Protein-compound docking is a key technology in structure-guided drug development (SGDD), and some combinations of computational methods including the protein-compound docking have been used in the SGDD. Ligand-binding site prediction is the first step in the SGDD. The second step is the ensemble docking, in which compounds in a database are docked onto the protein surfaces of a structural ensemble of the target protein. The third step is the information analysis of the docking results. Finally, suitable docking results are selected for an assay experiment. Topics around the protein-compound docking and the SGDD are briefly explained.
Actin assembly activates ATP hydrolysis, which provides structural cues for flament turnover. Polymerized actin supports cellular signaling, intracellular trafficking, and cytokinesis. We present the cryo-electron microscopic structure of F-actin in the presence of phosphate, with the visualization of some α-helical backbones and large side chains. A complete atomic model based on the cryo-EM identified intermolecular interactions, some of which were mediated by magnesium or phosphate ions. A critical role for bending of the proline-rich loop (residues 108-112) in activating ATPase was revealed. Crystal structures of G-actin mutants, which trap the catalytic site in two intermediate states, were solved. These structures combined with cryo-EM data allows us to propose a molecular mechanism for actin assembly and ATPase activation, critical for filament dynamics.
F-actin is a helical assembly of actin, an essential component of muscle fibers for contraction, and plays crucial roles in numerous cellular processes, such as lamellipodia and filopodia as the most abundant component and regulator of cytoskeletons by dynamic assembly and disassembly processes (from G-actin to F-actin and vice versa). While actin is a ubiquitous protein and is involved in important biological functions, the definitive high-resolution structure of F-actin remains unknown. Here we report the F-actin structure at 6.6 Å resolution, made obtainable by recent advances in electron cryomicroscopy. The density map clearly resolves all the secondary structures, such as α-helices, β-structures and loops, having made unambiguous modeling and refinement possible. Complex domain motions that open up the nucleotide binding pocket upon F-actin formation, specific D-loop and terminal conformations, and relatively tight axial but markedly loose interprotofilament interactions of hydrophilic nature revealed in the F-actin model all appear to be important for dynamic functions of actin.
So far stimuli-responsive polymer gels and their application to smart materials have been widely studied. On the other hand, as a novel biomimetic gel, we have been studying gels with an autonomous self-oscillating function, since firstly reported in 1996. We succeeded in developing novel self-oscillating polymers and gels by utilizing the oscillating reaction, called the Belousov-Zhabotinsky (BZ) reaction. The self-oscillating polymer is composed of a poly(N-isopropylacrylamide) network in which the catalyst for the BZ reaction is covalently immobilized. In the presence of the reactants, the polymer gel undergoes spontaneous cyclic swelling-deswelling changes or soluble-insoluble changes (in the case of uncrosslinked polymer) without any on-off switching of external stimuli. Potential applications of the self-oscillating polymers and gels include several kinds of functional material systems, such as biomimetic actuators and mass transport surface.