The KcsA channel is a prototypical potassium channel, exhibiting pH-dependent gating. The structure of the transmembrane pore-domain of the KcsA channel was examined using atomic force microscopy (AFM) under the membrane-embedded condition. In the closed conformation, the cytoplasmic end of the pore domain was protruded from the membrane surface. In the open conformation, the open pore at the center of the tetrameric channel was resolved, and the protrusion was substantially shortened relative to the closed conformation. High-speed AFM revealed the clustering–dispersion dynamics upon pH changes, and this collective behavior was closely related to the gating conformational changes.
MazF is an mRNA interferase, which cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest. During normal growth conditions, the MazF toxin is inactivated through binding to its cognate antitoxin, MazE. How MazF specifically recognizes its mRNA target and carries out cleavage and how the formation of the MazE-MazF complex inactivates MazF remain unclear. We determined crystal structures of MazF in complex with mRNA substrate and antitoxin MazE in Bacillus subtilis. In this review, I present the mechanism of the sequence-specific RNA recognition of MazF and the neutralization of MazF activity by MazE antitoxin.
A wide class of dynamical systems exhibit early signals of state transitions, such as increased fluctuations. Here, we show that prefrontal neurons exhibit increased fluctuations in firing prior to switching codes for behavioral goals. We also demonstrated that decreasing the stability of neural network models resulted in increased firing variability before bifurcations. These results suggest that dynamical transitions in neural networks underlie prefrontal functioning, enabling flexible adaptation in ever-changing environments.
The proteasome is a 2.5-MDa multisubunit protease complex that degrades polyubiquitylated proteins. Although its functions and structure have been extensively characterized, little is known about its molecular dynamics in living cells. By using fluorescence correlation spectrometry, a method for quantitative imaging, we determined the absolute concentration, dynamics, and complex formation of the proteasome in living cells. The proteasome is a highly mobile complex and almost all proteasome subunits are stably incorporated into the proteasomes. We also revealed that the proteasome completes its assembly process in the cytoplasm and translocates into the nucleus as a holoenzyme.
In the F1-ATPase complex, the conformational change of the catalytically active β subunit is propagated to the entire α3β3 ring, resulting in an asymmetry in the hexamer. With the sequential nucleotide perturbations, the asymmetrical α3β3 structure changes from one state to the other, which rotates the γ subunit axis. Basically, the two elements: the β structural change and the asymmetrical α3β3 are essential for the molecular motor rotation. Therefore, we have been studying them using molecular dynamics (MD) simulations. The results in a series of our studies deepen the understanding of the rotational mechanism of the motor.
Since nearly all protein molecules acting in cell are working dynamically, dynamic aspects of them are indispensable to understand each biological system. Recent advances in synchrotron-based crystallography and computational chemistry have allowed to provide dynamic aspect in high-resolution crystal structures. Here we review our structural and functional studies on multi-drug efflux transporter, AcrB. Crystal structure analysis and molecular dynamics (MD) simulation are complemental techniques. And synergy between them makes static crystal structures more animate. Proton is another nuisance in protein crystallography, since it is almost invisible technically. MD simulation can allow systematic examination of protonation states in titratable residues.