Crystal structure of (S)-4-carbamoyl-4-(1,3-dioxo-isoindolin-2-yl)butanoic acid

The title compound is a one of the first-step hydrolysis products of thalidomide. In the crystal, each mol­ecule is linked via six neighbouring mol­ecules into a three-dimensional network through N—H⋯O and O—H⋯O hydrogen bonds.

In the title compound, C₁₃H₁₂N₂O₅, the phthalimide ring system is essentially planar, with a maximum deviation of 0.0479 (14) Å. In the crystal, each mol­ecule is linked via six neighbouring mol­ecules into a three-dimensional network through N—H⋯O and O—H⋯O hydrogen bonds, which form an R₃²(8) ring motif.

[OPTIMIZATION OF THE METHOD OF SUPRAPANCREATIC LYMPH NODE DISSECTION IN LAPAROSCOPY-ASSISTED GASTRECTOMY (IN THE FINAL ANALYSIS OF INTERNATIONAL CONFERENCES <<SCHOOL OF STOMACH SURGERY>>)]

The article analyzed the methods of suprapancretic lymph node dissection in laparoscopic gastrectomy which were devel- oped and applied in Japan. The authors described the details of operation technique. There were noted the advantages of medial approach for suprapancreatic lymph node dissection.

Modulation of the osteoconductive property and immune response of poly(ether ether ketone) by modification with calcium ions

A Ca-modified PEEK facilitates osteoblastic cell proliferation and differentiation and shifts macrophage phenotype towards anti-inflammatory/wound healing type.

Contribution of a family 1 carbohydrate-binding module in thermostable glycoside hydrolase 10 xylanase from Talaromyces cellulolyticus toward synergistic enzymatic hydrolysis of lignocellulose

BACKGROUND

Enzymatic removal of hemicellulose components such as xylan is an important factor for maintaining high glucose conversion from lignocelluloses subjected to low-severity pretreatment. Supplementation of xylanase in the cellulase mixture enhances glucose release from pretreated lignocellulose. Filamentous fungi produce multiple xylanases in their cellulase system, and some of them have modular structures consisting of a catalytic domain and a family 1 carbohydrate-binding module (CBM1). However, the role of CBM1 in xylanase in the synergistic hydrolysis of lignocellulose has not been investigated in depth.

RESULTS

Thermostable endo-β-1,4-xylanase (Xyl10A) from Talaromyces cellulolyticus, which is recognized as one of the core enzymes in the fungal cellulase system, has a modular structure consisting of a glycoside hydrolase family 10 catalytic domain and CBM1 at the C-terminus separated by a linker region. Three recombinant Xyl10A variants, that is, intact Xyl10A (Xyl10Awt), CBM1-deleted Xyl10A (Xyl10AdC), and CBM1 and linker region-deleted Xyl10A (Xyl10AdLC), were constructed and overexpressed in T. cellulolyticus. Cellulose-binding ability of Xyl10A CBM1 was demonstrated using quartz crystal microbalance with dissipation monitoring. Xyl10AdC and Xyl10AdLC showed relatively high catalytic activities for soluble and insoluble xylan substrates, whereas Xyl10Awt was more effective in xylan hydrolysis of wet disc-mill treated rice straw (WDM-RS). The enzyme mixture of cellulase monocomponents and intact or mutant Xyl10A enhanced the hydrolysis of WDM-RS glucan, with the most efficient synergism found in the interactions with Xyl10Awt. The increased glucan hydrolysis yield exhibited a linear relationship with the xylan hydrolysis yield by each enzyme. This relationship revealed significant hydrolysis of WDM-RS glucan with lower supplementation of Xyl10Awt.

CONCLUSIONS

Our results suggest that Xyl10A CBM1 has the following two roles in synergistic hydrolysis of lignocellulose by Xyl10A and cellulases: enhancement of lignocellulosic xylan hydrolysis by binding to cellulose, and the efficient removal of xylan obstacles that interrupt the cellulase activity (because of similar binding target of CBM1). The combination of CBM-containing cellulases and xylanases in a fugal cellulase system could contribute to reduction of the enzyme loading in the hydrolysis of pretreated lignocelluloses.

Crystallization and preliminary X-ray crystallographic analysis of a putative acetylxylan esterase from Talaromyces cellulolyticus

Acetylxylan esterase (AXE) catalyzes the hydrolytic cleavage of the ester bond between acetic acid and hemicellulose in plant cell walls. A putative AXE gene exhibiting high homology to carbohydrate esterase family 3 was found in the genome database of the fungus Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus). A truncated form of the protein, the catalytic domain of the enzyme, was prepared and crystallized. The best crystal was obtained at 293 K using 0.17 M ammonium sulfate, 28% PEG 4000, 5%(v/v) glycerol, 0.5%(w/v) n-octyl-β-D-glucoside. X-ray diffraction data were collected to 1.50 Å resolution. The crystal belonged to space group P41212 or P43212, with unit-cell parameters a = 70.90, b = 70.90, c = 87.09 Å. One enzyme molecule per asymmetric unit gave a crystal volume per protein mass (VM) of 2.62 Å(3) Da(-1) and a solvent content of 53.0%(v/v).

Crystallization and preliminary X-ray crystallographic analysis of a putative feruloyl esterase from Talaromyces cellulolyticus

Feruloyl esterase (FAE; EC 3.1.1.73) catalyzes the cleavage of the ester bond between ferulic acid and polysaccharides in plant cell walls, and thus holds significant potential for the industrial utilization of biomass saccharification. A feruloyl esterase was identified from the genome database of Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus). The gene consists of the catalytic domain and a carbohydrate-binding module connected through a serine/threonine-rich linker region. The recombinant enzyme was prepared, purified and crystallized at 293 K using 0.1 M imidazole pH 8.0, 0.2 M calcium acetate, 14% PEG 8000 as the precipitant. The crystal diffracted to 2.6 Å resolution and the crystal system is primitive orthorhombic, with unit-cell parameters a = 90.9, b = 123.4, c = 135.4 Å. Four molecules are assumed to be present per asymmetric unit, corresponding to a Matthews coefficient of 2.50 Å(3) Da(-1) and a solvent content of 50.88%(v/v).

Heterologous expression of hyperthermophilic cellulases of archaea Pyrococcus sp. by fungus Talaromyces cellulolyticus

Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) is one of the high cellulolytic enzyme-producing fungi. T. cellulolyticus exhibits the potential ability for high amount production of enzyme proteins. Using the homologous expression system under the control of a glucoamylase promoter, some kinds of cellulases of T. cellulolyticus can be expressed by T. cellulolyticus. On the other hand, hyperthermophilic cellulase has been expected to be useful in the industrial applications to biomass. The hyperthermophilic archaea Pyrococcus horikoshii and P. furiosus have GH family 5 and 12 hyperthermophilic endocellulase, respectively. The two kinds of hyperthermophilic endocellulases were successfully produced by T. cellulolyticus using the above expression system under the control of a glucoamylase promoter of T. cellulolyticus. These recombinant cellulases exhibited the same characteristics as those of the recombinant cellulases prepared in E. coli. The productions of the recombinant enzymes were estimated to be over 100 mg/L. In this study, we first report the overexpression of the hyperthermophilic enzymes of archaea using the fungal expression system.

Characterization of the xylanase regulator protein gene, xlnR, in Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus)

We cloned a putative Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) xlnR gene and isolated a xlnR disruptant strain. XlnR protein was localized in the nucleus. Xylanase production by the xlnR disruptant was lower than in the control strain at both the enzyme and transcriptional level. These data suggest that the XlnR protein regulates xylanase production in T. cellulolyticus.

Gene targeting by RNAi-mediated knockdown of potent DNA ligase IV homologue in the cellulase-producing fungus Talaromyces cellulolyticus

The genome of the cellulase-producing fungus Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) was screened for a potent DNA ligase IV gene (ligD homologue). Homologous recombination efficiency in T. cellulolyticus is very low. Therefore, suppression of a non-homologous end-joining system was attempted to enable specific gene knockouts for molecular breeding. The transcript levels of ligD homologue were 0.037 of those of the parental YP-4 strain in the Li20 transformant carrying the RNAi construct targeting the ligD homologue. Transformation of the hairpin-type RNAi vector into T. cellulolyticus could be useful in fungal gene knockdown experiments. Cellulase production and protein secretion were similar in the parental YP-4 strain and the Li20 transformant. Knockout transformation of ligD homologue using the Li20 transformant led to 23.1 % double crossover gene targeting. Our results suggest that the potent DNA ligase IV gene of T. cellulolyticus is related to non-homologous end joining and that the knockdown of the ligD homologue is useful in gene targeting.

Crystal structure of Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) GH family 11 xylanase

Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) is one of the mesophilic fungi that can produce high levels of cellulose-related enzymes and are expected to be used for the degradation of polysaccharide biomass. In silico analysis of the genome sequence of T. cellulolyticus detected seven open reading frames (ORFs) showing homology to xylanases from glycoside hydrolase (GH) family 11. The gene encoding the GH11 xylanase C (TcXylC) with the highest activity was used for overproduction and purification of the recombinant enzyme, permitting solving of the crystal structure to a resolution of 1.98 Å. In the asymmetric unit, two kinds of the crystal structures of the xylanase were identified. The main structure of the protein showed a β-jelly roll structure. We hypothesize that one of the two structures represents the open form and the other shows the close form. The changing of the flexible region between the two structures is presumed to induce and accelerate the enzyme reaction. The specificity of xylanase toward the branched xylan is discussed in the context of this structural data and by comparison with the other published structures of xylanases.

Determination of Chirality of the Chiral Space Groups with Two-fold Screw Axis

Crystals are classified according to their symmetry operations into 230 space groups. A two-fold screw axis, 21, a symmetry operation, is frequently found in the crystal, especially non-centrosymmetric organic crystals. The two-fold screw axis shows a chiral character when molecules in the crystal tilt against the screw axis as shown in Figure. The crystals belonging to a chiral space group with two-fold screw axis such as a P21or P212121exhibit two different types with opposite chirality. However, although the two crystals are not identical in a molecular arrangement, we cannot distinguish them with the present notation of space group. Recently, the idea of determining the handedness of two-fold screw axis have been successfully proposed using hierarchical interpretation of the crystals.(I. Hisaki, T. Sasaki et al., 2012) Nevertheless, the issue on a notation to distinguish chiral crystals with two-fold screw axis still remains unsettled as far as we know. Therefore, we attempt to propose a novel notation for the crystals belonging to chiral space groups with two-fold screw axis. We focus on the relationship between the absolute structure and optical activity of the crystals. We have selected alanine crystals, which belong to P212121, as model crystals to discuss the notation. We have determined the absolute structure of the alanine crystals by X-ray diffraction and have measured their optical activity with Generalized High Accuracy Universal Polarimeter (G-HAUP).(M. Tanaka, N. Nakamura et al., 2012) G-HAUP is an apparatus that can measure simultaneously the linear birefringence, linear dichroism, circular birefringence, i.e., optical activity, and circular dichroism in any solid material. These experimental results have successfully correlated the absolute structure to the optical activity of the alanine crystals.

Measurement of chiroptical properties of nickel sulfate hexahydrate with G-HAUP

A crystal, which belongs to a lower crystal system than cubic one, exhibits optical anisotropies. The optical anisotropies originate from the difference in refraction and absorption between orthogonally linearly polarized lights. When molecules forming a crystal are enantiomers with the same chirality or form helical structures with the same handedness, the crystal shows chiroptical properties, which originate from the difference in refraction and absorption between right and left circularly polarized lights. The four optical phenomena are called linear birefringence (LB), linear dichroism (LD), circular birefringence (CB) and circular dichroism (CD), respectively. It had been difficult to measure CB and CD in chiral crystals with optical anisotropies because the signals of the anisotropies are three or four orders of magnitude larger than those of chiroptical properties. The Generalized High Accuracy Universal Polarimeter (G-HAUP) [1] enables us to simultaneously measure LB, LD, CB and CD of any anisotropic crystal. Nickel sulfate (NS) is achiral in the solution state. However, in the crystalline state, it forms hexahydrate and exhibits chirality since molecules are put in helical arrangements. The NS crystal belongs to an enantiomorphous space group, P41212 or P43212. Many researchers have reported the optical properties of NS crystal because large and good-quality crystals are readily grown. However, we consider the LB, LD, CB and CD in NS crystal should be simultaneously and completely investigated. The purpose of this study is to obtain LB, LD, CB and CD along the a axis with G-HAUP and compare the CB and CD with the results along the c axis. We measured optical rotatory power (ORP) along the c axis with G-HAUP, which agrees with the previous results [2,3]. We then prepared for some samples with chirality and anisotropy. We measured LB, LD, CB and CD spectra, respectively and will demonstrate the relation between their optical properties and structures.

Structural and thermal analyses of a hydrolysis compound of thalidomide

Thalidomide (TD) is a historically famous chiral drug. After prescription as a safe hypnotic, TD was suspected of contributing to teratogenicity, resulting in prohibition of the use of TD. TD and its derivatives, however, have attracted a renewed attention since their therapeutic effects for Hansen's disease and multiple myeloma were demonstrated. Meanwhile TD has been known to suffer from spontaneous hydrolysis with complicated pathways, leading to the production of various metabolites of TD. Therefore, we are now facing the difficulty in specifying the compounds which cause desired and/or adverse effects in the drug mechanism of TD. In a previous study, pure hydrolytic products of TD were synthesized and assayed for production-inhibitory activity of TNF-α, a kind of cytokine that induces inflammation. This study has showed that some products, especially α-(2-carboxybenzamido)glutarimide (CBG), exhibit high potency for the inhibition of TNF-α production compared to original TD. The hydrolytic products of TD thus are found to greatly attribute to the pharmacological effect of TD. For comprehending effects of the hydrolytic products, it is much significant to perform physicochemical analysis of them because their properties are deeply related to molecular stability and interaction with receptor proteins. In this study, we thus aim to investigate the physicochemical properties of CBG employing X-ray crystal structural analysis and thermal analyses. Single crystals of racemic and enantiomeric CBG were grown by solvent evaporation methods. On the crystallization, we chose alcoholic solvents such as methanol and ethanol. Surprisingly, crystals grown from the CBG solutions have indicated the same crystal structure of TD with high reproducibility. This unique result is likely to represent dehydration of CBG in non-aqueous solvents, which has not been reported so far. The detailed mechanism is under investigation.

Efficacy and safety of the dipeptidyl peptidase-4 inhibitor sitagliptin compared with α-glucosidase inhibitor in Japanese patients with type 2 diabetes inadequately controlled on sulfonylurea alone (SUCCESS-2): a multicenter, randomized, open-label, non-inferiority trial

We assessed the efficacy and safety of sitagliptin compared with α-glucosidase inhibitor (αGI) in 120 of Japanese patients with type 2 diabetes mellitus (T2DM) inadequately controlled on stable ≤2 mg/day glimepiride alone [mean hemoglobin A1c (HbA1c) 7.7%] by the randomized, active-controlled, non-inferiority trial. Patients were randomly assigned to receive additional sitagliptin or αGI for 24 weeks. The primary endpoint was change in HbA1c from baseline to week 12. After 12 weeks, sitagliptin reduced HbA1c by -0.44% (p < 0.001) relative to αGI. At 24 weeks, the reduction was almost identical between the groups (-0.091%, p = 0.47). Gastrointestinal disorders were more common with αGI than with sitagliptin, but only minor hypoglycaemia occurred in both groups at similar frequency. These data suggested that sitagliptin was not inferior to αGI for reduction of HbA1c in Japanese T2DM patients receiving glimepiride alone, and well tolerated with minimum risk of gastrointestinal symptoms and hypoglycaemia.

Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form

A protein-engineering study revealed that the C-terminal domain of a thermostable β-glucosidase contributes to its polymeric state.

One of the β-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability.

A new crystal form of a hyperthermophilic endocellulase

The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal.

Complete saccharification of β-glucan using hyperthermophilic endocellulase and β-glucosidase from Pyrococcus furiosus

Hyperthermophilic cellulase is an industrially important enzyme for biomass saccharification at high temperature. Two hyperthermophilic cellulases from the hyperthermophile Pyrococcus furiosus, endocellulase (EGPf) and β-glucosidase (BGLPf), exhibit optimal activity at 90-105 °C and a combination of two enzymes can hydrolyze a wide range of β-linked substrates. EGPf cleaves the β(1→4) bond of various substrates containing either only the β(1→4) linkage or β(1→3),(1→4) mixed-linkages. In contrast, BGLPf preferentially hydrolyzes the β(1→3) linkage over the β(1→4) linkage of disaccharides. β-Glucans are polysaccharides of D-glucose monomers formed by β(1→3),(1→4) mixed-linkage bonds. They occur most commonly as cellulose in plants, in the bran of cereal grains, the cell wall of baker's yeast, and in certain fungi, mushrooms, and bacteria. We reveal that β-glucan can be completely degraded to glucose at high temperature with a combination of EGPf and BGLPf.

Analysis of the Hyperthermophilic Chitinase fromPyrococcus furiosus: Activity toward Crystalline Chitin

Chitinase [EC 3.2.1.14] is an enzyme that can hydrolyze the beta-1,4 linkage between N-acetyl-D-glucosamine in chitin. In the genome database of the hyperthermophilic archaeon Pyrococcus furiosus, we found two adjacent genes (PF1233 and PF1234) homologous to those of the chitinase of Thermococcus kodakaraensis. In the cultured medium of P. furiosus, however, no chitinase activity was detected. On analysis of the structural gene of P. furiosus, it appears that one nucleotide insertion in PF1234 caused a frame shift and separated a gene. By deletion of one nucleotide in PF1234, the best match was achieved between chitinases of T. kodakaraenesis and P. furiosus. We succeeded in constructing an artificial recombinant chitinase exhibiting hydrolytic activity toward not only colloidal but also crystalline chitins at high temperature. Furthermore, by analyzing the characteristics of the domains, a recombinant enzyme comprising two domains exhibiting high activity toward crystalline chitin was prepared.

Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

Substitutive mutations that convert a tetrameric β-glucosidase into a dimeric state lead to improvement of its crystal quality.

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed.