Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II

High-speed atomic force microscopy and 3D modeling reveal the structural dynamics of ADAR1 complexes

Targeting abnormal dysregulation of adenosine-to-inosine deamination by ADAR enzymes offers a promising therapeutic strategy in cancer research. However, the development of effective inhibitors is impeded by the incomplete structural information on ADAR1 complexes. In this study, we employ a combination of computational 3D modeling and high-speed atomic force microscopy to elucidate the atomic and molecular dynamics of ADAR1. Two distinct interface regions (IFx and IFy) on the surface of the deaminase domain and oligomerization structural models are identified. Single-molecule-level insights into the structural dynamics of ADAR1 reveal the oligomerization of ADAR1 monomers through the self-assembly of deaminase domains. In the presence of the substrate dsRNA, the N-terminal region, including RNA-binding domains, of ADAR1 dimer exhibits a controlled flexible conformation and promotes a stable dimeric interaction with dsRNA for RNA editing. These findings provide the basis for the development of targeted inhibitors to regulate ADAR1 activity in therapeutic applications.

Hierarchical Assembly of Hemin-Peptide Catalytic Systems on Graphite Surfaces

The formation of molecular hybrid systems with cofactors and peptides on graphite electrodes has recently been demonstrated. The design of peptide sequences is crucial for forming robust catalytic molecular systems on electrodes. However, the relationship between peptide sequences, molecular structure, and catalytic performance has not been fully explored. In this study, we employed peptides with simple dipeptide repeats, which effectively immobilize hemin, to construct a stable catalytic system and investigated the molecular basis of their self-assembly and catalytic activity by varying the sequence. Among peptides containing the dipeptide sequences (YH, VH, and LH), YH demonstrated the most efficient immobilization of hemin, which is catalytically active in electrochemical reactions. Using advanced molecular visualization techniques, specifically frequency modulation atomic force microscopy (FM-AFM), we characterized the well-ordered structures of these peptides on graphite electrodes, revealing their molecular-scale organization. Our findings in electrochemical characterizations include a quantitative evaluation of the surface density of hemin immobilized by self-assembled peptides and the catalytic activity of the peptide-hemin hybrid system under electrochemical conditions in the presence of H2O2. The strong peptide-peptide and peptide-hemin interactions, facilitated by π-π interactions of tyrosine residues, contribute to the system's stability and efficiency. The dipeptide repeats serve as a useful platform to investigate the role of important amino acids, beyond histidine, in stably immobilizing cofactors. These results highlight the potential for developing durable and efficient catalytic interfaces in electrochemical applications.

Multiple Mechanisms to Regulate Actin Functions: "Fundamental" Versus Lineage-Specific Mechanisms and Hierarchical Relationships

Eukaryotic actin filaments play a central role in numerous cellular functions, with each function relying on the interaction of actin filaments with specific actin-binding proteins. Understanding the mechanisms that regulate these interactions is key to uncovering how actin filaments perform diverse roles at different cellular locations. Several distinct classes of actin regulatory mechanisms have been proposed and experimentally supported. However, these mechanisms vary in their nature and hierarchy. For instance, some operate under the control of others, highlighting hierarchical relationships. Additionally, while certain mechanisms are fundamental and ubiquitous across eukaryotes, others are lineage-specific. Here, we emphasize the fundamental importance and functional significance of the following actin regulatory mechanisms: the biochemical regulation of actin nucleators, the ATP hydrolysis-dependent aging of actin filaments, thermal fluctuation- and mechanical strain-dependent conformational changes of actin filaments, and cooperative conformational changes induced by actin-binding proteins.

PQBP3/NOL7 is an intrinsically disordered protein

PQBP3 is a protein binding to polyglutamine tract sequences that are expanded in a group of neurodegenerative diseases called polyglutamine diseases. The function of PQBP3 was revealed recently as an inhibitor protein of proteasome-dependent degradation of Lamin B1 that is shifted from nucleolus to peripheral region of nucleus to keep nuclear membrane stability. Here, we address whether PQBP3 is an intrinsically disordered protein (IDP) like other polyglutamine binding proteins including PQBP1, PQBP5 and VCP. Multiple bioinformatics analyses predict that N-terminal region of PQBP3 is unstructured. High-speed atomic force microscopy (HS-AFM) reveals that N-terminal region of PQBP3 is dynamically changed in the structure consistently with the predictions of the bioinformatics analyses. These data support that PQBP3 is also an IDP.

Deciphering the actin structure-dependent preferential cooperative binding of cofilin

The mechanism underlying the preferential and cooperative binding of cofilin and the expansion of clusters toward the pointed-end side of actin filaments remains poorly understood. To address this, we conducted a principal component analysis based on available filamentous actin (F-actin) and C-actin (cofilins were excluded from cofilactin) structures and compared to monomeric G-actin. The results strongly suggest that C-actin, rather than F-ADP-actin, represented the favourable structure for binding preference of cofilin. High-speed atomic force microscopy explored that the shortened bare half helix adjacent to the cofilin clusters on the pointed end side included fewer actin protomers than normal helices. The mean axial distance (MAD) between two adjacent actin protomers along the same long-pitch strand within shortened bare half helices was longer (5.0-6.3 nm) than the MAD within typical helices (4.3-5.6 nm). The inhibition of torsional motion during helical twisting, achieved through stronger attachment to the lipid membrane, led to more pronounced inhibition of cofilin binding and cluster formation than the presence of inorganic phosphate (Pi) in solution. F-ADP-actin exhibited more naturally supertwisted half helices than F-ADP.Pi-actin, explaining how Pi inhibits cofilin binding to F-actin with variable helical twists. We propose that protomers within the shorter bare helical twists, either influenced by thermal fluctuation or induced allosterically by cofilin clusters, exhibit characteristics of C-actin-like structures with an elongated MAD, leading to preferential and cooperative binding of cofilin.

Unraveling the mechanisms and evolution of a two-domain module in IQGAP proteins for controlling eukaryotic cytokinesis

The IQGAP family of proteins plays a crucial role in cytokinesis across diverse organisms, but the underlying mechanisms are not fully understood. In this study, we demonstrate that IQGAPs in budding yeast, fission yeast, and human cells use a two-domain module to regulate their localization as well as the assembly and disassembly of the actomyosin ring during cytokinesis. Strikingly, the calponin homology domains (CHDs) in these IQGAPs bind to distinct cellular F-actin structures with varying specificity, whereas the non-conserved domains immediately downstream of the CHDs in these IQGAPs all target the division site, but differ in timing, localization strength, and binding partners. We also demonstrate that human IQGAP3 acts in parallel to septins and myosin-IIs to mediate the role of anillin in cytokinesis. Collectively, our findings highlight the two-domain mechanism by which IQGAPs regulate cytokinesis in distantly related organisms as well as their evolutionary conservation and divergence.

Technical advances in high-speed atomic force microscopy

It has been 30 years since the outset of developing high-speed atomic force microscopy (HS-AFM), and 15 years have passed since its establishment in 2008. This advanced microscopy is capable of directly visualizing individual biological macromolecules in dynamic action and has been widely used to answer important questions that are inaccessible by other approaches. The number of publications on the bioapplications of HS-AFM has rapidly increased in recent years and has already exceeded 350. Although less visible than these biological studies, efforts have been made for further technical developments aimed at enhancing the fundamental performance of HS-AFM, such as imaging speed, low sample disturbance, and scan size, as well as expanding its functionalities, such as correlative microscopy, temperature control, buffer exchange, and sample manipulations. These techniques can expand the range of HS-AFM applications. After summarizing the key technologies underlying HS-AFM, this article focuses on recent technical advances and discusses next-generation HS-AFM.