• 한국언어정보학회:학술대회논문집
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• 한국언어정보학회 2002년도 Language, Information, and Computation Proceedings of The 16th Pacific Asia Conference
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• pp.2-27
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• 2002

As pact of a long-ranged project that aims at establishing database-theoretic semantics as a model of computational semantics, this presentation focuses on the development of a syntactic component for processing strings of words or sentences to construct semantic data structures. For design arid modeling purposes, the present treatment will be restricted to the analysis of some problematic constructions of Korean involving semi-free word order, conjunction arid temporal anchoring, and adnominal modification and antecedent binding. The present work heavily relies on Hausser's (1999, 2000) SLIM theory for language that is based on surface compositionality, time-linearity arid two other conditions on natural language processing. Time-linear syntax for natural language has been shown to be conceptually simple and computationally efficient. The associated semantics is complex, however, because it must deal with situated language involving interactive multi-agents. Nevertheless, by processing input word strings in a time-linear mode, the syntax cart incrementally construct the necessary semantic structures for relevant queries and valid inferences. The fragment of Korean syntax will be implemented in Malaga, a C-type implementation language that was enriched for both programming and debugging purposes arid that was particluarly made suitable for implementing in Left-Associative Grammar. This presentation will show how the system of syntactic rules with constraining subrules processes Korean sentences in a step-by-step time-linear manner to incrementally construct semantic data structures that mainly specify relations with their argument, temporal, and binding structures.

• Corrosion Science and Technology
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• 제8권2호
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• pp.81-88
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• 2009

Chloride induced corrosion of steel reinforcement inside concrete is a major concern for concrete structures exposed to a marine environment. It is well known that transport of chloride ions in concrete occurs mainly through ionic/molecular diffusion, as a gradient of chloride concentration in the concrete pore solution is set. In the process of chloride transport, a portion of chlorides are bound in cement matrix then to be removed in the pore solution, and thus only the rest of chlorides which are not bound (i.e. free chlorides) leads the ingress of chlorides. However, since the measurement of free/bound chloride content is much susceptible to environmental conditions, chloride profiles expressed in total chlorides are evaluated to use in many studies In this study, the capacity of chloride binding in cement matrix was monitored for 150 days and then quantified using the Langmuir isotherm to determine the portions of free chlorides and bound chlorides at given total chlorides and the redistribution of free chlorides. Then, the diffusion of chloride ion in concrete was modeled by considering the binding capacity for the prediction of chloride profiles with the redistribution. The predicted chloride profiles were compared to those obtained from conventional model. It was found that the prediction of chloride profiles obtained by the model has shown slower diffusion than those by the conventional ones. This reflects that the prediction by total chloride may overestimate the ingress of chlorides by neglecting the redistribution of free chlorides caused by the binding capacity of cement matrix. From the evaluation, it is also shown that the service life prediction using the free chloride redistribution model needs different expression for the chloride threshold level which is expressed by the total chlorides in the conventional diffusion model.

• Molecules and Cells
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• 제39권11호
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• pp.814-820
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• 2016

FtsZ, a tubulin homologue, is an essential protein of the Z-ring assembly in bacterial cell division. It consists of two domains, the N-terminal and C-terminal core domains, and has a conserved C-terminal tail region. Lateral interactions between FtsZ protofilaments and several Z-ring associated proteins (Zaps) are necessary for modulating Z-ring formation. ZapD, one of the positive regulators of Z-ring assembly, directly binds to the C-terminal tail of FtsZ and promotes stable Z-ring formation during cytokinesis. To gain structural and functional insights into how ZapD interacts with the C-terminal tail of FtsZ, we solved two crystal structures of ZapD proteins from Salmonella typhimurium (StZapD) and Escherichia coli (EcZapD) at a 2.6 and $3.1{\AA}$ resolution, respectively. Several conserved residues are clustered on the concave sides of the StZapD and EcZapD dimers, the suggested FtsZ binding site. Modeled structures of EcZapD-EcFtsZ and subsequent binding studies using bio-layer interferometry also identified the EcFtsZ binding site on EcZapD. The structural insights and the results of bio-layer interferometry assays suggest that the two FtsZ binding sites of ZapD dimer might be responsible for the binding of ZapD dimer to two protofilaments to hold them together.

• Molecules and Cells
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• 제45권8호
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• pp.575-587
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• 2022

Human ABCB6 is an ATP-binding cassette transporter that regulates heme biosynthesis by translocating various porphyrins from the cytoplasm into the mitochondria. Here we report the cryo-electron microscopy (cryo-EM) structures of human ABCB6 with its substrates, coproporphyrin III (CPIII) and hemin, at 3.5 and 3.7 Å resolution, respectively. Metal-free porphyrin CPIII binds to ABCB6 within the central cavity, where its propionic acids form hydrogen bonds with the highly conserved Y550. The resulting structure has an overall fold similar to the inward-facing apo structure, but the two nucleotide-binding domains (NBDs) are slightly closer to each other. In contrast, when ABCB6 binds a metal-centered porphyrin hemin in complex with two glutathione molecules (1 hemin: 2 glutathione), the two NBDs end up much closer together, aligning them to bind and hydrolyze ATP more efficiently. In our structures, a glycine-rich and highly flexible "bulge" loop on TM helix 7 undergoes significant conformational changes associated with substrate binding. Our findings suggest that ABCB6 utilizes at least two distinct mechanisms to fine-tune substrate specificity and transport efficiency.

• Steel and Composite Structures
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• 제28권6호
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• pp.671-679
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• 2018

The paper is devoted to the stability analysis of a simply supported five layer sandwich beam. The beam consists of five layers: two metal faces, the metal foam core and two binding layers between faces and the core. The main goal is to elaborate a mathematical and numerical model of this beam. The beam is subjected to an axial compression. The nonlinear hypothesis of deformation of the cross section of the beam is formulated. Based on the Hamilton's principle the system of four stability equations is obtained. This system is approximately solved. Applying the Bubnov-Galerkin's method gives an ordinary differential equation of motion. The equation is then numerically processed. The equilibrium paths for a static and dynamic load are derived and the influence of the binding layers is considered. The main goal of the paper is an analytical description including the influence of binding layers on stability, especially on critical load, static and dynamic paths. Analytical solutions, in particular mathematical model are verified numerically and the results are compared with those obtained in experiments.

• EDISON SW 활용 경진대회 논문집
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• 제6회(2017년)
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• pp.32-38
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• 2017

Prion is a group of the proteins known for its infection mechanisms of Creutzfeldt-Jakob disease (CJD) and other diseases. Solved structures and proven biological roles of fungal prions add tremendous potential to conducting computational simulations. Our research focuses on the binding dynamics of HET-s(218-289), one of the heterokaryon fungal prion originated from Podospora anserina, by calculating the binding free energy using umbrella sampling at 300 K. The binding free energy calculated was $-54.5kcal\;mol^{-1}$, relatively similar to the binding energy of other amyloid fibrils. The simulation result suggests the thermodynamic properties of ${\beta}$-solenoid of HET-s prion and its similarity in dissociation pathways compared to amyloids.

• Journal of Electrical Engineering and information Science
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• 제2권6호
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• pp.106-110
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• 1997

The binding energies of the ground state of both the heavy-hole and light-hole excitons in a GaAs(In\ulcornerGa\ulcornerAs) quantum well sandwiched between two semi-infinite Al\ulcornerGa\ulcornerAs(InP) layers are calculated as a function of well width in the presence of an arbitray magnetic field. A variational approach is followed using very simple trial wave function. The applied magnetic field is assumed to be parallel to the axis of growth and the binding energies are calculated for a finite value of the height of the potential barrier. The exciton binding energies for a given value of the magnetic field are found to be increased than their values in a zero magnetic field due to the compression of their wave functions within the well with the applied magnetic field.

• BMB Reports
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• 제31권4호
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• pp.307-327
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• 1998

Cytochrome c peroxidase (CcP) is a yeast mitochondrial enzyme which catalyzes the reduction of hydrogen peroxide to water using two equivalents of ferrocytochrome c. The CcP/cytochrome c system has many features which make it a very useful model for detailed investigation of heme protein structure/function relationships including activation of hydrogen peroxide, protein-protein interactions, and long-range electron transfer. Both CcP and cytochrome c are single heme, single subunit proteins of modest size. High-resolution crystallographic structures of both proteins, of one-to-one complexes of the two proteins, and a number of active-site mutants are available. Site-directed mutagenesis studies indicate that the distal histidine in CcP is primarily responsible for rapid utilization of hydrogen peroxide implying significantly different properties of the distal histidine in the peroxidases compared to the globins. CcP and cytochrome c bind to form a dynamic one-to-one complex. The binding is largely electrostatic in nature with a small, unfavorable enthalpy of binding and a large positive entropy change upon complex formation. The cytochrome c-binding site on CcP has been mapped in solution by measuring the binding affinities between cytochrome c and a number of CcP surface mutations. The binding site for cytochrome c in solution is consistent with the crystallographic structure of the one-to-one complex. Evidence for the involvement of a second, low-affinity cytochrome c-binding site on CcP in long-range electron transfer between the two proteins is reviewed.

• Journal of Microbiology and Biotechnology
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• 제28권8호
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• pp.1339-1345
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• 2018

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, which catalyzes aldol cleavage and condensation reactions, has two distinct substrate-binding sites. The substrate-binding mode at the catalytic site and Schiff-base formation have been well studied. However, structural information on the phosphate-binding loop (P-loop) is limited. Zymomonas mobilis KDPG aldolase is one of the aldolases with a wide substrate spectrum. Its structure in complex with the substrate-mimicking 3-phosphoglycerate (3PG) shows that the phosphate moiety of 3PG interacts with the P-loop and a nearby conserved serine residue. 3PG-binding to the P-loop replaces water molecules aligned from the P-loop to the catalytic site, as observed in the apostructure. The extra electron density near the P-loop and comparison with other aldolases suggest the diversity and flexibility of the serine-containing loop among KDPG aldolases. These structural data may help to understand the substrate-binding mode and the broad substrate specificity of the Zymomonas KDPG aldolase.

• BMB Reports
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• 제50권10호
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• pp.485-486
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• 2017

Many intrinsically unstructured/unfolded proteins (IUPs) contain transient local secondary structures even though they are "unstructured" in a tertiary sense. These local secondary structures are named "pre-structured motifs (PreSMos)" and in fact are the specificity determinants for IUP-target binding, i.e., the active sites in IUPs. Using high-resolution NMR we have delineated a PreSMo active site in the intrinsically unfolded mid-domain (residues 201-300) of SUMO-specific protease 4 (SUSP4). This 29-residue motif which we termed a p53 rescue motif can protect p53 from mdm2 quenching by binding to the p53-helix binding pocket in mdm2(3-109). Our work demonstrates that the PreSMo approach is quite effective in providing a structural rationale for interactions of p53-mdm2-SUSP4 and opens a novel avenue for designing mdm2-inhibiting anticancer compounds.