• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.438-444
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• 2008

A self-assembled monolayer of 2,2'-bipyridine (22BPY) molecules on Au(111) underwent a structural phase transition when the polarity of a bias voltage was switched in scanning tunneling microscopy (STM) experiments. The nature of two bright spots representing each 22BPY molecule on Au(111) in the high-resolution STM images was identified by calculating the partial density plots for a monolayer of 22BPY molecules adsorbed on Au(111) using tight-binding electronic structure calculations. The stacking pattern of the chains of 22BPY molecules on Au(111) was explained by examining the intermolecular interactions between the 22BPY molecules based on first principles electronic structure calculations for a 22BPY dimer, (22BPY)2. The structural instability of the 22BPY molecule arrangement caused by a change in the bias voltage switch was investigated by estimating the adsorbate-surface interaction energy using a point-charge approximation for Au(111).

• Journal of the Korean Magnetics Society
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• v.5 no.5
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• pp.846-853
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• 1995

In order to study electronic structures for locally disordered systems, we have developed a first-principle self-con-sistent-spin-polarized real space band method (TB-LMTO-R), which combines the tight-binding(TB) linear-muffin-tin orbital(LMTO) band rrethod and the recursion(R) rrethod. The TB-LMTO-R rrethod has been applied to fer-romagnetic bec Fe, hcp Co, and fcc Ni. With varying cluster sizes, recursion coefficients, and the order of the TB-Hamiltonian, we have calculated the local density of states(LDOS) and magnetic moments. It is found that the calculation with 5,000 atoms cluster, 40 continued fractions, and the second-order TB-Hamiltonian yields a conver¬gent result in agreement with those from the conventional LMTO. In this way, we have demonstrated a physical transparency of the TB-LMTO-R method as a real space description.

• Advances in nano research
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• v.14 no.1
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• pp.1-15
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• 2023

Driven by the scaling down of transistor node technology, graphene became of interest to many researchers following the success of its fabrication as graphene nanoribbons (GNRs). However, during the fabrication of GNRs, it is not uncommon to have defects within the GNR structures. Scaling down node technology also changes the modelling approach from the classical Boltzmann transport equation to the quantum transport theory because the quantum confinement effects become significant at sub-10 nanometer dimensions. The aim of this study is to examine the effect of Stone-Wales defects on the electronic properties of GNRs using a tight-binding model, based on Non-Equilibrium Green's Function (NEGF) via numeric computation methods using MATLAB. Armchair and zigzag edge defects are also implemented in the GNR structures to mimic the practical fabrication process. Electronic properties of pristine and defected GNRs of various lengths and widths were computed, including their band structure and density of states (DOS). The results show that Stone-Wales defects cause fluctuation in the band structure and increase the bandgap values for both armchair GNRs (AGNRs) and zigzag GNRs (ZGNRs) at every simulated width. In addition, Stone-Wales defects reduce the numerical computation DOS for both AGNRs and ZGNRs. However, when the lengths of the structures increase with fixed widths, the effect of the Stone-Wales defects become less significant.

• Advances in nano research
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• v.15 no.5
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• pp.385-399
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• 2023

Hexagonal boron nitride (h-BN), commonly referred to as Boron Nitride Nanoribbons (BNNRs), is an electrical insulator characterized by high thermal stability and a wide bandgap semiconductor property. This study delves into the electronic properties of two BNNR configurations: Armchair BNNRs (ABNNRs) and Zigzag BNNRs (ZBNNRs). Utilizing the nearest-neighbour tight-binding approach and numerical methods, the electronic properties of BNNRs were simulated. A simplifying assumption, the Hamiltonian matrix is used to compute the electronic properties by considering the self-interaction energy of a unit cell and the interaction energy between the unit cells. The edge perturbation is applied to the selected atoms of ABNNRs and ZBNNRs to simulate the electronic properties changes. This simulation work is done by generating a custom script using numerical computational methods in MATLAB software. When benchmarked against a reference study, our results aligned closely in terms of band structure and bandgap energy for ABNNRs. However, variations were observed in the peak values of the continuous curves for the local density of states. This discrepancy can be attributed to the use of numerical methods in our study, in contrast to the semi-analytical approach adopted in the reference work.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.531-535
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• 2011

It was regarded that the $^{31}P$ resonances of inherent nucleotides in $F_1$-ATPase (EF1), as large as 380KDa, could not be observed by $^{31}P$ NMR spectroscopy. However, our $^{31}P$ NMR spectroscopy could differentiate between different nucleotide binding sites on EF1 from Escherichia coli. When EF1 was prepared in the absence of $Mg^{2+}$, EF1 contained only ADP. Multiple $^{31}P$ resonances from $\beta$-phosphates of ADP bound to the EF1 were observed from the enzyme prepared without $Mg^{2+}$, suggesting asymmetry or flexibility amongst nucleotide binding sites. $^{31}P$ resonances from enzyme bound ATP could be observed only from EF1, when the enzyme was prepared in the presence of $Mg^{2+}$. This $Mg^{2+}$ dependent ATP binding was very tight that, once bound, nucleotide could not be removed even after removal of $Mg^{2+}$. $^{31}P$ NMR proved to be a valuable tool for investigating phosphorous related enzymes.

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.2019-2024
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• 2010

Insulin-like growth factor binding protein 5 (IGFBP-5) plays an important role in controlling cell survival, differentiation and apoptosis. Apoptosis can be induced by an extrinsic pathway involving the ligand-mediated activation of death receptors such as tumor necrosis factor receptor 1 (TNFR1). To determine whether IGFBP-5 and TNFR1 interact as members of the same apoptosis pathway, recombinant IGFBP-5 and TNFR1 were isolated. The expression and purification of the full-length TNFR1 and truncated IGFBP-5 proteins were successfully performed in E. coli. The binding of both IGFBP-5 and TNFR1 proteins was detected by surface plasmon resonance spectroscopy (BIAcore), fluorescence measurement, electron microscopy, and size-exclusion column (SEC) chromatography. IGFBP-5 indeed binds to TNFR1 with an apparent $K_D$ of 9 nM. After measuring the fluorescence emission spectra of purified IGFBP-5 and TNFR1, it was found that the tight interaction of these proteins is accompanied by significant conformational changes of one or both. These results indicate that IGFBP-5 acts potently as a novel ligand for TNFR1.

• Reproductive and Developmental Biology
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• v.40 no.2
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• pp.23-26
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• 2016

Transcription factor called activating enhancer binding protein 2C (AP2-gamma) is found in a variety of species and expressed from oocyte stage onwards, particularly restricted to the trophectoderm. Recent studies demonstrated that ablation of Tfap2c led to failure of tight junction biogenesis, particularly the knock-down embryos of Tfap2c did not form cavity from morula to blastocyst in mouse and pig. We speculated that the Tfa2pc may also be involved in desmosome biogenesis because blastocoel formation is coincident with the establishment of desmosome. To determine this, we depleted Tfap2c injecting siRNA into one-cell zygote and analysed the expression levels of genes that are required for desmosome complex such as PkP2, Pkp3, Dsc2, and Dsg2. We found only Pkp3 was up-regulated in the knockdowned morula embryos. Interestingly, upstream region of Pkp3 had putative Tfap2c binding sites. In conclusion, our results suggest that Tfap2c is not a crucial factor but somehow it might be involved in desmosome biogenesis directly or indirectly via Pkp3.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.63-63
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• 2003

$\alpha$$_1$-Antityrpsin is a member of the serine protease inhibitor (SERPIN) family that shares a common tertiary structure. The reactive site loop (RSL) of serpins is exposed at one end of the molecule for protease binding. Upon cleavage by a target protease, the RSL is inserted into the major $\beta$-sheet A, which is a necessary process for formation of a tight inhibitory complex. Various biochemical and structural studies suggest that the rate of the RSL insertion upon binding a target protease is critical for inhibitory activity, and it is thought that helix F region (thFs3A and helix F) located in front of $\beta$-sheet A, should be lifted for the loop insertion during complex formation.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.9 no.1
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• pp.49-55
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• 2023

Tumors are encircled by various non-cancerous cell types in the extracellular matrix, including fibroblasts, endothelial cells, immune cells, and cytokines. Fibroblasts are the most critical cells in the tumor stroma and play an important role in tumor development, which has been highlighted in some epithelial cancers. Many studies have shown a tight connection between cancerous cells and fibroblasts in the last decade. Regulatory factors secreted into the tumor environment by special fibroblast cells, cancer-associated fibroblasts (CAFs), play an important role in tumor and vessel development, metastasis, and therapy resistance. This review addresses the development of FAP inhibitors, emphasizing the first, second, and latest generations. First-generation inhibitors exhibit low selectivity and chemical stability, encouraging researchers to develop new scaffolds based on preclinical and clinical data. Second-generation enzymes such as UAMC-1110 demonstrated enhanced FAP binding and better selectivity. Targeted treatment and diagnostic imaging have become possible by further developing radionuclide-labeled fibroblast activation protein inhibitors (FAPIs). Although all three FAPIs (01, 02, and 04) showed excellent preclinical and clinical findings. The final optimization of these FAPI scaffolds resulted in FAPI-46 with the highest tumor-to-background ratio and better binding affinity.

• BMB Reports
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• v.29 no.6
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• pp.519-524
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• 1996

Peptidylprolyl cis-trans isomerase (PPlase) catalyzes the cis-trans isomerization of prolyl peptide and facilitates the folding of cellular proteins and peptides. PPlase consists of two distinct immunophilins, each specifically binding to the immunosupressive drug cyclosporin A (CsA) or FK506, respectively. A PPlase was isolated and partially purified from porcine spleen. The molecular weight of porcine spleen PPlase was determined to be ~14,000 on the basis of SDS-PAGE. The purified enzyme was strongly inhibited by FK506, but not by CsA. The inhibition constant and the true concentration of enzyme preparations were determined by active site titration using the tight binding inhibitor FK506: $K_{i}=18.7$ nM and $E_{t}=172$ nM. The equilibrium ratio of conformer. [cis]/[trans], of prolyl peptide substrates (N-Suc-Ala-Xaa-Pro-Phe-p-NA) in anhydrous trifluoroethanol/LiCl solvent system varied from 0.24 to 0.85 depending on the nature of Xaa. Overall. in this solvent-salt system, the populations of the cis conformer of substrates in equilibrium are higher than in an aqueous solution so that the substantial error caused by high background absorption can be reduced. The reactivities of porcine spleen PPlase are shown to be highly sensitive to changes in the structure of substrates. Thus, $k_{cat}/K_m$ value for the most reactive substrate (Xaa Leu) is $4.007+10^{6}M^{1}s^{1}$ and, is 2,636 fold higher than that for the least reactive peptide substrate tested, Xaa=Glu.