• Journal of the Korean Magnetic Resonance Society
• /
• v.17 no.1
• /
• pp.59-66
• /
• 2013

BldD, a developmental transcription factor from Streptomyces coelicolor, is a homodimeric, DNA-binding protein with 167 amino acids in each subunit. Each monomer consists of two structurally distinct domains, the N-terminal domain (BldD-NTD) responsible for DNA-binding and dimerization and the C-terminal domain (BldD-CTD). In contrast to the BldD-NTD, of which crystal structure has been solved, the BldD-CTD has been characterized neither in structure nor in function. Thus, in terms of structural genomics, structural study of the BldD-CTD has been conducted in solution, and in the present work, mainchain NMR assignments of the recombinant BldD-CTD (residues 80-167 of BldD) could be achieved by a series of heteronuclear multidimensional NMR experiments on a [$^{13}C/^{15}N$]-enriched protein sample. Finally, the secondary structure prediction by CSI and TALOS+ analysis using the assigned chemical shifts data identified a ${\beta}-{\alpha}-{\alpha}-{\beta}-{\alpha}-{\alpha}-{\alpha}$ topology of the domain. The results will provide the most fundamental data for more detailed approach to the atomic structure of the BldD-CTD, which would be essential for entire understanding of the molecular function of BldD.

• Journal of the Optical Society of Korea
• /
• v.16 no.2
• /
• pp.166-169
• /
• 2012

We propose a high-transmittance multi-domain vertical alignment liquid crystal device with a protrusion structure. Disclination lines, which inevitably appear at the boundaries of domains in a multi-domain structure, can be reduced by adding a protrusion structure on the top substrate. The transmittance was improved by 11% using the proposed structure with no change of either the dark state or the operating voltage.

• Journal of the Society of Naval Architects of Korea
• /
• v.45 no.2
• /
• pp.168-174
• /
• 2008

To calculate the fluid-structure interaction(FSI) problem rationally, it should be the basic technology to analyse each domain of fluid and structure accurately. In this paper, a new FSI analysis algorithm was introduced using the 3D solid finite element for structural analysis and CFD code based on the HCIB method for viscous flow analysis. The fluid and structural domain were analysed successively and alternatively in time domain. The structural domain was analysed by the Newmark-b direct time integration scheme using the pressure field calculated by the CFD code. The results for example calculation were compared with other research and it was shown that those coincided each other. So we can conclude that the developed algorithm can be applied to the general FSI problems.

• Molecules and Cells
• /
• v.44 no.3
• /
• pp.179-185
• /
• 2021

Vancomycin response regulator (VncR) is a pneumococcal response regulator of the VncRS two-component signal transduction system (TCS) of Streptococcus pneumoniae. VncRS regulates bacterial autolysis and vancomycin resistance. VncR contains two different functional domains, the N-terminal receiver domain and C-terminal effector domain. Here, we investigated VncR C-terminal DNA binding domain (VncRc) structure using a crystallization approach. Crystallization was performed using the micro-batch method. The crystals diffracted to a 1.964 Å resolution and belonged to space group P212121. The crystal unit-cell parameters were a = 25.71 Å, b = 52.97 Å, and c = 60.61 Å. The structure of VncRc had a helix-turn-helix motif highly similar to the response regulator PhoB of Escherichia coli. In isothermal titration calorimetry and size exclusion chromatography results, VncR formed a complex with VncS, a sensor histidine kinase of pneumococcal TCS. Determination of VncR structure will provide insight into the mechanism by how VncR binds to target genes.

• Journal of the Korean Magnetic Resonance Society
• /
• v.12 no.1
• /
• pp.1-13
• /
• 2008

Acetyl-CoA carboxylase (ACC) catalyzes the first step in fatty acid biosynthesis: the synthesis of malonyl-CoA from acetyl-CoA. As essential regulators of fatty acid biosynthesis and metabolism, ACCs are regarded as therapeutic targets for the treatment of metabolic diseases such as obesity, In ACC, the biotinoyl domain performs a critical function by transferring an activated carboxyl group from the biotin carboxylase domain to the carboxyl transferase domain, followed by carboxyl transfer to malonyl-CoA. Despite the intensive research on this enzyme, only the bacterial and yeast ACC structures are currently available, To explore the mechanism of ACC holoenzyme function, we determined the structure of the biotinoyl domain of human ACC2 and analyze its characteristics using NMR spectroscopy. The 3D structure of the hACC2 biotinoyl domain has a similar folding topology to the previously determined domains from E. coli and P. Shermanii, however, the 'thumb' structure is absent in the hACC2 biotinoyl domain. Observations of the NMR signals upon the biotinylation indicate that the biotin group of hACC2 does not affect the structure of the biotinoyl domain, while the biotin group for E. coli ACC interacts directly with the thumb residues that are not present in the hACC2 structure. These results imply that, in the E. coli ACC reaction, the biotin moiety carrying the carboxyl group from BC to CT can pause at the thumb of the BCCP domain. The human biotinoyl domain, however, lacks the thumb structure and does not have additional non-covalent interactions with the biotin moiety; thus, the flexible motion of the biotinylated lysine residue must underlie the "swinging arm" motion. This study provides insight into the mechanism of ACC holoenzyme function and supports the "swinging arm" model in human ACCs.

• Journal of the Korea Safety Management & Science
• /
• v.15 no.3
• /
• pp.133-141
• /
• 2013

As a work analysis technique, Work Domain Analysis (WDA) aims to identify the design knowledge structure of a work domain that human operators interact with through human-system interfaces. Abstraction hierarchy (AH) is a multi-level, hierarchical knowledge representation framework for modeling the functional structure of any kinds of systems. Thus, WDA based on AH aims to identify the functional knowledge structure of a work domain. AH has been used in a range of work domains and problems to model their functional knowledge structure and has proven its generality and usefulness. However, many of researchers and system designers have reported that it is never easy to understand the concepts underlying AH and use it effectively for WDA. This would be because WDA is a form of work analysis that is different from other types of work analysis techniques such as task analysis and AH has several unique characteristics that are differentiated from other types of function analysis techniques used in systems engineering. With this issue in mind, this paper introduces the concepts of WDA based on AH and offers a comprehensive list of references. Next, this paper proposes a set of principles for effectively applying AH for work domain analysis, which are developed based on the author's experiences, consultation with experts, and literature reviews.

• Journal of the Earthquake Engineering Society of Korea
• /
• v.22 no.7
• /
• pp.379-390
• /
• 2018

In this study, a numerical approach based on mid-point integrated finite elements and a viscous boundary is proposed for time-domain wave-propagation analyses in infinite poroelastic media. The proposed approach is accurate, efficient, and easy to implement in time-domain analyses. In the approach, an infinite domain is truncated at some distance. The truncated domain is represented by mid-point integrated finite elements with real element-lengths and a viscous boundary is attached to the end of the domain. Given that the dynamic behaviors of the proposed model can be expressed in terms of mass, damping, and stiffness matrices only, it can be implemented easily in the displacement-based finite-element formulation. No convolutional operations are required for time-domain calculations because the coefficient matrices are constant. The proposed numerical approach is applied to typical wave-propagation and soil-structure interaction problems. The model is verified to produce accurate and stable results. It is demonstrated that the numerical approach can be applied successfully to nonlinear soil-structure interaction problems.

• Korean Journal of Materials Research
• /
• v.14 no.2
• /
• pp.94-100
• /
• 2004

We have investigated the magnetic domain structure and the thermal stability of magnetotransport properties of IrMn biased spin-valves containing Co, CoFe and NiFe. The magnetic domain structures were imaged using a magneto-optical indicator film(MOIF) technique. To investigate the thermal stability, magnetoresistance(MR) was measured at annealing temperature(TANN) and room temperature($T_{RT}$) followed by the annealing. Domain imaging reveal that the increase of annealing temperature led to changes in the exchange coupling between the two ferromagnet(FM) layers through nonmagnetic layer rather than between FM and antiferromagnet. unlike the NiFe biased IrMn spin valve with large domains, MOIF pictures of Co and CoFe biased IrMn spin valve structures show the formation of many small microdomains. The magnetic structure, as revealed by the domain images, appeared unchanged while the MR dropped dramatically. From the combined giant magnetoresistance(GMR) and MOIF results, it was apparent that the decrease of MR ratio was not related to the spin valve magnetic structure up to about $350^{\circ}C$($T_{RT}$ ).

• Journal of the Korean Chemical Society
• /
• v.68 no.1
• /
• pp.25-31
• /
• 2024

The p97 adenosine triphosphatase is a key player in protein homeostasis, responsible for unfolding ubiquitylated substrates. It engages with various adaptor proteins through its N-terminal domain, with the p97-p47 complex attracting particular attention for its involvement in membrane remodeling. Although the structures of p97 in complex with the Ubiquitin regulatory X (UBX) domain from various adaptors have been reported, the stoichiometry is conflicting. Here, we report the crystal structure of the p97 N-D1 hexamer in complex with the p47 UBX domain at a resolution of 2.7 Å. The structure reveals a stoichiometry of 6:6 between the p97 N-D1 and the p47 UBX domain. These findings provide valuable insights into the binding stoichiometry of p97 N-D1 and p47 UBX domain, which are crucial for understanding the role of p97 and adaptor proteins in cellular processes such as the ubiquitin-proteasome pathway, membrane fusion, and cell cycle regulation.

• Structural Engineering and Mechanics
• /
• v.86 no.1
• /
• pp.93-107
• /
• 2023

In this paper, a density based topology optimization is proposed for generating of supports required in additive manufacturing to maintain the overhanging regions of main structures during layer by layer fabrication process. For this purpose, isogeometric analysis method is employed to model geometry and structural analysis of main and support structures. In order to model the problem two cases are investigated. In the first case, design domain of supports can easily be separated from the main structure by using distinct isogeometric patches. The second case happens when the main structure itself is optimized by using topology optimization and the supports should be designed in the voids of optimum layout. In this case, in order to avoid boundary identification and re-meshing process for separating design domain of supports from main structure, a parameterization technique is proposed to identify the design domain of supports. To achieve this, two density functions are defined over the entire domain to describe the main structure and supporting areas. On the other hand, since supports are under gravity loads while main structure and its stiffness is not completed during manufacturing process, in the proposed method, stiffness of the main structure is considered to be trivial and the gravity loads are also naturally applied to design support structures. By doing so, the results show reasonable supports are created to protect, continuously, overhanging surfaces of the main structure. Several examples are presented to demonstrate the efficiency of the proposed method and compare the results with literature.