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Soichi Takeda

Publications and source records attributed to Soichi Takeda.

11 recordsLinked to original sources
PubMed2006

Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom.

VAPs are haemorrhagic snake-venom toxins belonging to the reprolysin family of zinc metalloproteinases. In vitro, VAPs induce apoptosis specifically in cultured vascular endothelial cells. VAPs have a modular structure that bears structural homology to mammalian ADAMs (a disintegrin and metalloproteinases). VAP1 is a homodimer with a MW of 110 kDa in which the monomers are connected by a single disulfide bridge. VAP2 is homologous to VAP1 and exists as a monomer with a MW of 55 kDa. In the current study, several crystal forms of VAP1 and VAP2 were obtained using the vapour-diffusion method and diffraction data sets were collected using SPring-8 beamlines. The best crystals of VAP1 and VAP2 generated data sets to 2.5 and 2.15 angstroms resolution, respectively.

Animals↗
PubMed2006

Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms.

The crescent-shaped BAR (Bin/Amphiphysin/Rvs-homology) domain dimer is a versatile protein module that senses and generates positive membrane curvature. The BAR domain dimer of human endophilin-A1, solved at 3.1 A, has a unique structure consisting of a pair of helix-loop appendages sprouting out from the crescent. The appendage's short helices form a hydrophobic ridge, which runs across the concave surface at its center. Examining liposome binding and tubulation in vitro using purified BAR domain and its mutants indicated that the ridge penetrates into the membrane bilayer and enhances liposome tubulation. BAR domain-expressing cells exhibited marked plasma membrane tubulation in vivo. Furthermore, a swinging-arm mutant lost liposome tubulation activity yet retaining liposome binding. These data suggested that the rigid crescent dimer shape is crucial for the tubulation. We here propose that the BAR domain drives membrane curvature by coordinate action of the crescent's scaffold mechanism and the ridge's membrane insertion in addition to membrane binding via amino-terminal amphipathic helix.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Crystal structure of CHP2 complexed with NHE1-cytosolic region and an implication for pH regulation.

The plasma membrane Na+/H+ exchangers (NHE) require calcineurin B homologous protein (CHP) as an obligatory binding partner for ion transport. Here, we report the first crystal structure of CHP (CHP2 isoform) in complex with its binding domain in NHE1. We show that the cytoplasmic alpha-helix of NHE1 is inserted into the hydrophobic cleft formed by N- and C-lobes of CHP2 and that the size and shape of this crevice together with hydrogen bond formation at multiple positions assure a high degree of specificity for interaction with NHE members. Structure-based mutagenesis revealed the importance of hydrophobic interactions between CHP/NHE1 for the function of NHE1. Furthermore, the crystal structure shows the existence of a protruding CHP-unique region, and deletion of this region in CHP2 inhibited the NHE1 activity by inducing the acidic shift of intracellular pH dependence, while preserving interaction with NHE1. These findings suggest that CHP serves as an obligatory subunit that is required both for supporting the basic activity and regulating the pH-sensing of NHE1 via interactions between distinct parts of these proteins.

Amino Acid Sequence↗
PubMed2006

Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold.

ADAMs (a disintegrin and metalloproteinase) are sheddases possessing extracellular metalloproteinase/disintegrin/cysteine-rich (MDC) domains. ADAMs uniquely display both proteolytic and adhesive activities on the cell surface, however, most of their physiological targets and adhesion mechanisms remain unclear. Here for the first time, we reveal the ADAMs' MDC architecture and a potential target-binding site by solving crystal structures of VAP1, a snake venom homolog of mammalian ADAMs. The D-domain protrudes from the M-domain opposing the catalytic site and constituting a C-shaped arm with cores of Ca2+ ions. The disintegrin-loop, supposed to interact with integrins, is packed by the C-domain and inaccessible for protein binding. Instead, the hyper-variable region (HVR) in the C-domain, which has a novel fold stabilized by the strictly conserved disulfide bridges, constitutes a potential protein-protein adhesive interface. The HVR is located at the distal end of the arm and faces toward the catalytic site. The C-shaped structure implies interplay between the ADAMs' proteolytic and adhesive domains and suggests a molecular mechanism for ADAMs' target recognition for shedding.

ADAM Proteins↗
PubMed2006

Preparation of protein crystals for X-ray structural study.

The knowledge of accurate molecular structures obtained by X-ray protein crystallography is now inevitable for rational drug design and for understanding the molecular basis underlying genetic disorders found in patients. However, preparing protein crystals suitable for structural analysis is currently the bottleneck in structure determination by this method. The intent of this chapter is to present current methods of preparing protein crystals for structural studies for a wide range of biologists who have access to macromolecules but do not know how to handle them for crystallization. The chapter includes the pretreatment of a protein prior to the crystallization experiment, initial screens, and optimization of the crystallization conditions for further X-ray study. Finally, handling considerations that are important for a protein intended for crystallization experiments are discussed.

Crystallization↗
PubMed2006

[Nano -level imaging for analyzing protein structure and function].

The present manuscript outlines the nano-level imaging project, which is under promotion by the three national research institutes and supported by a research grant from the Ministry of Health, Labor and Welfare (nano-001). This research project targets collecting fundamental information regarding comprehensive understanding of cardiovascular, neurological and the other disorders, developing new diagnostic and therapeutic methods by visualizing protein structure and function in atomic(sub-nano level) or molecular (nano-level) resolution. The results of the current projects will be extended into drug design, clinical diagnostic technology and medical materials in near future.

Nanotechnology↗
PubMed2005

Crystallization and preliminary crystallographic analysis of the human calcineurin homologous protein CHP2 bound to the cytoplasmic region of the Na+/H+ exchanger NHE1.

Calcineurin homologous protein (CHP) is a Ca2+-binding protein that directly interacts with and regulates the activity of all plasma-membrane Na+/H+-exchanger (NHE) family members. In contrast to the ubiquitous isoform CHP1, CHP2 is highly expressed in cancer cells. To understand the regulatory mechanism of NHE1 by CHP2, the complex CHP2-NHE1 (amino acids 503-545) has been crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as precipitant. The crystals diffract to 2.7 A and belong to a tetragonal space group, with unit-cell parameters a = b = 49.96, c = 103.20 A.

Calcineurin↗
PubMed2005

Crystal structure of troponin and the molecular mechanism of muscle regulation.

Troponin plays a central role in the regulation of skeletal and cardiac muscle contraction. The protein consists of three polypeptide chains (TnT, TnI and TnC) and is located on polymerized actin together with tropomyosin, forming muscle thin filament. We have determined the molecular structures of the core domains (relative molecular mass of 46,000 and 52,000) of human cardiac troponin in the Ca2+-saturated form by X-ray crystallography. Analysis of the four structures derived from the two crystal forms reveals that the core domain is further divided into sub-domains, connected by linkers, making the entire molecule highly flexible. The structures of the troponin ternary complex suggests that the Ca2+-binding to the regulatory TnC site displaces the carboxyl-terminal portion of TnI from actin/tropomyosin, thereby altering mobility and/or flexibility of the troponin/tropomyosin strand on the actin filament. These Ca2+-dependent changes in the properties of the tropomyosin strand on the actin filament may in turn alter accessibility of myosin heads (motor protein) to the actin filament.

Calcium↗
PubMed2003

Structure of the core domain of human cardiac troponin in the Ca(2+)-saturated form.

Troponin is essential in Ca(2+) regulation of skeletal and cardiac muscle contraction. It consists of three subunits (TnT, TnC and TnI) and, together with tropomyosin, is located on the actin filament. Here we present crystal structures of the core domains (relative molecular mass of 46,000 and 52,000) of human cardiac troponin in the Ca(2+)-saturated form. Analysis of the four-molecule structures reveals that the core domain is further divided into structurally distinct subdomains that are connected by flexible linkers, making the entire molecule highly flexible. The alpha-helical coiled-coil formed between TnT and TnI is integrated in a rigid and asymmetric structure (about 80 angstrom long), the IT arm, which bridges putative tropomyosin-anchoring regions. The structures of the troponin ternary complex imply that Ca(2+) binding to the regulatory site of TnC removes the carboxy-terminal portion of TnI from actin, thereby altering the mobility and/or flexibility of troponin and tropomyosin on the actin filament.

Calcium↗