologies of MLOs and mutations in MLO components have been reported in various tumors and diseases.

Recent biochemical and microscopic measurements have revealed fluctuating chromatin structures of 10^–7 to 10^–5 m. These structures are intrinsically related to DNA transcription and replication; therefore, elucidating the physical principles of chromatin structural dynamics is essential for understanding cell functions. A three-dimensional computational model of the whole human genome was developed through the physics-based bottom-up approach, which quantitatively explained various genomic and microscopic data on chromatin. The model suggests that the difference in the functional activity among chromatin domains leads to the heterogeneous domain movement in the genome, which entropically drives chromatin phase separation to form A and B compartments.

During collective migration of epithelial cells, leader cells show sustained ERK activity, while follower cells exhibit oscillatory ERK activation in conjunction with the intercellular propagation of the ERK activity. These different ERK activations govern the spatiotemporal organization of cell specification and coordinated movement. By employing the visualization and manipulation of cell signaling activity with biosensors and optogenetic tools, we revealed that free space-dependent cell protrusions and intercellular pulling forces are required for the ERK activation dynamics in the leader and follower cells, respectively. These findings highlight the novel aspects of growth factor signaling pathways dependent on physical and mechanical stimuli.

Hydrogen bond (H-bond) is an essential factor for the secondary structure formation in proteins. In this review, we will introduce our recent studies in which H-bond interaction energies in three helical secondary structures were systematically analyzed by using the negative fragmentation approach (NFA). We found that the H-bond energies in the helical conformations are weaker than those of the isolated ones. We conclude that H-bond destabilization is originated from the depolarization of the H-bond acceptor and donor groups by their neighboring peptide groups and that the difference of the orientation of neighboring groups cause differences in H-bond energies.