Molecular Mechanism for the Regulation of Rho-Kinase by Dimerization and Its Inhibition by Fasudil

SummaryRho-kinase is a key regulator of cytoskeletal events and a promising drug target in the treatment of vascular diseases and neurological disorders. Unlike other protein kinases, Rho-kinase requires both N- and C-terminal extension segments outside the kinase domain for activity, although the details of this requirement have been elusive. The crystal structure of an active Rho-kinase fragment containing the kinase domain and both the extensions revealed a head-to-head homodimer through the N-terminal extension forming a helix bundle that structurally integrates the C-terminal extension. This structural organization enables binding of the C-terminal hydrophobic motif to the N-terminal lobe, which defines the correct disposition of helix αC that is important for the catalytic activity. The bound inhibitor fasudil significantly alters the conformation and, consequently, the mode of interaction with the catalytic cleft that contains local structural changes. Thus, both kinase and drug conformational pliability and stability confer selectivity

Interaction between the CheY response regulator and the histidine-containing phosphotransfer (HPt) domain of the ArcB sensory kinase in Escherichia coli

AbstractBacteria have devised sophisticated His–Asp phosphorelay signaling systems for eliciting a variety of adaptive responses to their environment. The histidine-containing phosphotransfer (HPt) domain, found in many signal transduction protein, functions as a mediator of the His–Asp phosphorelay. The ArcB anaerobic sensor of E. coli contains such a HPt domain, although its function is not fully understood. In this study, we provide in vivo and in vitro evidence that the HPt domain is capable of interacting with the CheY receiver, which contains a phospho-accepting aspartate residue

Real-time TIRF observation of vinculin recruitment to stretched α-catenin by AFM

Adherens junctions (AJs) adaptively change their intensities in response to intercellular tension; therefore, they integrate tension generated by individual cells to drive multicellular dynamics, such as morphogenetic change in embryos. Under intercellular tension, α-catenin, which is a component protein of AJs, acts as a mechano-chemical transducer to recruit vinculin to promote actin remodeling. Although in vivo and in vitro studies have suggested that α-catenin-mediated mechanotransduction is a dynamic molecular process, which involves a conformational change of α-catenin under tension to expose a cryptic vinculin binding site, there are no suitable experimental methods to directly explore the process. Therefore, in this study, we developed a novel system by combining atomic force microscopy (AFM) and total internal reflection fluorescence (TIRF). In this system, α-catenin molecules (residues 276–634; the mechano-sensitive M1-M3 domain), modified on coverslips, were stretched by AFM and their recruitment of Alexa-labeled full-length vinculin molecules, dissolved in solution, were observed simultaneously, in real time, using TIRF. We applied a physiologically possible range of tensions and extensions to α-catenin and directly observed its vinculin recruitment. Our new system could be used in the fields of mechanobiology and biophysics to explore functions of proteins under tension by coupling biomechanical and biochemical information

Mechano-adaptive sensory mechanism of α-catenin under tension

The contractile forces in individual cells drive the tissue processes, such as morphogenesis and wound healing, and maintain tissue integrity. In these processes, α-catenin molecule acts as a tension sensor at cadherin-based adherens junctions (AJs), accelerating the positive feedback of intercellular tension. Under tension, α-catenin is activated to recruit vinculin, which recruits actin filaments to AJs. In this study, we revealed how α-catenin retains its activated state while avoiding unfolding under tension. Using single-molecule force spectroscopy employing atomic force microscopy (AFM), we found that mechanically activated α-catenin fragment had higher mechanical stability than a non-activated fragment. The results of our experiments using mutated and segmented fragments showed that the key intramolecular interactions acted as a conformational switch. We also found that the conformation of α-catenin was reinforced by vinculin binding. We demonstrate that α-catenin adaptively changes its conformation under tension to a stable intermediate state, binds to vinculin, and finally settles into a more stable state reinforced by vinculin binding. Our data suggest that the plastic characteristics of α-catenin, revealed in response to both mechanical and biochemical cues, enable the functional-structural dynamics at the cellular and tissue levels

The PHCCEx domain of Tiam1/2 is a novel protein- and membrane-binding module

Tiam1 and Tiam2 (Tiam1/2) are guanine nucleotide-exchange factors that possess the PH–CC–Ex (pleckstrin homology, coiled coil and extra) region that mediates binding to plasma membranes and signalling proteins in the activation of Rac GTPases. Crystal structures of the PH–CC–Ex regions revealed a single globular domain, PHCCEx domain, comprising a conventional PH subdomain associated with an antiparallel coiled coil of CC subdomain and a novel three-helical globular Ex subdomain. The PH subdomain resembles the β-spectrin PH domain, suggesting non-canonical phosphatidylinositol binding. Mutational and binding studies indicated that CC and Ex subdomains form a positively charged surface for protein binding. We identified two unique acidic sequence motifs in Tiam1/2-interacting proteins for binding to PHCCEx domain, Motif-I in CD44 and ephrinB's and the NMDA receptor, and Motif-II in Par3 and JIP2. Our results suggest the molecular basis by which the Tiam1/2 PHCCEx domain facilitates dual binding to membranes and signalling proteins

A comprehensive survey on quantum computer usage: How many qubits are employed for what purposes?

Quantum computers (QCs), which work based on the law of quantum mechanics, are expected to be faster than classical computers in several computational tasks such as prime factoring and simulation of quantum many-body systems. In the last decade, research and development of QCs have rapidly advanced. Now hundreds of physical qubits are at our disposal, and one can find several remarkable experiments actually outperforming the classical computer in a specific computational task. On the other hand, it is unclear what the typical usages of the QCs are. Here we conduct an extensive survey on the papers that are posted in the quant-ph section in arXiv and claim to have used QCs in their abstracts. To understand the current situation of the research and development of the QCs, we evaluated the descriptive statistics about the papers, including the number of qubits employed, QPU vendors, application domains and so on. Our survey shows that the annual number of publications is increasing, and the typical number of qubits employed is about six to ten, growing along with the increase in the quantum volume (QV). Most of the preprints are devoted to applications such as quantum machine learning, condensed matter physics, and quantum chemistry, while quantum error correction and quantum noise mitigation use more qubits than the other topics. These imply that the increase in QV is fundamentally relevant, and more experiments for quantum error correction, and noise mitigation using shallow circuits with more qubits will take place.Comment: 14 pages, 5 figures, figures regenerate

Structure of the RecQ C-terminal Domain of Human Bloom Syndrome Protein

Bloom syndrome is a rare genetic disorder characterized by genomic instability and cancer predisposition. The disease is caused by mutations of the Bloom syndrome protein (BLM). Here we report the crystal structure of a RecQ C-terminal (RQC) domain from human BLM. The structure reveals three novel features of BLM RQC which distinguish it from the previous structures of the Werner syndrome protein (WRN) and RECQ1. First, BLM RQC lacks an aromatic residue at the tip of the β-wing, a key element of the RecQ-family helicases used for DNA-strand separation. Second, a BLM-specific insertion between the N-terminal helices exhibits a looping-out structure that extends at right angles to the β-wing. Deletion mutagenesis of this insertion interfered with binding to Holliday junction. Third, the C-terminal region of BLM RQC adopts an extended structure running along the domain surface, which may facilitate the spatial positioning of an HRDC domain in the full-length protein

Structure of dimerized radixin FERM domain suggests a novel masking motif in C-terminal residues 295–304

The crystal structure of dimerized radixin FERM domain has been determined. It was found that the adhesion molecule-binding site of one molecule is masked by the C-terminal residues of the other molecule

Crystallographic characterization of the membrane-targeting domains of the Rac-specific guanine nucleotide-exchange factors Tiam1 and Tiam2

The membrane-targeting domains of the Rac-specific guanine nucleotide-exchange factors Tiam1 and Tiam2 were purified and crystallized