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Targeting aberrant glycoforms has been validated for in vitro cancer diagnostic development, and several assays are currently in routine clinical use. Because N-glycans in Fc region of antibodies show cross-reactivity with various lectins, high-quality aglycosylated antibodies are exceptionally important for immunoassay platform-based quantitative measurements. Previously, aglycosylated antibody acquisition relied on incomplete, uneconomical and onerous enzymatic and chemical methods. Here, we edited four murine immunoglobulin G genes using adenine base-editing and homology-directed recombination (HDR)-mediated gene editing methods to generate aglycosylated antibody-producing mice. Resulting aglycosylated antibodies showed required analytical performances without compromised protein stability. Thus, this aglycosylated monoclonal antibody-lectin coupled immunoassay for the quantification of tumour markers (ALIQUAT) method can provide a robust, versatile and accessible immunoassay platform to quantify specific glycoforms in precision cancer diagnostics. Moreover, the engineered mice can be used as a host to produce various aglycosylated antibodies in a convenient and robust fashion, thereby expanding in vitro diagnostic development opportunities that utilize glycoforms as a disease-specific biomarkers., Lee et al. describe the generation of aglycosylated antibody-producing mice. These aglycosylated antibodies, lacking glycans prevent unwanted interactions with the lectins, and are used as reagents in a tool they developed called ALIQUAT. This aglycosylated antibody and lectin-based immunoassay diagnostic platform can be used to detect disease specific glycan biomarkers.

Lon proteases degrade defective or denature proteins as well as some folded proteins for the control of cellular protein quality. There are two types of Lon proteases, LonA and LonB. Each consists of two functional components: a protease component and an ATPase associated with various cellular activities (AAA+ module). Here, we report the 2.03 —resolution crystal structure of the isolated AAA+ module (iAAA+ module) of LonB from Thermococcus onnurineus NA1 (TonLonB). The iAAA+ module, having no bound nucleotide, adopts a conformation virtually identical to the ADP-bound conformation of AAA+ modules in the hexameric structure of TonLonB; this provides insights into the ATP-independent proteolytic activity observed in a LonB protease. Structural comparison of AAA+ modules between LonA and LonB revealed that the AAA+ modules of Lon proteases are separated into two distinct clades depending on their structural features. The AAA+ module of LonB belongs to the -H2 & Ins1 insert clade (HINS clade)- defined for the first time in this study, while the AAA+ module of LonA is a member of the HCLR clade.

High Performance Computer (also called "supercomputer") is a computer which can process the complex and large-scale operation in computational science. In general, High Performance Computer represents the top 500 computers which is based on the computer performance in the world. After the successful commercialization of CDC6600 which has the 9MFLOPS performance in 1964, TFLOPS and PFLOPS High Performance Computer have been developed. High Performance Computer is the public resource which can be developed and provided by government. For the efficient application of High Performance Computer, government has to support the related activities such as research, resource allocation, and professional manpower training. To build a basis of the development of High Performance Computing can improve the quality of life and develop the national economy. For this reason, Korean government preceded the establishment of law for national supercomputing promotion from 2009. As a result of this effort, Korean government enacted the 'National Supercomputing Promotion Act' in 2011. This study provides the domestic and international trend of High Performance Computer, and analyses the major contents of National Supercomputing Promotion Act. This effort will be helpful to propose the strategy in order to provide more efficient service as a momentum of national supercomputing center.

AMSH plays a critical role in the ESCRT (endosomal sorting complexes required for transport) machinery, which facilitates the down-regulation and degradation of cell-surface receptors. It displays a high level of specificity toward cleavage of Lys63-linked polyubiquitin chains, the structural basis of which has been understood recently through the crystal structure of a highly related, but ESCRT-independent, protein AMSH-LP (AMSH-like protein). We have determined the X-ray structure of two constructs representing the catalytic domain of AMSH: AMSH244, the JAMM (JAB1/MPN/MOV34)-domain-containing polypeptide segment from residues 244 to 424, and AMSH219(E280A), an active-site mutant, Glu280 to Ala, of the segment from 219 to 424. In addition to confirming the expected zinc coordination in the protein, the structures reveal that the catalytic domains of AMSH and AMSH-LP are nearly identical; however, guanidine-hydrochloride-induced unfolding studies show that the catalytic domain of AMSH is thermodynamically less stable than that of AMSH-LP, indicating that the former is perhaps structurally more plastic. Much to our surprise, in the AMSH219(E280A) structure, the catalytic zinc was still held in place, by the compensatory effect of an aspartate from a nearby loop moving into a position where it could coordinate with the zinc, once again suggesting the plasticity of AMSH. Additionally, a model of AMSH244 bound to Lys63-linked diubiquitin reveals a type of interface for the distal ubiquitin significantly different from that seen in AMSH-LP. Altogether, we believe that our data provide important insight into the structural difference between the two proteins that may translate into the difference in their biological function.

Two different bacteriocins, carotovoricin and carocin S1, had been found in Pectobacterium carotovorum subsp. carotovorum , which causes soft-rot disease in diverse plants. Previously, we reported that the particular strain Pcc21, producing only one high-molecular-weight bacteriocin, carried a new antibacterial activity against the indicator strain Pcc3. Here, we report that this new antibacterial activity is due to a new bacteriocin produced by strain Pcc21 and named carocin D. Carocin D is encoded by the caro DK gene located in the genomic DNA together with the caro DI gene, which seems to encode an immunity protein. N-terminal amino acid sequences of purified carocin D were determined by Edman degradation. In comparison with the primary translation product of caro DK, it was found that 8 amino acids are missing at the N terminus. This finding proved that carocin D is synthesized as a precursor peptide and that 8 amino acids are removed from its N terminus during maturation. Carocin D has two putative translocation domains; the N-terminal and C-terminal domains are homologous to those of Escherichia coli colicin E3 and Pseudomonas aeruginosa S-type pyocin, respectively. When caro DK and caro DI genes were transformed into carocin D-sensitive bacteria such as Pcc3, the bacteria became resistant to this bacteriocin. Carocin D has one putative DNase domain at the extreme C terminus and showed DNase activity in vitro . This bacteriocin had slight tolerance to heat but not to proteases. The caro DK gene was present in only 5 of 54 strains of P. carotovorum subsp. carotovorum . These results indicate that carocin D is a third bacteriocin found in P. carotovorum subsp. carotovorum , and this bacteriocin can be readily expressed in carocin D-sensitive nonpathogenic bacteria, which may have high potential as a biological control agent in the field.

Auxin-binding protein 57 (ABP57), a soluble auxin-binding protein, acts as a receptor to activate plasma membrane (PM) H+-ATPase. Here, we report the cloning of abp57 and the biochemical characterization of its protein expressed in E. coli. The analysis of internal amino acid sequences of ABP57 purified from rice shoots enabled us to search for the corresponding gene in protein DB of NCBI. Further BLAST analysis showed that rice has four abp57-like genes and maize has at least one homolog. Interestingly, Arabidopsis seems to have no homolog. Recombinant ABP57 expressed in E. coli caused the activation of PM H+-ATPase regardless of the existence of IAA. Scatchard analysis showed that the recombinant protein has relatively low affinity to IAA as compared to natural ABP57. These results collectively support the notion that the cloned gene is responsible for ABP57.

A thick film of patterned heterogeneous surface is introduced, in which the surface heterogeneity arises due to a difference in the characteristics of interfacial potential. When a liquid film is coated onto such a surface, the film is unstable only on certain parts of the surface and, consequently, dewetting takes place. In the other parts, the film is stable and no dewetting takes place. This heterogeneous surface is utilized for patterning low-duty-ratio patterns, which has proved challenging for any mold-based unconventional lithographies. Only the natural forces associated with capillarity and dewetting are responsible for the patterning. As a result, defect-free and uniform patterning is possible over a large area.

Porous carbon beads were prepared by carbonizing at 700 and 1000 °C under N 2 (NN-series) or CO 2 atmospheres (CO-series) and a subsequent oxidization with boiling nitric acid solution (13%, v/v) for 3 h (ANN- and ACO-series). BET surface area of both CO- and NN-series samples tends to increase with increasing carbonization temperature, but CO-series samples show higher BET surface areas (700 °C: 610 m 2 /g, 1000 °C: 780 m 2 /g) compared with those of NN-series samples (700 °C: 380 m 2 /g, 1000 °C: 580 m 2 /g). After acid oxidation, BET surface areas of NN-series samples increased from 580 to 650 m 2 /g, whereas those of CO-series samples decreased from 780 to 600 m 2 /g. On subsequent acid oxidation, acidic surface functional groups increased in both CO- and NN-series samples, but the CO-series samples tend to have much more acidic surface functional groups. Adsorption of halogenated methanes, such as tetra-, tri- and dichloromethanes, onto the samples of CO-, NN-, ACO- and ANN-series was thought to be driven initially by the basicity, but the acidic functional groups that could attract adsorbates via dipole–dipole interaction might hinder the adsorption of subsequently incoming adsorbates.

Ubiquitin C-terminal hydrolase 37 (UCH37) is a deubiquitinating enzyme capable of dismantling Lys48-linked polyubiquitin chains when associated with the 26S proteasome. Upon binding to the proteasomal subunit ADRM1, UCH37 is activated for cleavage of the distal monomer in a chain, an exo-specific activity. Prior to binding with ADRM1, it is thought that UCH37 is inhibited by its own C-terminal UCHL5-like domain (ULD). Our interests lie in UCH37’s mechanism of activation by ADRM1 as well as its exo-specificity. Previously we have reported the crystal structure of T. spiralis UCH37 bound to ubiquitin vinyl methyl ester, which revealed that the ULD domain interacts with ubiquitin’s Lys48, an event we believe accounts for its exo-specificity. In order to further examine specificity and activation, we have generated a series of ULD mutants of UCH37. To probe exo-specificity, we are purifying the 19S regulatory particle of the proteasome from rabbit skeletal muscle, will reconstitute each ULD mutant within the ...

High performance computer is one that processes complex largescale computing tasks in the area of scientific calculations difficult to solve with ordinary computer, which is also called supercomputer. Generally, a high performance computer refers to one within the world's top 500 based on computer performance. Currently, 50 years past since the successful commercialization of CDC6600 with 9MFLOPS (One million times/second) operation processing capability in 1964, developing high performance computers of TFLOPS (One trillion times/second) and PFLOPS (Quadrillion times/second) is in progress and application. The high performance computer can be said to be a public resource the government should develop and provide. To apply the public resource effectively, at the state level, high performance computer related technologies should be promoted such as high performance computer related research and development, effective distribution of the resources and training of professional manpower. Through this, a high performance computer development base should be created and contribute to the people's quality of life improvement and national economy development. By this necessity, South Korea carried out procedures for the enactment of a law for high performance computer related technology development, application and promotion since 2009. Accordingly, in June, 2011, ‘National Supercomputing Promotion Act’ was enacted. This paper will investigate the trend of the domestic/overseas policies for high performance computer, analyze and sum up the major contents of this law. Keyword: High Performance Computer, Cyberinfrastructure, Supercomputer, Promotion Act, Computational Science

Ubiquitination is countered by a group of enzymes collectively called deubiquitinases (DUBs) - about 100 of them can be found in the human genome. One of the most interesting aspects of these enzymes is the ability of some members to selectively recognize specific linkage types between ubiquitin in polyubiquitin chains and their endo and exo specificity. The structural basis of exo-specific deubiquitination catalyzed by a DUB is poorly understood. UCH37, a cysteine DUB conserved from fungi to humans, is a proteasome-associated factor that regulates the proteasome by sequentially cleaving polyubiquitin chains from their distal ends, i.e., by exo-specific deubiquitination. In addition to the catalytic domain, the DUB features a functionally uncharacterized UCH37-like domain (ULD), presumed to keep the enzyme in an inhibited state in its proteasome-free form. Herein we report the crystal structure of two constructs of UCH37 from Trichinella spiralis in complex with a ubiquitin-based suicide inhibitor, ubiquitin vinyl methyl ester (UbVME). These structures show that the ULD makes direct contact with ubiquitin stabilizing a highly unusual intra-molecular salt bridge between Lys48 and Glu51 of ubiquitin, an interaction that would be favored only with the distal ubiquitin but not with the internal ones in a Lys48-linked polyubiquitin chain. An inspection of 39 DUB-ubiquitin structures in the protein data bank reveals the uniqueness of the salt bridge in ubiquitin bound to UCH37, an interaction that disappears when the ULD is deleted, as revealed in the structure of the catalytic domain alone bound to UbVME. The structural data are consistent with previously reported mutational data on the mammalian enzyme, which, together with the fact that the ULD residues that bind to ubiquitin are conserved, points to a similar mechanism behind the exo specificity of the human enzyme. To the best of our knowledge, these data provide the only structural example so far of how the exo specificity of a DUB can be determined by its non-catalytic domain. Thus, our data show that, contrary to its proposed inhibitory role, the ULD actually contributes to substrate recognition and could be a major determinant of proteasome-associated function of UCH37. Moreover, our structures show that the unproductively oriented catalytic cysteine in the free enzyme is aligned correctly when ubiquitin binds, suggesting a mechanism for ubiquitin selectivity.

Levan is β-2,6-linked polymeric fructose and serves as reserve carbohydrate in some plants and microorganisms. Mobilization of fructose is usually mediated by enzymes such as glycoside hydrolase (GH), typically releasing a monosaccharide as a product. The enzyme levan fructotransferase (LFTase) of the GH32 family catalyzes an intramolecular fructosyl transfer reaction and results in production of cyclic difructose dianhydride, thus exhibiting a novel substrate specificity. The mechanism by which LFTase carries out these functions via the structural fold conserved in the GH32 family is unknown. Here, we report the crystal structure of LFTase from Arthrobacter ureafaciens in apo form, as well as in complexes with sucrose and levanbiose, a difructosacchride with a β-2,6-glycosidic linkage. Despite the similarity of its two-domain structure to members of the GH32 family, LFTase contains an active site that accommodates a difructosaccharide using the -1 and -2 subsites. This feature is unique among GH32 proteins and is facilitated by small side chain residues in the loop region of a catalytic β-propeller N-domain, which is conserved in the LFTase family. An additional oligosaccharide-binding site was also characterized in the β-sandwich C-domain, supporting its role in carbohydrate recognition. Together with functional analysis, our data provide a molecular basis for the catalytic mechanism of LFTase and suggest functional variations from other GH32 family proteins, notwithstanding the conserved structural elements.

Nitrogen metabolism is one of essential processes in living organisms. The catabolic pathways of nitrogenous compounds play a pivotal role in the storage and recovery of nitrogen. In Escherichia coli, two different, interconnecting metabolic routes drive nitrogen utilization through purine degradation metabolites. The enzyme (S)-ureidoglycolate dehydrogenase (AllD), which is a member of l-sulfolactate dehydrogenase-like family, converts (S)-ureidoglycolate, a key intermediate in the purine degradation pathway, to oxalurate in an NAD(P)-dependent manner. Therefore, AllD is a metabolic branch-point enzyme for nitrogen metabolism in E. coli. Here, we report crystal structures of AllD in its apo form, in a binary complex with NADH cofactor, and in a ternary complex with NADH and glyoxylate, a possible spontaneous degradation product of oxalurate. Structural analyses revealed that NADH in an extended conformation is bound to an NADH-binding fold with three distinct domains that differ from those of the canonical NADH-binding fold. We also characterized ligand-induced structural changes, as well as the binding mode of glyoxylate, in the active site near the NADH nicotinamide ring. Based on structural and kinetic analyses, we concluded that AllD selectively utilizes NAD(+) as a cofactor, and further propose that His116 acts as a general catalytic base and that a hydride transfer is possible on the B-face of the nicotinamide ring of the cofactor. Other residues conserved in the active sites of this novel l-sulfolactate dehydrogenase-like family also play essential roles in catalysis.

Pathogenic bacteria synthesize and secrete toxic low molecular weight compounds as virulence factors. These microbial toxins play essential roles in the pathogenicity of bacteria in various hosts, and are emerging as targets for antivirulence strategies. Toxoflavin, a phytotoxin produced by Burkholderia glumae BGR1, has been known to be the key factor in rice grain rot and wilt in many field crops. Recently, toxoflavin-degrading enzyme (TxDE) was identified from Paenibacillus polymyxa JH2, thereby providing a possible antivirulence strategy for toxoflavin-mediated plant diseases. Here, we report the crystal structure of TxDE in the substrate-free form and in complex with toxoflavin, along with the results of a functional analysis. The overall structure of TxDE is similar to those of the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. The active site is located at the end of the hydrophobic channel, 9 Å in length, and contains a Mn(II) ion interacting with one histidine residue, two glutamate residues, and three water molecules in an octahedral coordination. In the complex, toxoflavin binds in the hydrophobic active site, specifically the Mn(II)-coordination shell by replacing a ligating water molecule. A functional analysis indicated that TxDE catalyzes the degradation of toxoflavin in a manner dependent on oxygen, Mn(II), and the reducing agent dithiothreitol. These results provide the structural features of TxDE and the early events in catalysis.

Allantoinase acts as a key enzyme for the biogenesis and degradation of ureides by catalyzing the conversion of (S)-allantoin into allantoate, the final step in the ureide pathway. Despite limited sequence similarity, biochemical studies of the enzyme suggested that allantoinase belongs to the amidohydrolase family. In this study, the crystal structure of allantoinase from Escherichia coli was determined at 2.1 A resolution. The enzyme consists of a homotetramer in which each monomer contains two domains: a pseudo-triosephosphate-isomerase barrel and a beta-sheet. Analogous to other enzymes in the amidohydrolase family, allantoinase retains a binuclear metal center in the active site, embedded within the barrel fold. Structural analyses demonstrated that the metal ions in the active site ligate one hydroxide and six residues that are conserved among allantoinases from other organisms. Functional analyses showed that the presence of zinc in the metal center is essential for catalysis and enantioselectivity of substrate. Both the metal center and active site residues Asn94 and Ser317 play crucial roles in dictating enzyme activity. These structural and functional features are distinctively different from those of the metal-independent allantoinase, which was very recently identified.

Neisseria polysaccharea amylosucrase (NpAS), a transglucosidase of glycoside hydrolase family 13, is a hydrolase and glucosyltransferase that catalyzes the synthesis of amylose-like polymer from a sucrose substrate. Recently, an NpAS homolog from Xanthomonas axonopodis pv. glycines was identified as a member of the newly defined carbohydrate utilization locus that regulates the utilization of plant sucrose in phytopathogenic bacteria. Interestingly, this enzyme is exclusively a hydrolase and not a glucosyltransferase; it is thus known as sucrose hydrolase (SUH). Here, we elucidated the novel functional features of SUH using X-ray crystallography and site-directed mutagenesis. Four different crystal structures of SUH, including the SUH-Tris and the SUH-sucrose and SUH-glucose complexes, represent structural snapshots along the catalytic reaction coordinate. These structures show that SUH is distinctly different from NpAS in that ligand-induced conformational changes in SUH cause the formation of a pocket-shaped active site and in that SUH lacks the three arginine residues found in the NpAS active site that appear to be crucial for NpAS glucosyltransferase activity. Mutation of SUH to insert these arginines failed to confer glucosyltransferase activity, providing evidence that its enzymatic activity is limited to sucrose hydrolysis by its pocket-shaped active site and the identity of residues in the vicinity of the active site.

In order to provide a fast moving mobile host (MH) supporting multimedia applications with a consistent quality of service (QoS), an efficient call admission mechanism is in need. This paper proposes the 2-level call admission (2LCAC) scheme based on a call admission scheme using the priority to guarantee the consistent QoS for mobile multimedia applications. The 2LCAC consists of the basic call admission and advanced call admission; the former determines call admission based on bandwidth available in each cell and the latter determines call admission by utilizing delay tolerance time (DTT) and priority queue (PQueue) algorithms. In order to evaluate the performance of our scheme, we measure the metrics such as the blocking probability of new calls, dropping probability of handoff calls and bandwidth utilization. The result shows that the performance of our scheme is superior to that of existing schemes such as complete sharing policy (CSP), guard channel policy (GCP) and adaptive guard channel policy (AGCP).