Construction of the plasmid, expression by Chinese hamster ovary cell, purification and characterization of the first three short consensus repeat modules of human complement receptor type 1.

Short consensus repeat (SCR1-3), the first three SCR modules from N-terminus of type 1 complement receptor (CR1), is expected to accelerate dissociation of complement components and suppress complement activity by binding the main component of complement C4b. In order to clarify the three-dimensional structure, which triggers the activity of SCR1-3 on complement, we constructed an over-expression system in CHO DG44 cells which facilitated mass production of SCR1-3. The mass production was achieved by a two-stage culture system and optimum culture conditions using ASF104N medium and MTX-, NaBu-containing alpha-MEM/10% FBS medium, respectively.

Crystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells.

Parasporin-2 is a protein toxin that is isolated from parasporal inclusions of the Gram-positive bacterium Bacillus thuringiensis. Although B. thuringiensis is generally known as a valuable source of insecticidal toxins, parasporin-2 is not insecticidal, but has a strong cytocidal activity in liver and colon cancer cells.

Supramolecular complex formation and crystallization of isocitrate dehydrogenase from Thermus thermophilus HB8: preliminary studies with X-Ray crystallography and atomic force microscopy.

Atomic force microscopy (AFM) observation of a crystal surface of the thermostable isocitrate dehydrogenase (ICDH) from a thermophilic eubacterium, Thermus thermophilus HB8, suggested that the crystal consists of huge homo-complexed ellipsoidal bodies of the protein, with averaged long- and short-axis diameters of 18.6 nm and 10.9 nm respectively.

Linking the clinical vocabulary of diseases to the genes by mapping UMLS to OMIM allelic variant fields.

To link clinical vocabulary of diseases to gene entries in Online Mendelian Inheritance in Man (OMIM), we comprehensively matched diseases from Unified Medical Language System (UMLS) Metathesaurus to the OMIM text in Allelic Variant fields that describe relations between the mutations or polymorphisms of the genes and the phenotypes. Out of 1,786 genes having the field, 1,445 genes (80.9%) had matches with 2,417 types of diseases or disorders.

Stawamycin analog, JBIR-11 from Streptomyces viridochromogenes subsp. sulfomycini NBRC 13830.

A stawamycin analog, JBIR-11 (1) was isolated from mycelium of Streptomyces viridochromogenes subsp. sulfomycini NBRC 13830. The structure was determined on the basis of the spectroscopic data.

CAATT/enhancer-binding proteins alpha and delta interact with NKX2-1 to synergistically activate mouse secretoglobin 3A2 gene expression.

Secretoglobin (SCGB) 3A2 is a small molecular weight secreted protein predominantly expressed in lung airways. We previously demonstrated that the expression of SCGB3A2 is regulated by homeodomain transcription factor NKX2-1. Here we show that CCAAT/enhancer-binding proteins, C/EBPalpha and C/EBPdelta, regulate mouse Scgb3a2 gene transcription in vivo and in vitro by binding to specific sites located in the Scgb3a2 promoter and the activity is synergistically enhanced through cooperative interaction with NKX2-1.

A thermostable dolichol phosphoryl mannose synthase responsible for glycoconjugate synthesis of the hyperthermophilic archaeon Pyrococcus horikoshii.

Dolichol phosphoryl mannose synthase (DPM synthase) is an essential enzyme in the synthesis of N- and O-linked glycoproteins and the glycosylphosphatidyl-inositol anchor. An open reading frame, PH0051, from the hyperthermophilic archaeon Pyrococcus horikoshii encodes a DPM synthase ortholog, PH0051p. A full-length version of PH0051p was produced using an E.

A novel antimycin-like compound, JBIR-06, from Streptomyces sp. ML55.

A novel compound of antimycin family, JBIR-06 (1), was isolated from Streptomyces sp. ML55. The structure of 1 was established as a twelve-membered macrocyclic skeleton with a 3-(formylamino)-2-hydroxybenzamide based on the spectroscopic data.

Improved secretion of human Fas ligand extracellular domain by N-terminal part truncation in Pichia pastoris and preparation of the N-linked carbohydrate chain trimmed derivative.

Human Fas ligand is a medically important transmembrane glycoprotein directing the induction of apoptosis. The influence of N-terminal part (Q103-P138) truncation of human Fas ligand extracellular domain (hFasLECD) on the expression of N-terminal FLAG-(Gly)(5)-tagged hFasLECD (NFG5-hFasLECD) with partial N-glycosylation-sites deletion in Pichia pastoris was investigated. The N-terminal part truncation significantly improved the secretion level of both singly (N184Q) and doubly (N184Q, N250Q) N-glycosylation-sites deleted NFG5-hFasLECD.

Structure of six-transmembrane cation channels revealed by single-particle analysis from electron microscopic images.

Six-transmembrane (6-TM) cation channels are plasma membrane-integral components of cellular signaling pathways conserved in almost all species, including animals, plants and some kinds of prokaryotes. These channels selectively permeate cations in response to various signals. In excitable and non-excitable mammalian cells, 6-TM cation channels play fundamental roles, including the generation of action potential and its transmission, the regulation of intracellular ion concentrations, and the activation of signaling cascades by humoral or mechanical pathways.

Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions.

Background: It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and their positional distribution.

Results: We predicted the positions of 228 known binding motifs for transcription factors in phylogenetically conserved regions within -2000 and +1000 bp of transcriptional start sites (TSSs) of human genes and visualized their correlated non-overlapping occurrences. In the 8,454 significantly correlated motif pairs, two major classes were observed: 248 pairs in Class 1 were mainly found around TSSs, whereas 4,020 Class 2 pairs appear at rather arbitrary distances from TSSs.

Gold nanoparticles used as a carrier enhance production of anti-hapten IgG in rabbit: a study with azobenzene-dye as a hapten presented on the entire surface of gold nanoparticles.

The azobenzene moiety, well-known not only for its reversible cis-to-trans photoisomerization but also as a hapten, does not induce antibodies on its own, but it reacts with antibodies raised against conjugates with protein carriers. Hence we selected azobenzene dye as an indicator to assess the possibility of having gold nano-particles act as an immunological carrier instead of protein carriers. In rabbits, we confirmed an in vivo response against azobenzene dye presented on the entire surface of gold nanoparticles (azo-nanoparticles), where the gold nanoparticles appeared to play a role as a carrier for the hapten.

Improvement of protein-compound docking scores by using amino-acid sequence similarities of proteins.

The low accuracy of predicted docking scores is critical at in silico drug screening. In order to improve the accuracy of docking scores, we approximated the protein-compound binding free energy as a linear combination of the raw docking scores of a target compound with many different protein pockets. The coefficients of the linear combination were estimated by the similarities among proteins, simply by using the amino-acid sequence similarities or identities of the proteins.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts.

The motor protein prestin is a bullet-shaped molecule with inner cavities.

Prestin is a transmembrane motor protein localized at the outer hair cells (OHCs) of the mammalian inner ear. Voltage-dependent conformational changes in prestin generate changes in the length of OHCs. A loss of prestin function is reported to induce severe auditory deficiencies, suggesting prestin-dependent changes of OHC length may be at least a part of cochlear amplification.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology information is prerequisite for further studies. However, detection of orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, are utilized.

Novel GRP78 molecular chaperone expression down-regulators JBIR-04 and -05 isolated from Streptomyces violaceoniger.

In the course of our screening program for regulators of the expression of GRP78 molecular chaperone, JBIR-04 (1) and -05 (2) were isolated from Streptomyces violaceoniger 4541-SVS3 as congeners of prunustatin A (3). The structures of 1 and 2 were determined by the analyses of the spectroscopic data. These compounds mainly consist of an amino acid and amino acid derived alpha-hydroxy acid residues.

Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin.

The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD-containing NADH-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3).

Docking of protein molecular surfaces with evolutionary trace analysis.

We have developed a new method to predict protein- protein complexes based on the shape complementarity of the molecular surfaces, along with sequence conservation obtained by evolutionary trace (ET) analysis. The docking is achieved by optimization of an object function that evaluates the degree of shape complementarity weighted by the conservation of the interacting residues. The optimization is carried out using a genetic algorithm in combination with Monte Carlo sampling.

A novel nuclear export inhibitor JBIR-02, a new piericidin discovered from Streptomyces sp. ML55.

A new member of the piericidin family, JBIR-02, was isolated from mycelium of Streptomyces sp. ML55 together with two known piericidin derivatives, piericidin A(1) and IT-143-B. The structure was determined on the basis of spectroscopic data.

Effect of a sodium ion on the dehydration-induced phase transition of monoclinic lysozyme crystals.

A monoclinic lysozyme crystal grown in NaCl solution was transformed into a new monoclinic crystal form by controlled dehydration. This crystal-to-crystal phase transition was accompanied by 20-40% solvent loss and the transformed crystal diffracted to prominently high resolution. The structures of the native and transformed crystals were determined at 1.

Prediction of protein-ligand complex structure by docking software guided by other complex structures.

We developed a new scoring method that selects a protein-ligand complex structure with higher geometrical accuracy than the top-scoring complex structure, using the structural information of known protein-ligand complexes. To apply this method, one or more protein-ligand complex structures must be known for the target protein. A number of predicted structures were generated by the protein-compound docking program for a new ligand, and one of these structures, which showed the maximum overlap with the ligand coordinates of the known protein-ligand complex, was selected as the most probable complex structure.

Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.

Understanding the structural basis of thermostability and thermoactivity, and their interdependence, is central to the successful future exploitation of extremophilic enzymes in biotechnology. However, the structural basis of thermostability is still not fully characterized. Ionizable residues play essential roles in proteins, modulating protein stability, folding and function.