Deuteration and selective labeling of alanine methyl groups of β-adrenergic receptor expressed in a baculovirus-insect cell expression system.

G protein-coupled receptors (GPCRs) exist in equilibrium between multiple conformations, and their populations and exchange rates determine their functions. However, analyses of the conformational dynamics of GPCRs in lipid bilayers are still challenging, because methods for observations of NMR signals of large proteins expressed in a baculovirus-insect cell expression system (BVES) are limited. Here, we report a method to incorporate methyl-CH-labeled alanine with > 45% efficiency in highly deuterated proteins expressed in BVES.

Protein F-labeling using transglutaminase for the NMR study of intermolecular interactions.

The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies.

Conductance of P2X4 purinergic receptor is determined by conformational equilibrium in the transmembrane region.

Ligand-gated ion channels are partially activated by their ligands, resulting in currents lower than the currents evoked by the physiological full agonists. In the case of P2X purinergic receptors, a cation-selective pore in the transmembrane region expands upon ATP binding to the extracellular ATP-binding site, and the currents evoked by α,β-methylene ATP are lower than the currents evoked by ATP. However, the mechanism underlying the partial activation of the P2X receptors is unknown although the crystal structures of zebrafish P2X4 receptor in the apo and ATP-bound states are available.

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment.

Rapid identification of ligand-binding sites by using an assignment-free NMR approach.

In this study, we developed an assignment-free approach for rapid identification of ligand-binding sites in target proteins by using NMR. With a sophisticated cell-free stable isotope-labeling procedure that introduces (15)N- or (13)C-labels to specific atoms of target proteins, this approach requires only a single series of ligand titrations with labeled targets. Using titration data, ligand-binding sites in the target protein can be identified without time-consuming assignment procedures.

The structure of brazzein, a sweet-tasting protein from the wild African plant Pentadiplandra brazzeana.

Brazzein is the smallest sweet-tasting protein and was isolated from the wild African plant Pentadiplandra brazzeana. The brazzein molecule consists of 54 amino-acid residues and four disulfide bonds. Here, the first crystal structure of brazzein is reported at 1.

Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.

Protein-protein interactions are necessary for various cellular processes, and therefore, information related to protein-protein interactions and structural information of complexes is invaluable. To identify protein-protein interfaces using NMR, resonance assignments are generally necessary to analyze the data; however, they are time consuming to collect, especially for large proteins. In this paper, we present a rapid, effective, and unbiased approach for the identification of a protein-protein interface without resonance assignments.

Crystal structure of Bifidobacterium Longum phosphoketolase; key enzyme for glucose metabolism in Bifidobacterium.

The crystal structure of Bifidobacterium longum phosphoketolase, a thiamine diphosphate (TPP) dependent enzyme, has been determined at 2.2A resolution. The enzyme is a dimer with the active sites located at the interface between the two identical subunits with molecular mass of 92.

Direct determination of the insulin-insulin receptor interface using transferred cross-saturation experiments.

Insulin initiates metabolic control by binding to the insulin receptor (IR) on target cells. Kinetic and mutational analyses have revealed two binding sites on the insulin molecule and the residues that compose them. However, direct determination of the insulin-IR interface is required to distinguish those residues that contribute to receptor binding from those required for structural stability.

Substrate specificity of microbial transglutaminase as revealed by three-dimensional docking simulation and mutagenesis.

Transglutaminases (TGases) are used in fields such as food and pharmaceuticals. Unlike other TGases, microbial transglutaminase (MTG) activity is Ca(2+)-independent, broadening its application. Here, a three-dimensional docking model of MTG binding to a peptide substrate, CBZ-Gln-Gly, was simulated.

A simple stabilization method of reduced albumin in blood and plasma for the reduced/oxidized albumin ratio measurement.

Albumin (Alb) is mixture of reduced and oxidized forms. It is physiologically significant to determine Alb(red)%, which is the proportion of reduced Alb in the sum of Alb. However, reduced Alb in both blood and plasma samples is easily converted to oxidized Alb.

Crystal structure and enhanced activity of a cutinase-like enzyme from Cryptococcus sp. strain S-2.

The structural and enzymatic characteristics of a cutinase-like enzyme (CLE) from Cryptococcus sp. strain S-2, which exhibits remote homology to a lipolytic enzyme and a cutinase from the fungus Fusarium solani (FS cutinase), were compared to investigate the unique substrate specificity of CLE. The crystal structure of CLE was solved to a 1.

Monitoring the hydrolysis and transglycosylation activity of alpha-glucosidase from Aspergillus niger by nuclear magnetic resonance spectroscopy and mass spectrometry.

Alpha-glucosidase from Aspergillus niger is an enzyme that catalyzes hydrolysis of alpha-1,4 linkages and transglucosylation to form alpha-1,6 linkages. In this study, an analytical method of oligosaccharides by nuclear magnetic resonance (NMR) was used to provide quantitative estimation of the fractions of each sugar unit and was applied to characterize the alpha-glucosidase reaction. Our data indicated that alpha-glucosidase reacts with the nonreducing end of oligosaccharides to form an alpha-1,6 linkage, and then a sugar unit with two alpha-1,6 linkages is gradually produced.

Proteome analysis for rat saliva.

Proteome analysis is a popular method to discover biomarkers for the prevention and diagnosis of diseases. Since saliva is a non-invasively available body fluid, gathering of saliva causes minimal harm to patients. Therefore, detection of proteins for the prevention and diagnosis from the saliva sample may be the preferred method, especially for children and elderly people.

Hepatectomy for hepatocellular carcinoma patients who meet the Milan criteria.

Background/aims: Although hepatocellular carcinoma patients who meet the Milan criteria are optimal candidates for liver transplantation, most such patients in Japan have been treated without liver transplantation.

Methodology: In this retrospective analysis, the patient selection criteria were (1) admission between 1992 and 2005, (2) fulfillment of the Milan criteria, (3) classification within the Barcelona Clinic Liver Cancer stages A1-A4, and (4) no previous anticancer treatment.

Results: Of 451 patients who met the selection criteria, 162 underwent hepatectomy.

[Structure and function changes of oxidized human serum albumin: physiological significance of the biomarker and importance of sampling conditions for accurate measurement].

Human serum albumin (HSA) exists in both reduced and oxidized forms, and the percentage of oxidized albumin increases in several diseases; however, little is known regarding the pathological and physiological significance of oxidation due to poor characterization of the precise structural and functional properties of oxidized HSA. Here, we characterize both structural and functional differences between reduced and oxidized HSA. Using LC-ESITOFMS and FTMS analysis, we determined that the major structural change in oxidized HSA in healthy human plasma is a disulfide-bonded cysteine at the thiol of Cys34 of reduced HSA.

Curculin exhibits sweet-tasting and taste-modifying activities through its distinct molecular surfaces.

Curculin isolated from Curculigo latifolia, a plant grown in Malaysia, has an intriguing property of modifying sour taste into sweet taste. In addition to this taste-modifying activity, curculin itself elicits a sweet taste. Although these activities have been attributed to the heterodimeric isoform and not homodimers of curculin, the underlying mechanisms for the dual action of this protein have been largely unknown.

Prognostic factors in patients with gemcitabine-refractory pancreatic cancer.

Objective: The purpose of this study was to identify prognostic factors in patients with gemcitabine-refractory pancreatic cancer and to determine criteria for selecting candidates for second-line treatment.

Methods: The records of 74 patients who were treated with gemcitabine (GEM) and followed up until disease progression were reviewed retrospectively. Sixteen clinical variables at the time of disease progression after GEM chemotherapy were chosen for analysis in this study.

Top-down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry.

A system of microchip capillary electrophoresis/electrospray ionization mass spectrometry (microchip-CE/ESI-MS) for rapid characterization of proteins has been developed. Capillary electrophoresis (CE) enables rapid analysis of a sample present in very small quantity, such as at femtomole levels, at high resolution. Faster CE/MS analysis is expected by downsizing the normal capillary to the microchip (microchip) capillary.

Effective novel dissociation methods for intact protein: heat-assisted nozzle-skimmer collisionally induced dissociation and infrared multiphoton dissociation using a Fourier transform ion cyclotron resonance mass spectrometer equipped with a micrometal electrospray ionization emitter.

Heating of a nano-electrospray ionization (nanoESI) source can improve the dissociation efficiency of collisionally induced dissociation (CID) methods, such as nozzle-skimmer CID (NS-CID) and infrared multiphoton dissociation (IRMPD), for large biomolecule fragmentation. A metal nanoESI emitter was used due to its resistance to heating above 250 degrees C. This novel method for the dissociation of large biomolecular ions is termed "heat-assisted NS-CID" (HANS-CID) or "heat-assisted IRMPD" (HA-IRMPD).

High performance in protease refolding by application of a continuous system using immobilized inhibitor.

In the reoxidative refolding of Streptomyces griseus trypsin, which is a serine protease having three S-S bonds per molecule, a synthetic inhibitor immobilized on agarose beads was applied in order to avoid the digestion of non-renatured protease molecules by renatured ones. A semi-continuous refolding system was fabricated by packing such inhibitor-immobilized gels in a glass column and the optimal operating conditions were investigated. Taking account of the effective conditions surveyed in the system, a continuous refolding system was constructed and operated to achieve higher performance.

Primary tumor of pancreatic cancer as a measurable target lesion in chemotherapy trials.

Background: It is unclear whether primary pancreatic cancer (PC) tumors can be accepted as measurable target lesions in chemotherapy trials. We reviewed recent PC patients to clarify the significance of their computed tomography (CT) responses of the primary tumor after chemotherapy.

Methods: The patient selection criteria were (i) having been admitted between January 2002 and December 2004, (ii) diagnosed as having histologically or cytologically proven adenocarcinoma of the pancreas, (iii) treated with chemotherapy with no previous anticancer treatment and (iv) having been evaluated by follow-up CT to assess the response according to the Response Evaluation Criteria in Solid Tumors criteria.

Treatment cost of pancreatic cancer in Japan: analysis of the difference after the introduction of gemcitabine.

Background: Recent advances in cancer chemotherapy have increased not only the survival rate but also the treatment cost, although there has been little interest in cost analyses in Japan.

Method: The actual cost of pancreatic cancer treatment was surveyed especially with respect to the difference after April 2001, which was the date that gemcitabine was introduced in Japan.

Results: A total of 113 patients were admitted consecutively from April 2000 to March 2002.