The cofilin family accelerates actin dynamics in the cell by more than 100 times, by enhancing severing and depolymerization. We predicted that fluctuations in the actin filament are essential for cofilin binding based on the cryo-EM structure of the cofilin-bound actin filament, and this has been confirmed by several recent studies with many collaborators. Three types of fluctuations—1) actin domain fluctuation, 2) D-loop fluctuation, and 3) fluctuations of the helical twist—regulate cofilin binding without altering the averaged structure. This highlights the importance of protein fluctuation, not only in understanding how cofilin functions, but also in broader biological contexts.

In metazoan cells, microtubules (MTs), intermediate filaments (IFs), and actin filaments (AFs) are involved in maintaining cell integrity and regulating cell motility. Unlike MTs and AFs, IFs are nonpolar filaments composed of elongated units. It has been postulated that type 3 IFs and AFs interact directly, which may facilitate the organization of cytoplasmic networks. We observed colocalization between desmin IFs (type 3 IFs in muscle cells) and AFs in cell-sized droplets in vitro via fluorescence microscopy. Direct observation of individual desmin IFs and moving AFs on myosins demonstrated a nematic behavior of AFs along desmin IFs due to loose interactions.

The actin cytoskeleton drives various biological functions, including intracellular positioning of the nucleus and mitotic spindle, and cell motility. To gain physical insights into the regulatory mechanisms, we use water-in-oil droplets containing cytoplasmic extracts as a model system. We successfully reconstituted the symmetric/asymmetric positioning of a nucleus-sized object and actomyosin-based cell motility. A combination of physical modeling and molecular perturbation experiments identified the key physical parameters responsible for these processes, highlighting the roles of mechanical interactions among cytoskeletal proteins in organizing intracellular structures and biological functions.

Just as humans build houses, some unicellular organisms also construct structures outside their bodies. In testate amoebae, the mother cell constructs a shell for the daughter cell in the extracellular, template-free space before cell division. During the process of shell construction, testate amoebae show surprisingly complex behavior. How do unicellular organisms without eyes, hands, or brains construct a shell outside the cell? In this review, we introduce recent findings on the process of shell construction and the shell structure of the testate amoeba Paulinell micropora.

Proteins perform various functions in living organisms, and understanding their 3D structures is essential to understanding their functions. The 3D Zernike descriptor (3DZD) provides a compact, rotationally and translationally invariant description of protein surface shapes. These features are desirable when applying 3DZD to describe the shape of proteins. Therefore, 3DZD is widely used for comparing protein structures and for shape-based searches. In this review, we describe the properties of 3DZD and their various applications in protein structure analysis.