• Journal of Microbiology and Biotechnology
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• v.31 no.2
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• pp.233-239
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• 2021

Cyanobacteriochromes (CBCRs) are phytochrome-related photoreceptor proteins in cyanobacteria and cover a wide spectral range from ultraviolet to far-red. A single GAF domain that they contain can bind bilin(s) autocatalytically via heterologous recombination and then fluoresce, with potential applications as biomarkers and biosensors. Here, we report that a novel red/green CBCR GAF domain, SPI1085g2 from Spirulina subsalsa, covalently binds both phycocyanobilin (PCB) and phycoerythrobilin (PEB). The PCB-binding GAF domain exhibited canonical red/green photoconversion with weak fluorescence emission. However, the PEB-binding GAF domain, SPI1085g2-PEB, exhibited an intense orange fluorescence (λabs.max = 520 nm, λfluor.max = 555 nm), with a fluorescence quantum yield close to 1.0. The fluorescence of SPI1085g2-PEB was selectively and instantaneously quenched by copper ions in a concentration-dependent manner and exhibited reversibility upon treatment with the metal chelator EDTA. This study identified a novel PEB-binding cyanobacteriochrome-based fluorescent protein with the highest quantum yield reported to date and suggests its potential as a biosensor for the rapid detection of copper ions.

• BMB Reports
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• v.31 no.4
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• pp.370-376
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• 1998

Src-Homology 2 (SH2) domains have a capacity to bind phosphotyrosine-containing sequence context and play essential roles in various cellular signaling pathways. Due to the specific nature of the binding between SH2 domains and their counterpart proteins, inhibitors of SID domain binding have drawn extensive attention as a potential candidate for therapeutic agents. Here, we describe the binding assay system to screen for the ligands or blockers of the SH2 domains with an emphasis on the $p56^{lck}$ SH2 domain. In our assay system, SID domains expressed and purified as fusion proteins to Glutathione-S-transferase (GST) were covalently attached to 96-well microtitre plates through amide bond formation, which were subsequently allowed to bind the biotinylated phosphotyrosine (pY)containing synthetic pep tides. The binding of biotinylated pY peptides was detected by the horseradish peroxidase (HRP)-conjugated streptavidin. Using the various combinations of SH2 domain-pY peptides, we observed that: (1) The binding of pY-peptides to its counterpart SH2 domain is concentration-dependent and saturable; (2) The binding is highly specific for a particular combination of SH2 domain-pY peptide pair; and (3) The binding of Lck SH2-cognate pY-peptides is specifically competed by the nonbiotinylated peptides with expected relative affinity. These results indicate that the established assay system detects the SH2-pY peptide interaction with reproducible sensitivity and specificity and is suitable for screening the specific inhibitors of $p56^{lck}$ SH2 function.

• YAKHAK HOEJI
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• v.39 no.1
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• pp.10-13
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• 1995

As a continuation of the previous studies, a third group of thirty five hot aqueous extracts from natural products were screened for platelet activating factor(PAF) receptor binding antagonistic acitivities using rabbit platelet. The results demonstrate that Arctium lappa is potential source of PAF antagonist.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1168-1169
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• 2005

• Molecules and Cells
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• v.43 no.11
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• pp.899-908
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• 2020

Intrinsically disordered proteins or regions (IDPs or IDRs) are widespread in the eukaryotic proteome. Although lacking stable three-dimensional structures in the free forms, IDRs perform critical functions in various cellular processes. Accordingly, mutations and altered expression of IDRs are associated with many pathological conditions. Hence, it is of great importance to understand at the molecular level how IDRs interact with their binding partners. In particular, discovering the unique interaction features of IDRs originating from their dynamic nature may reveal uncharted regulatory mechanisms of specific biological processes. Here we discuss the mechanisms of the macromolecular interactions mediated by IDRs and present the relevant cellular processes including transcription, cell cycle progression, signaling, and nucleocytoplasmic transport. Of special interest is the multivalent binding nature of IDRs driving assembly of multicomponent macromolecular complexes. Integrating the previous theoretical and experimental investigations, we suggest that such IDR-driven multiprotein complexes can function as versatile allosteric switches to process diverse cellular signals. Finally, we discuss the future challenges and potential medical applications of the IDR research.

• Food Science of Animal Resources
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• v.32 no.3
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• pp.301-307
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• 2012

We investigated the effects of non-meat protein binders combined with glucono-${\delta}$-lactone (GdL) on the binding properties regarding restructured pork prepared by high-pressure treatment. Soy protein isolate (SPI), casein (CS), whey protein concentrate (WPC), and egg white (EW) were used as non-meat protein binders and compared with the control (no binder) and with the ${\kappa}$-carrageenan (KC) treatment. The compression and depression rates were 2.3 and 37 MPa/s, respectively, and pressurization was conducted at 200 MPa for 30 min at $4^{\circ}C$. After pressurization, the physical properties (pH, water-holding capacity, color, tensile strength, and microscopic structure) of the sample were evaluated. The combination of pressurization with acidification enabled cold-set meat binding, and the binding strength of restructured pork was enhanced by the addition of non-meat proteins. Among binders, SPI demonstrated the best efficiency in binding meat pieces. Therefore, the present study demonstrated that the combination of acidification and pressurization processes with the utilization of non-meat protein binders has a potential benefit in meat restructuring.

• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.127-136
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• 2015

Cupredoxin-like proteins are mainly copper-binding proteins that conserve a typical rigid Greek-key arrangement consisting of an eight-stranded β-sandwich, even though they share as little as 10-15% sequence similarity. The electron transport function of the Cupredoxins is critical for respiration and photosynthesis, and the proteins have therapeutic potential. Despite their crucial biological functions, the identification of the distant Cupredoxin homologs has been a difficult task due to their low sequence identity. In this study, the overlapped conserved residue (OCR) fingerprint for the Cupredoxin superfamily, which consists of conserved residues in three aspects (i.e., the sequence, structure, and intramolecular interaction), was used to detect the novel Cupredoxin homologs in the NCBI non-redundant protein sequence database. The OCR fingerprint could identify 54 potential Cupredoxin sequences, which were validated by scanning them against the conserved Cupredoxin motif near the Cu-binding site. This study also attempted to model the 3D structures and to predict the functions of the identified potential Cupredoxins. This study suggests that the OCR-based approach can be used efficiently to detect novel homologous proteins with low sequence identity, such as Cupredoxins.

• Journal of Biosystems Engineering
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• v.38 no.2
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• pp.129-137
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• 2013

Purpose: Modeling has been used for elucidating the mechanism of complex biosystems. In spite of importance and uniqueness of adolescent calcium (Ca) metabolism characterized by a threshold Ca intake, its regulatory mechanism has not been covered and even not proposed. Hence, this study aims at model-based proposing potential mechanisms regulating adolescent Ca metabolism. Methods: Two different hypothetic mechanisms were proposed. The main mechanism is conceived based on Ca-protein binding which induces renal Ca filtration, while additional mechanism assumed that active renal Ca re-absorption regulated Ca metabolism in adolescents. Mathematical models were developed to represent the proposed mechanism and simulated them whether they could produce adolescent Ca profiles in serum and urine. Results: Simulation showed that both mechanisms resulted in the unique behavior of Ca metabolism in adolescents. Based on the simulation insulin-like growth factor-1 (IGF-1) is suggested as a potential regulator because it is related to both growth, a remarkable characteristic of adolescence, and Ca metabolism including absorption and bone accretion. Then, descriptive modeling is employed to conceptualize the hypothesized mechanisms governing adolescent Ca metabolism. Conclusions: This study demonstrated that modeling is a powerful tool for elucidating an unknown mechanism by simulating potential regulatory mechanisms in adolescent Ca metabolism. It is expected that various analytic applications would be plausible in the study of biosystems, particularly with combination of experimental and modeling approaches.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3644-3652
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• 2010

The metallo-$\beta$-lactamases ($M{\beta}Ls$) are clinically significant enzymes which readily hydrolyze most $\beta$-lactam antibiotics. Discovering potential inhibitors for the $M{\beta}Ls$ is an expensive, time consuming endeavor. Virtual screening can sieve out inhibitor candidates with incompatible features prior to synthesis, decreasing these costs. Using Autodock 4.0, the binding locations and energies of four previously-studied potential inhibitors and four additional compounds obtained from the National Cancer Institute (NCI) database were computationally calculated. Based on the docking models of these eight compounds, we then designed several hypothetical inhibitor structures, compounds A through F, and performed their respective docking experiments. The docking results for compound F showed that it binds to the zinc containing active sites with a lowest predicted binding energy of -6.70 kcal/mol, suggesting F is the most likely potential $M{\beta}L$ inhibitor.