G-CSF receptor-binding cyclic peptides designed with artificial amino-acid linkers

Designing small molecules that mimic the receptor-binding local surface structure of large proteins such as cytokines or growth factors is fascinating and challenging. In this study, we designed cyclic peptides that reproduce the receptor-binding loop structures of G-CSF. We found it is important to select a suitable linker to join two or more discontinuous sequences and both termini of the peptide corresponding to the receptor-binding loop. Structural simulations based on the crystallographic structure of KW-2228, a stable and potent analog of human G-CSF, led us to choose 4-aminobenzoic acid (Abz) as a part of the linker. A combination of 4-Abz with beta-alanine or glycine, and disulfide bridges between cysteins or homocysteins, gave a structure suitable for receptor binding. In this structure, the side-chains of several amino acids important for the interactions with the receptor are protruding from one side of the peptide ring. This artificial peptide showed G-CSF antagonistic activity in a cell proliferation assay.     

Structures of homoleptic eight- and nine-coordinate uranium(IV) perchlorate complexes with sulfoxide molecules as ligands

Homoleptic eight- and nine-coordinate U(IV) perchlorate complexes with sulfoxide ligands have been characterized crystallographically. Crystals of [U(dmso)₈](ClO₄)₄ · 0.75CH₃NO₂, [U(dmso)₉](ClO₄)₄ · 4dmso (dmso = dimethyl sulfoxide), and [U(tmso)₈](ClO₄)₄ · 2tmso (tmso = tetramethylene sulfoxide) were found to have dodecahedral, tricapped trigonal prismatic, and square antiprismatic geometries, respectively. Average U-O bond distances in [U(dmso)₈](ClO₄)₄ · 0.75CH₃NO₂, [U(dmso)₉](ClO₄)₄ · 4dmso, and [U(tmso)₈](ClO₄)₄ · 2tmso are 2.35(3), 2.41 (4), and 2.35(3) Å, respectively. Furthermore, it was found that [U(dmso)₈]⁴⁺ is in equilibrium with [U(dmso)₉]⁴⁺ in CH₃NO₂ solution containing dmso. Thermodynamic parameters for such an equilibrium are as follows: K (25 °C) = 3.4 ± 0.2 dm³ mol⁻¹, ΔH = −54.9 ± 4.5 kJ mol⁻¹, and ΔS = −174 ± 15 J K⁻¹ mol⁻¹.     

A possible role of vimentin on the cell surface for the activation of latent transforming growth factor-β

Latent TGF-β (LTGF-β) has to be converted to active TGF-β for its activities. Previously, we reported that certain fragments of latency associated peptide (LAP) augmented LTGF-β activation via increase in binding of LTGF-β to the endothelial cell (EC) surface followed by cell-associated proteolysis. By searching for EC membrane proteins crosslinked with the LAP fragment, we identified the molecule bound to LAP fragment as vimentin. Moreover, the LAP fragment-induced LTGF-β activation was attenuated by anti-vimentin antibody. These results indicate that binding of the LAP fragment to vimentin on the cell surface is indispensable for LTGF-β activation by the LAP fragment.

Structured summary

MINT-6806227:vimentin (uniprotkb:P48616) binds (MI:0407) to LAP (uniprotkb:P18341) by competition binding (MI:0405)MINT-6806183:LAP (uniprotkb:P18341) binds (MI:0407) to vimentin (uniprotkb:P48616) by cross-linking studies (MI:0030)     

Abundance of Zetaproteobacteria within crustal fluids in back‐arc hydrothermal fields of the Southern Mariana Trough

To extend knowledge of subseafloor microbial communities within the oceanic crust, the abundance, diversity and composition of microbial communities in crustal fluids at back‐arc hydrothermal fields of the Southern Mariana Trough (SMT) were investigated using culture‐independent molecular techniques based on 16S rRNA gene sequences. Seafloor drilling was carried out at two hydrothermal fields, on‐ and off‐ridge of the back‐arc spreading centre of the SMT. 16S rRNA gene clone libraries for bacterial and archaeal communities were constructed from the fluid samples collected from the boreholes. Phylotypes related to Thiomicrospira in the Gammaproteobacteria (putative sulfide‐oxidizers) and Mariprofundus in the Zetaproteobacteria (putative iron‐oxidizers) were recovered from the fluid samples. A number of unique archaeal phylotypes were also recovered. Fluorescence in situ hybridization (FISH) analysis indicated the presence of active bacterial and archaeal populations in the fluids. The Zetaproteobacteria accounted for up to 32% of the total prokaryotic cell number as shown by FISH analysis using a specific probe designed in this study. Our results lead to the hypothesis that the Zetaproteobacteria play a role in iron oxidation within the oceanic crust.     

Direct and efficient production of ethanol from cellulosic material with a yeast strain displaying cellulolytic enzymes

For direct and efficient ethanol production from cellulosic materials, we constructed a novel cellulose-degrading yeast strain by genetically codisplaying two cellulolytic enzymes on the cell surface of Saccharomyces cerevisiae. By using a cell surface engineering system based on alpha-agglutinin, endoglucanase II (EGII) from the filamentous fungus Trichoderma reesei QM9414 was displayed on the cell surface as a fusion protein containing an RGSHis6 (Arg-Gly-Ser-His(6)) peptide tag in the N-terminal region. EGII activity was detected in the cell pellet fraction but not in the culture supernatant. Localization of the RGSHis6-EGII-alpha-agglutinin fusion protein on the cell surface was confirmed by immunofluorescence microscopy. The yeast strain displaying EGII showed significantly elevated hydrolytic activity toward barley beta-glucan, a linear polysaccharide composed of an average of 1,200 glucose residues. In a further step, EGII and beta-glucosidase 1 from Aspergillus aculeatus No. F-50 were codisplayed on the cell surface. The resulting yeast cells could grow in synthetic medium containing beta-glucan as the sole carbon source and could directly ferment 45 g of beta-glucan per liter to produce 16.5 g of ethanol per liter within about 50 h. The yield in terms of grams of ethanol produced per gram of carbohydrate utilized was 0.48 g/g, which corresponds to 93.3% of the theoretical yield. This result indicates that efficient simultaneous saccharification and fermentation of cellulose to ethanol are carried out by a recombinant yeast cells displaying cellulolytic enzymes.     

Model complexes of the active site of galactose oxidase. Effects of the metal ion binding sites

Model compounds of the active site of galactose oxidase have been developed by using new cofactor model ligands, L1H (2-methylthio-4-tert-butyl-6-[{bis(pyridin-2-ylmethyl)amino}methyl]phenol) and L2H (2-methylthio-4-tert-butyl-6-[{bis(6-methylpyridin-2-ylmethyl)amino}methyl]phenol). Treatment of the ligands with copper(II) and zinc(II) perchlorate in the presence of triethylamine followed by anion exchange reaction with NaPF₆ or NaBPh₄ provided the corresponding copper(II) and zinc(II) complexes, the crystal structures of which have been determined by X-ray crystallographic analysis. All the copper(II) and zinc(II) complexes have been isolated as a dimeric form in which the phenolate oxygen of each ligand acts as the bridging ligand to form a rhombic M₂(OAr)₂ core (M=Cu or Zn). The dimeric complexes can be converted into the corresponding monomer complexes by the treatment with exogenous ligand such as acetate ion. The redox potential and the spectroscopic features of the monomer complexes have also been examined. Furthermore, the copper(II)- and zinc(II)-complexes of the phenoxyl radical species of the ligands have been generated in situ by the oxidation of the phenolate complexes with (NH₄)₂[Ce^IV(NO₃)₆] (CAN) in CH₃CN, and their spectroscopic features have been explored. The structures and physicochemical properties of the phenolate and phenoxyl radical complexes of L1 and L2 have been compared to those of the previously reported copper(II) and zinc(II) complexes of L3 (2-methylthio-4-tert-butyl-6-[{bis(2-pyridin-2-ylethyl)amino}methyl]phenol) in order to get insights into the interaction between the metal ions and the organic cofactor moiety.     

Nucleophilic reaction by carbonic anhydrase model zinc compound: characterization of intermediates for CO2 hydration and phosphoester hydrolysis

The partially hydrophilic and hydrophobic tripodal ligands, tris(hydroxy-2-benzimidazolylmethyl)amine L1h and tris(2-benzimidazolyl)amine L1 were used for the preparation of biomimetic complex of carbonic anhydrase. The CO(2) hydration using [L1hZn(OH)]ClO(4).1.5H(2)O provided the zinc-bound and free HCO(3)(-)s, which were formed by nucleophilic attack of Zn-OH toward CO(2) in dimethyl sulfoxide (DMSO). The phenolic OH in L1h can recognize water molecules through hydrogen bonds to facilitate the collection of the water molecules around a biomimetic zinc compound; the molecular structure of [L1hZn(OH)](+) was revealed. The packing diagram has demonstrated the all the water molecules are hydrogen bonded to each phenolic OH. The nucleophilic attack of zinc-bound OH(-) to substrate is used to catalyze the CO(2) hydration and phosphoester hydrolysis. The carbonic anhydrase model compound [L1Zn(OH(2))](2+) was applied for the hydrolysis of phosphoesters, parathion and bis(p-nitrophenyl)phosphate (BNPP(-)). The low reactivity of [L1Zn(OH)](+) for parathion hydrolysis is attributed to the stability of the intermediate [L1Zn(OP(S)(OEt)(2))](+). Since the structures of the intermediates [L1Zn(OH(2))](BNPP)(2) (1) and [L1Zn(OP(S)(OEt)(2))]ClO(4) (2) formed on the way of hydrolysis are too stable to realize the catalytic cycle and are not active for hydrolysis, carbonic anhydrase model compound [L1Zn(OH(2))](2+) was not suitable for phosphoester hydrolysis; the zinc model compound surrounded by three benzimidazolyl groups is used to have the steric hindrance for bulky substrate, such as parathion and BNPP(-).     

Kinetic study of catalytic CO(2) hydration by water-soluble model compound of carbonic anhydrase and anion inhibition effect on CO(2) hydration

A kinetic study of CO(2) hydration was carried out using the water-soluble zinc model complex with water-soluble nitrilotris(2-benzimidazolylmethyl-6-sulfonate) L1S, [L1SZn(OH(2))](-), mimicking the active site of carbonic anhydrase, in the presence and absence of anion inhibitors NCS(-) and Cl(-). The obtained rate constants k(cat) for CO(2) hydration were 5.9x10(2), 1. 7x10(3), and 3.1x10(3) M(-1) s(-1) at 5, 10, and 15 degrees C, respectively: the k(cat)=ca. 10(4) M(-1) s(-1) extrapolated towards 25 degrees C has been the largest among the reported k(cat) using zinc model complexes for carbonic anhydrase. It was also revealed that NCS(-), Cl(-) and acetazolamide play a role of inhibitors by the decrease of k(cat): 7x10(2) and 2x10(3) M(-1) s(-1) for NCS(-) and Cl(-) at 15 degrees C, respectively. The sequence of their magnitudes in k(cat) is Cl(-) approximately acetazolamide>NCS(-), where the sequence Cl(-)>NCS(-) is confirmed for native carbonic anhydrase. The difference of k(cat) or k(obs) between NCS(-) and Cl(-) resulted from that between the stability constants K(st)=2x10(3) for [L1SZn(NCS)](2-) and 1x10(2) M(-1) for [L1SZnCl](2-) in D(2)O: for water-insoluble tris(2-benzimidazolylmethyl)amine L1, K(st)=1.8x10(4) for [L1Zn(NCS)](2-) and 1.5x10(3) M(-1) for [L1ZnCl](2-)in CD(3)CN/D(2)O (50% v/v). The crystal structure of anion-binding zinc model complexes [L1Zn(OH(2))](0.5)[L1ZnCl](0.5) (ClO(4))(1.5) 1(0.5)2(0.5)(ClO(4))(1.5) was revealed by X-ray crystallography. The geometry around Zn(2+) in 1 and 2 was tetrahedrally coordinated by three benzimidazolyl nitrogen atoms and one oxygen atom of H(2)O, or Cl(-).     

A novel type of family 19 chitinase from Aeromonas sp. No.10S-24. Cloning, sequence, expression, and the enzymatic properties.

A family 19 chitinase gene from Aeromonas sp. No.10S-24 was cloned, sequenced, and expressed in Escherichia coli. From the deduced amino acid sequence, the enzyme was found to possess two repeated N-terminal chitin-binding domains, which are separated by two proline-threonine rich linkers. The calculated molecular mass was 70 391 Da. The catalytic domain is homologous to those of plant family 19 chitinases by about 47%. The enzyme produced alpha-anomer by hydrolyzing beta-1,4-glycosidic linkage of the substrate, indicating that the enzyme catalyzes the hydrolysis through an inverting mechanism. When N-acetylglucosamine hexasaccharide [(GlcNAc)6] was hydrolyzed by the chitinase, the second glycosidic linkage from the nonreducing end was predominantly split producing (GlcNAc)2 and (GlcNAc)4. The evidence from this work suggested that the subsite structure of the enzyme was (-2)(-1)(+1)(+2)(+3)(+4), whereas most of plant family 19 chitinases have a subsite structure (-3)(-2)(-1)(+1)(+2)(+3). Thus, the Aeromonas enzyme was found to be a novel type of family 19 chitinase in its structural and functional properties.