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RanBPM and RanBP10 are non-canonical members of the Ran binding protein family that lack the Ran binding domain and do not associate with Ran GTPase in vivo . Rather, they have been shown to be scaffolding proteins that are important for a variety of cellular processes, and both of these proteins contain a SPRY domain, which has been implicated in mediating protein–protein interactions with a variety of targets including the DEAD-box containing ATP-dependent RNA helicase (DDX-4). In this study, we have determined the crystal structures of the SPIa and the ryanodine receptor domain and of approximately 70 upstream residues (immediate upstream to SPRY motif) of both RanBPM and RanBP10. They are almost identical, composed of a β-sandwich fold with a set of two helices on each side located at the edge of the sheets. A unique shallow binding surface is formed by highly conserved loops on the surface of the β-sheet with two aspartates on one end, a positive patch on the opposite end, and a tryptophan lining at the bottom of the surface. The 20-mer peptide (residues 228–247) of human DDX-4, an ATP-dependent RNA helicase known to regulate germ cell development, binds to this surface with a K D of ~ 13 μM. The crystal structure of the peptide complex and the mutagenesis studies elucidate how RanBPM can recognize its interaction partners to function in gametogenesis.

We report the synthesis of surface-composition-controlled gold–platinum (AuPt) bimetallic nanostructures on carbon nanotubes by peptide-based self-assembly and their catalytic responses to oxygen reduction. Our results can provide a great opportunity to construct various nanostructures with tailored properties.

Angular distortion caused by differential settlement critically influences the damage to and serviceability of a structure. The angular distortion criterion proposed by Bjerrum generally is used in practice. However, some measurements used in the field do not properly represent the angular distortion of a structure in a way that allows Bjerrum’s criterion to be applied. This paper includes a discussion of using the measured data obtained from ground and structures near road embankment sites over deep soft soil. The data analysis revealed several problems, such as an insufficient number of measurement gauges, improper installation of gauges, and incorrect understanding of the angular distortion during data interpretation. An improved measurement method, called “relative displacement measurement,” was suggested. The proposed method was demonstrated in the field. Compared to the previous measurement, this method provides more accurate measurement of the relative displacement between columns of the structure and better represents the angular distortion.

Peptide assemblies have received significant attention because of their important role in biology and applications in bionanotechnology. Despite recent efforts to elucidate the principles of peptide self-assembly for developing novel functional devices, peptide self-assembly on two-dimensional nanomaterials has remained challenging. Here, we report nature-inspired two-dimensional peptide self-assembly on pristine graphene via optimization of peptide–peptide and peptide–graphene interactions. Two-dimensional peptide self-assembly was designed based on statistical analyses of >104 protein structures existing in nature and atomistic simulation-based structure predictions. We characterized the structures and surface properties of the self-assembled peptide formed on pristine graphene. Our study provides insights into the formation of peptide assemblies coupled with two-dimensional nanomaterials for further development of nanobiocomposite devices.

Bacterial resistance to many existing antibiotics is a growing health concern worldwide. There is an urgent need to identify new antibiotics with unexploited modes of action. Peptide deformylase (PDF) is an essential enzyme involved in N-terminal protein processing in eubacteria but not in higher organisms. Therefore, PDF is considered an attractive target for the development of novel antibiotics. Here, we report the structures of the PDFs from Enterococcus faecalis (EfPDF) and Streptococcus pyogenes (SpyPDF) complexed with actinonin at 1.4 and 2.1 A resolutions, respectively. Actinonin, a naturally occurring, highly potent inhibitor, is bound tightly at the active site. The conformation of actinonin in the EfPDF and SpyPDF complexes was similar to those of all others. The detailed information from this study will facilitate the development of novel antibacterial molecules.

Expansion of a roadway on a soft ground can cause settlement of the existing road during embankment construction due to the consolidation characteristics of the soft soil. Many problems related to construction and maintenance, such as deterioration of the surface, decreased safety, and decreased structural stability, could affect the existing road. This scenario is especially true if the roadway foundation is a deep thick soft ground. Therefore, engineers should carefully select a proper design based on the characteristics of the soil layer. In this study, the expansion of the second branch of the Namhae Expressway was selected as the target site because this expressway has been constructing on a soft soil layer approximately 50 m thick. The original design was reviewed, problems were discussed and alternative was proposed through value engineering job plan phases: investigation, speculation, evaluation, development and presentation. In addition, the proposed alternative was evaluated on cost, function and value improvement. Compared to the original design, the proposed alternative saved cost and improved the function and overall value.

Protein kinase CK2 is a ubiquitous kinase that can phosphorylate hundreds of cellular proteins and plays important roles in cell growth and development. Deregulation of CK2 is related to a variety of human cancers, and CK2 is regarded as a suppressor of apoptosis; therefore, it is a target of anticancer therapy. Nucleolar phosphoprotein 140 (Nopp140), which is an intrinsically disordered protein, interacts with CK2 and inhibits the latter's catalytic activity in vitro. Interestingly, the catalytic activity of CK2 is recovered in the presence of d-myo-inositol 1,2,3,4,5,6-hexakisphosphate (IP6). IP6 is widely distributed in animal cells, but the molecular mechanisms that govern its cellular functions in animal cells have not been completely elucidated. In this study, the crystal structure of CK2 in complex with IP6 showed that the lysine-rich cluster of CK2 plays an important role in binding to IP6. The biochemical experiments revealed that a Nopp140 fragment (residues 568-596) and IP6 competitively bind to the catalytic subunit of CK2 (CK2α), and phospho-Ser574 of Nopp140 significantly enhances its interaction with CK2α. Substitutions of K74E, K76E, and K77E in CK2α significantly reduced the interactions of CK2α with both IP6 and the Nopp140-derived peptide. Our study gives an insight into the regulation of CK2. In particular, our work suggests that CK2 activity is inhibited by Nopp140 and reactivated by IP6 by competitive binding at the substrate recognition site of CK2.

Around 70% of Korea is mountainous, an increase in tunnel construction. It’s due to the growing interest of the public for the environment and land required for the road construction is very scarce. During construction of ‘Daedong 1 tunnel’ in the expressway expansion project between Naengjeong and Busan, there are shallow shaft due to this tunnel located in the valley and the shafts are separated, and penetrating location change was inevitable for construction was delayed because of complaint. So, we change the position of the penetrating by applying multi-channel TSP, and conducted a stability analysis. The analysis results showed that there is no problem on the stability of the tunnel. To secure the construction of additional stability, We installed instrument, performed mechanical excavation, added reinforcement at shallow shaft and conducted bench cut. Key words Shallow shaft, Change penetrating location, TSP using Multi-Channel초 록 국토의 70%가 산지인 우리나라는 도로건설 등에 필요한 토지가 매우 부족할 뿐만 아니라 환경에 대한 국민들의 관심이 고조되어 터널 시공이 증가하는 추세이다 . 남해고속도로 냉정～부산간 확장공사 대동1터널 시공 시 계곡부 위치 및 갱문 이격으로 저토피가 발생하였고 , 민원 등으로 착공이 지연되어 관통부 변경이 불가피하였다. 이에 다중TSP를 적용하여 관통부 위치를 변경하였고 안정해석을 실시하였다 . 해석결과 터널의 안정성에 문제가 없는 것으로 나타났으며 , 시공 중 추가적인 안정성을 확보하고자 계측기 설치 및 기계굴착 , 저토피 구간 추가 보강, 반단면 굴착을 실시하였다.핵심어 저토피, 관통부 변경, 다중채널TSP

Gold nanoparticles (AuNPs) encapsulated within reconstituted phospholipid bilayers have been utilized in various bioapplications due to their improved cellular uptake without compromising their advantages. Studies have proved that clustering AuNPs can enhance the efficacy of theranostic effects, but controllable aggregation or oligomerization of AuNPs within lipid membranes is still challenging. Here, we successfully demonstrate the formation of gold nanoparticle clusters (AuCLs), supported by reconstituted phospholipid bilayers with appropriate sizes for facilitating cellular uptake. Modulation of the lipid membrane curvatures influences not only the stability of the oligomeric state of the AuCLs, but also the rate of cellular uptake. Dynamic light scattering (DLS) data showed that 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), with its relatively small head group, is crucial for establishing an effective membrane curvature to encapsulate the AuCLs. The construction of phospholipid bilayers surrounding AuCLs was confirmed by analyzing the secondary structure of M2 proteins incorporated in the lipid membrane surrounding the AuCLs. When AuCLs were incubated with cells, accumulated clusters were found inside the cells without the lipids being removed or exchanged with the cellular membrane. We expect that our approach of clustering gold nanoparticles within lipid membranes can be further developed to design a versatile nanoplatform.

When the Z-type variant of human α(1)-antitrypsin was overexpressed in Saccharomyces cerevisiae, proteomics analysis identified YLR301w as one of the up-regulated proteins. YLR301w is a 27.5 kDa protein with no sequence homology to any known protein and has been reported to interact with Sec72 and Hrr25. The crystal structure of S. cerevisiae YLR301w has been determined at 2.3 Å resolution, revealing a novel β-structure. It consists of an N-terminal ten-stranded β-barrel with two short α-helices connected by a 23-residue linker to a seven-stranded half-barrel with two short helices at the C-terminus. The N-terminal barrel has a highly conserved hydrophobic channel that can bind hydrophobic molecules such as PEG. It forms a homodimer both in the crystal and in solution. YLR301w binds Sec72 with a K(d) of 6.2 µM, but the biological significance of this binding requires further investigation.

Early diagnosis of infectious diseases is important for treatment; therefore, selective and rapid detection of pathogenic bacteria is essential for human health. We report a strategy for highly selective detection and rapid separation of pathogenic microorganisms using magnetic nanoparticle clusters. Our approach to develop probes for pathogenic bacteria, including Salmonella, is based on a theoretically optimized model for the size of clustered magnetic nanoparticles. The clusters were modified to provide enhanced aqueous solubility and versatile conjugation sites for antibody immobilization. The clusters with the desired magnetic property were then prepared at critical micelle concentration (CMC) by evaporation-induced self-assembly (EISA). Two different types of target-specific antibodies for H- and O-antigens were incorporated on the cluster surface for selective binding to biological compartments of the flagella and cell body, respectively. For the two different specific binding properties, Salmonella were effectively captured with the O-antibody-coated polysorbate 80-coated magnetic nanoclusters (PCMNCs). The synergistic effect of combining selective targeting and the clustered magnetic probe leads to both selective and rapid detection of infectious pathogens.

Enoyl-[acyl carrier protein] reductase (ENR) is an essential enzyme in type II fatty-acid synthesis that catalyzes the last step in each elongation cycle. Thus far FabI, FabL and FabK have been reported to carry out the reaction, with FabI being the most characterized. Some bacteria have more than one ENR, and Bacillus cereus has two (FabI and FabL) reported. Here, we have determined the crystal structures of the later in the apo form and in the ternary complex with NADP(+) and an indole naphthyridinone inhibitor. The two structures are almost identical, except for the three stretches that are disordered in the apo form. The apo form exists as a homo-dimer in both crystal and solution, while the ternary complex forms a homo-tetramer. The three stretches disordered in the apo structure are important in the cofactor and the inhibitor binding as well as in tetramer formation.

PDF (peptide deformylase) plays a critical role in the production of mature proteins by removing the N-formyl polypeptide of nascent proteins in the prokaryote cell system. This protein is essential for bacterial growth, making it an attractive target for the design of new antibiotics. Accordingly, PDF has been evaluated as a drug target; however, architectural mechanism studies of PDF have not yet fully elucidated its molecular function. We recently reported the crystal structure of PDF produced by Enterococcus faecium [K.H. Nam, J.I. Ham, A. Priyadarshi, E.E. Kim, N. Chung, K.Y. Hwang, "Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure", Proteins 74 (2009) 261-265]. Here, we present the crystal structure of the EfPDF complex with MAS (Met-Ser-Ala), thereby not only delineating the architectural mechanism for the recognition of mimic-peptides by N-terminal cleaved expression peptide, but also suggesting possible targets for rational design of antibacterial drugs. In addition to their implications for drug design, these structural studies will facilitate elucidation of the architectural mechanism responsible for the peptide recognition of PDF.

d -Glutamic acid is a required biosynthetic building block for peptidoglycan, and the enzyme glutamate racemase (GluR) catalyzes the inter-conversion of D and L-glutamate enantiomers. Therefore, GluR is considered as an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of GluR from Streptococcus pyogenes in both inhibitor-free and inhibitor-bound forms. The inhibitor free GluR crystallized in two different forms, which diffracted to 2.25 A and 2.5 A resolution, while the inhibitor-bound crystal diffracted to 2.5 A resolution. GluR is composed of two domains of α/β protein that are related by pseudo-2-fold symmetry and the active site is located at the domain interface. The inhibitor, γ-2-naphthylmethyl- d -glutamate, which was reported earlier as a novel potent competitive inhibitor, makes several hydrogen bonds with protein atoms, and the naphthyl moiety is located in the hydrophobic pocket. The inhibitor binding induces a disorder in one of the loops near the active site. In both crystal forms, GluR exists as a dimer and the interactions seen at the dimer interface are almost identical. This agrees well with the results from gel filtration and dynamic light-scattering studies.

The setting and hardening of concrete is accompanied with nonlinear temperature distribution caused by development of hydration heat of cement. Especially at early ages, this nonlinear distribution has a large influence on the crack evolution. As a result, in order to predict the exact temperature history in concrete structures it is required to examine thermal properties of concrete. In this study, the coefficient of air convection, which presents thermal transfer between surface of concrete and air, was experimentally investigated with variables such as velocity of wind and types of form. From experimental results, the coefficient of air convection was calculated using equations of thermal equilibrium. Finally, the prediction model for equivalent coefficient of air convection including effects of velocity of wind and types of form was theoretically proposed. The coefficient of air convection in the proposed model increases with velocity of wind, and its dependance on wind velocity is vaned with types of form. This tendency is due to a combined heat transfer system of conduction through form and convection to air. From comparison with experimental results, the coefficient of air convection by this model was well agreed with those by experimental results.

Influencing factors on thermal conductivity of concrete are quantitatively investigated by QTM-D3—that is, a conductivity tester developed in Japan—and a prediction equation of thermal conductivity of concrete is suggested from the regression analysis of test results. To consider the interacted factors influencing thermal conductivity of concrete, mortar, and cement paste, seven testing variables such as age, water–cement (W/C) ratio, types of admixtures, aggregate volume fraction, fine aggregate faction, temperature, and humidity condition of specimen were adopted in this test. According to experimental results, aggregate volume fraction and moisture condition of specimen are revealed as mainly affecting factors on the conductivity of concrete. Meanwhile, the conductivities of mortar and cement paste are strongly affected by the W/C ratio and types of admixtures. However, age hardly changes the conductivity except for very early age. Finally, the conductivity of concrete is represented in terms of the aggregate volume fraction, fine aggregate fraction, W/C ratio, temperature, and humidity condition of specimen.

Muskelin is an intracellular kelch-repeat protein comprised of discoidin, LisH, CTLH and kelch-repeat domains. It is involved in cell adhesion and the regulation of cytoskeleton dynamics as well as being a component of a putative E3 ligase complex. Here, the first crystal structure of mouse muskelin discoidin domain (MK-DD) is reported at 1.55 Å resolution, which reveals a distorted eight-stranded β-barrel with two short α-helices at one end of the barrel. Interestingly, the N- and C-termini are not linked by the disulfide bonds found in other eukaryotic discoidin structures. A highly conserved MIND motif appears to be the determinant for MK-DD specific interaction together with the spike loops. Analysis of interdomain interaction shows that MK-DD binds the kelch-repeat domain directly and that this interaction depends on the presence of the LisH domain.

The reduction of hydration heat and the prediction of temperature history in massive concrete structures have been very important problems. In this study, a three-dimensional finite element program for thermal analysis of hydration heat in concrete structures with pipe cooling system was developed. A line element was adopted for modeling of pipe. Internal flow theory was applied for calculating the temperature variation of cooling water. The predicted results were compared with the measured data from the spread concrete footing of the Seo–Hae Bridge in Korea. The predicted results showed good agreements with the site measured data.

Malonyl-CoA:acyl-carrier protein transacylase (MCAT), encoded by the fabd gene, is a key enzyme in type II fatty-acid biosynthesis. It is responsible for transferring the malonyl group from malonyl-CoA to the holo acyl-carrier protein (ACP). Since the type II system differs from the type I system that mammals use, it has received enormous attention as a possible antibiotic target. In particular, only a single isoform of MCAT has been reported and a continuous coupled enzyme assay has been developed. MCAT from Staphylococcus aureus was overexpressed in Escherichia coli and the protein was purified and crystallized. Diffraction data were collected to 1.2 A resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 41.608, b = 86.717, c = 43.163 A, alpha = gamma = 90, beta = 106.330 degrees . The asymmetric unit contains one SaMCAT molecule.

Enoyl-[acyl-carrier protein] reductase (enoyl-ACP reductase; ENR) is a key enzyme in type II fatty-acid synthase that catalyzes the last step in each elongation cycle. It has been considered as an antibiotic target since it is an essential enzyme in bacteria. However, recent studies indicate that some pathogens have more than one ENR. Bacillus subtilis is reported to have two ENRs, namely BsFabI and BsFabL. While BsFabI is similar to other FabIs, BsFabL shows very little sequence similarity and is NADPH-dependent instead of NADH-dependent as in the case of FabI. In order to understand these differences on a structural basis, BsFabL has been cloned, expressed and and crystallized. The crystal belongs to space group P622, with unit-cell parameters a = b = 139.56, c = 62.75 A, alpha = beta = 90, gamma = 120 degrees and one molecule of FabL in the asymmetric unit. Data were collected using synchrotron radiation (beamline 4A at the Pohang Light Source, Korea). The crystal diffracted to 2.5 A resolution.

Enoyl-[acyl carrier protein] (ACP) reductase (ENR) is a key enzyme in type II fatty acid synthesis that catalyzes the last step in each elongation cycle. Therefore, it has been considered as a target for antibiotics. However, recent studies indicate that some pathogens have more than one ENR; in particular, Bacillus subtilis has two ENRs, FabI and FabL. The crystal structures of the ternary complexes of BsFaBI and BsFabL are found as a homotetramer showing the same overall structure despite a sequence identity of only 24%. The positions of the catalytic dyad of Tyr-(Xaa)(6)-Lys in FabL are almost identical to that of FabI, but a detailed structural analysis shows that FabL shares more structural similarities with FabG and other members of the SDR (short-chain alcohol dehydrogenase/reductase) family. The apo FabL structure shows significantly different conformations at the cofactor and the substrate-binding regions, and this resulted in a totally different tetrameric arrangement reflecting the flexibility of these regions in the absence of the cofactor and substrate/inhibitor.

Farnesoid X receptor (FXR) serves as a receptor for chenodeoxycholic acid (CDCA) and other bile acids, and it coordinates cholesterol and lipid metabolism. Because targeting the FXR-CDCA interaction might provide a way to regulate lipid homeostasis, we developed an FXR binding assay based on fluorescence polarization. Employing a fluorescently labeled CDCA (CDCA-F), we showed that CDCA-F selectively bound to the ligand binding domain of FXR (FXR-LBD) among nuclear receptors. The assay was then used for screening inhibitors against the FXR-CDCA interaction, thereby discovering four relatively potent inhibitors. The selected inhibitors were further studied for changes in intrinsic tryptophan fluorescence of FXR-LBD to gain structural insights into the interaction. Furthermore, transactivation effects of the inhibitors on the human bile salt excretory pump (BSEP) promoter were examined to reveal their cellular activities in the FXR-mediated pathway. Therefore, we demonstrated that the developed assay would offer an efficient primary screening tool for identifying FXR modulators.

Fe-M-O (M=Hf, AD films are fabricated by Ar+O2 reactive sputtering and their magnetic properties are investigated. Excellent soft magnetic properties at high frequency are obtained in Fe-Hf-O and Fe-Al-O thin films even in an as-deposited state; for example, Fe82Hf3.4O14.6 and Fe90.7Al2O7.3 films exhibit the values of 17.7 and 18.5 kG for saturation magnetization, 1.0 and 0.65 Oe for coercivity, and 2,200 and 3,000 for the effective permeability at 100 MHz, respectively. Microstructures, magnetic anisotropy and electrical resistivity are investigated to understand the magnetic properties of the thin films.

The nickel and cobalt resistance of Cupriavidus metallidurans CH34 is mediated by the CnrCBA efflux pump encoded by the cnrYHXCBAT metal resistance determinant. The products of the three genes cnrYXH transcriptionally regulate expression of cnr. CnrY and CnrX are membranebound proteins, probably functioning as anti-sigma factors, whereas CnrH is a cnr-specific extracytoplasmic functions (ECF) sigma factor. The periplasmic domain of CnrX (residues 29- 148) was cloned as a N-terminal His-tagged protein, expressed in Escherichia coli, and purified using affinity chromatography and gel filtration. The molecular mass was estimated to be about 13.6 kDa by size exclusion chromatography, corresponding to a monomer. The tetragonal bipyramid crystals were obtained by mixing an equal volume of protein in 50 mM Tris-HCl, pH 7.5, 1% glycerol, 100 mM NaCl, 1 mM DTT, and the reservoir solution of 15% w/v PEG 2000, 100 mM lithium chloride at 277 K in 2-4 days using hanging drop vapor diffusion. The protein concentration was 24 mg/ml. The crystal that diffracted to 2.42 A resolution belongs to space group P41 or P4(3) with unit cell parameters of a=b=32.14 A, c=195.31 A, alpha=beta=gamma=90 degrees, with one molecule of CnrX in the asymmetric unit.

Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, some bacteria including medically relevant pathogens possess two or more def-like genes. Here we have examined two PDFs from Bacillus cereus. The two share only 32% sequence identity and the crystal structures show overall similarity with PDF2 having a longer C-terminus. However, there are differences at the two active sites, and these differences appear to contribute to the activity difference seen between the two. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface.

In 1996, the concept of proxy signature was introduced by Mambo, Usuda and Okamoto in M. Mambo et al. (1996). A strong proxy signature scheme has been introduced in B. Lee et al. (2001), which we call LKK (B. Lee, H. Kim, K. Kim) scheme. In Z. Dong et al. (2003), the authors showed that the LKK scheme is vulnerable to their attack. In this paper, based on the vulnerability of the LKK scheme and blind Schnorr signature scheme, we propose a revised proxy signature and a proxy blind signature scheme. The basic idea is to propose the revised scheme resisting their attack and to make it difficult for the original signer to delete a delegation value.

These days in Internet, emerging various applications has become more complicated and needed large bandwidth under the necessity to securely use them. Network bandwidth has increased as much as to support those needs. But it becomes increasingly difficult to utilize them to their full capacity [I]. In other word, up-grading of network bandwidth is not enough solution to enhance performance experienced by end users. There are so many causes including TCP/IP protocol behaviors, application issues and network configuration issues etc. In this paper, I would suggest a new system diagnosis tool to settle specially enhancement of end user & E2E performance. The goals of this tool are to enable an end user & network operator to diagnose an end-host system and E2E performance weak point, offer some advises and optimize the systems by given auto or manual system metrics tuning guideline. And I wish to get an overlay network to understand network characteristics and utilize full network capacity. In this paper, we look over briefly other relative projects and introduce some key metrics to optimize end-host performance

Malonyl-CoA-acyl carrier protein transacylase (MCAT) transfers the malonyl group from malonyl-CoA to holo-acyl carrier protein (ACP), and since malonyl-ACP is a key building block for fatty-acid biosynthesis it is considered as a promising antibacterial target. The crystal structures of MCAT from Staphylococcus aureus and Streptococcus pneumoniae have been determined at 1.46 and 2.1Å resolution, respectively. In the SaMCAT structure, the N-terminal expression peptide of a neighboring molecule running in the opposite direction of malonyl-CoA makes extensive interactions with the highly conserved “Gly-Gln-Gly-Ser-Gln” stretch, suggesting a new design platform. Mutagenesis results suggest that Ser91 and His199 are the catalytic dyad.