• Molecules and Cells
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• v.45 no.7
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• pp.444-453
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• 2022

Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.

• Bulletin of the Korean Chemical Society
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• v.30 no.5
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• pp.1101-1106
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• 2009

Multivalent and multi-specific antibodies can provide valuable tools for bio-medical research, diagnosis and therapy. In antigen-antibody interactions, the avidity of antibodies depends on the affinity and the number of binding sites.$^1$ As artificial multivalent antibody agents, single chain Fv-streptavidin fusion tetramer proteins $(scFv-SA)_4$ have been previously tested.$^{1,\;2}$ Although, the Fab domain is known to be more stable than scFv in animal models,$^{3,\;4}$ it has never been used to make a multivalent agent with a streptavidin fusion. In this study, we prepared tetra-valent $(Fab-cSA)_4$ by fusing Fab with core streptavidin (cSA). This molecule was made using inclusion body production, refolding and chromatography purification. Affinities of the Fab-cSA tetramer and a scFv-cSA tetramer to a cell surface antigen were compared by ELISA using biotin-HRP. The Fab-cSA tetramer showed higher binding avidity than the scFv-cSA tetramer. The higher binding avidity of the Fab-cSA tetramer demonstrates its potential as a therapeutic agent for target-specific antibody therapy.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.265-265
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• 2006

Multivalent interactions, which are characterized by the simultaneous binding of multiple ligands on multiple receptors, are prevalent in biological system. We have shown that it is able to make a supramolecular aggregate coated with multiple functional molecules fairly easily by simply mixing one building block. In this particular example, a mannose-coated object was able to agglutinate bacterial cells with cognate binding partners through multivalent interactions. This kind of strategy can be applied in developing materials that can selectively remove pathogens. Supramolecular assembly of this type should be very useful in exploring multivalent biological interactions.

• 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.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.6
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• pp.460-464
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• 2000

Extracellular polymeric substances (EPS) are believed to play a role in the binding and formation of microbial flocs. However, the precise role is not well known. Sludge settling characteristics and the carbohydrate to protein ratio in EPS were tested with various airflow rates in this study. Sludge was collected from three modified sequencing batch reactors (SBRs), which were operated at 16$\^{C}$ with an airflow rate of 0.8L/min, 3L/min and 6L/min, respectively. During the operation, the reactor operated at an airflow rate of 0.8L/min showed sludge volume index (SVI) of 80 to 90ml/g and a constant ratio of carbohydrate to protein in the EPS, while a significant increase in the SVI was seen in the other reactors. Sludge bulking increased the amount of carbohydrate in the EPS, while kept protein almost constant in the airflow rate of 3L/min ad 6L/min. Surface charge also increased with increases in the carbohydrate to protein ratio in the EPS, which weakens the attraction between the EPS and multivalent cations. The ratio of carbohydrate to protein in the EPS was tween the EPS and multivalent cations. The ratio of carbohydrate to protein in the EPS was inferred to be essential for bioflocculation.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.789-797
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• 2010

The limited information on differential gene expression in the different serotypes of Actinobacillus pleuropneumoniae has significantly hampered the research on the pathogenic mechanisms of this organism and the development of multivalent vaccines against A. pleuropneumoniae infection. To compare the gene expressions in the A. pleuropneumoniae strains CVCC259 (serotype 1) and CVCC261 (serotype 3), we screened the differentially expressed genes in the two strains by performing representational difference analysis (RDA). Northern blot analyses were used to confirm the results of RDA. We identified 22 differentially expressed genes in the CVCC259 strain and 20 differentially expressed genes in the CVCC261 strain, and these genes were classified into 11 groups: (1) genes encoding APX toxins; (2) genes encoding transferrin-binding protein; (3) genes involved in lipopolysaccharide (LPS) biosynthesis; (4) genes encoding autotransporter adhesin; (5) genes involved in metabolism; (6) genes involved in the ATP-binding cassette (ABC) transporter system; (7) genes encoding molecular chaperones; (8) genes involved in bacterial transcription and nucleic acid metabolism; (9) a gene encoding protease; (10) genes encoding lipoprotein/membrane protein; and (11) genes encoding various hypothetical proteins. This is the first report on the systematic application of RDA for the analysis of differential gene expression in A. pleuropneumoniae serotypes 1 and 3. The determination of these differentially expressed genes will serve as an indicator for future research on the pathogenic mechanisms of A. pleuropneumoniae and the development of a multivalent vaccine against A. pleuropneumoniae infection.

• Biotechnology and Bioprocess Engineering:BBE
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• v.6 no.4
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• pp.293-300
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• 2001

A polyrotaxane-biotin conjugate was synthesized and its interaction with streptavidin measured using surface plasmon resonance(SPR) detection. A biodegradable polyrotaxane in which ca, 22 molecules of ${\alpha}$-cyclodextrina(${\alpha}$-CDs) were threaded onto a poly(ethylene oxide) chain(M$\sub$n:4,000) capped with benzyloxycarbonyl-L-phenylalanine was conjugated with a biotin hydorazide and 2-aminoethanol after activing the hydroxyl groups of ${\alpha}$-CDs in the polyrotaxane using N, N'-carbonyldiimidazole. The results of the high-resolution $^1$H-nyclear lmagnetic resonance($^1$H-NMR)spectra and gel permeation chromatography of the conjugate showed that ca, 11 biotin molecules were actually introduced to the polyrotaxane scaffold. An SPR analysis showed that the binding curves of the biotin molecules in the conjugate on the streptavidin-deposited surface changed in a concentration dependent manner, indicating that the biotin in the conjugate was ac-tually recognized by streptavidin. The association equilibrium constant(K$\sub$a/) of the interaction be-tween the conjugate and steptavidin tetramer was of the order 10$\^$7/. These results suggest that polyrotaxane is useful for scaffolds as a polymeric ligand in biomedical fields.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.330-342
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• 2018

The Streptavidin and Biotin system has been studied most extensively as the high affinity non-covalent binding of Biotin to STR ($K_D=10^{-14}M$) and four Biotin binding sites in tetrameric Streptavidin makes this system useful for the production of multivalent antibody. For the application of this system, we cloned Streptavidin amplified from Streptomyces avidinii chromosome by PCR and fused to gene of hAY4 single-chain Fv antibody specific to death receptor 4 (DR4) which is a receptor for tumor necrosis factor ${\alpha}$ related apoptosis induced ligand. The hAY4 single-chain Fv antibody fused to Streptavidin expressed in Escherichia coli showed 43 kDa monomer in heated SDS-PAGE. However, this fusion protein shown in both non-heated SDS-PAGE and Size-exclusion chromatography exhibited 172 kDa as a tetramer suggesting that natural tetramerization of Streptavidin by non-covalent association induced hAY4 single-chain Fv tetramerization. This fusion protein retained a Biotin binding activity similar to natural Streptavidin as shown in Ouchterlony assay and ELISA. Death receptor 4 antigen binding activity of purified hAY4 single-chain Fv fused to Streptavidin was also confirmed by ELISA and Westernblot. In addition, surface plasmon resonance analysis showed 60-fold higher antigen binding affinity of the hAY4-STR than monomeric hAY4 ScFv due to tetramerization. In summary, hAY4 single-chain Fv fused to Streptavidin fusion protein was successfully expressed and purified as a soluble tetramer in E. coli and showed both Biotin and DR4 antigen binding activity suggesting possible production of bifunctional and tetrameric ScFv antibody.

• Journal of the korean academy of Pediatric Dentistry
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• v.35 no.1
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• pp.73-82
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• 2008

Dental caries is an infectious disease caused by mutans streptococci, and is a primary etiologic agent of dental caries in humans. The molecular pathogenesis of mutans streptococcal-associated dental caries occurs in three phases. Firstly, S. mutans attaches to tooth surface via a cell surface adhesion termed antigen I/II. In the second phase, the glucosyltransferase(GTFs) synthesize polymers like glucans in the presence of sucrose. In the third phase, the multivalent glucans interacts with glucan binding proteins (GBPs) and they make dental plaque and accumulation of microorganisms. Many studies and clinical trials have indicated that a mucosal immune response to these antigens(Ag I/II, GTFs, GBPs) of S. mutans can influence the pathogenesis of dental caries. So these antigens can be important vaccine candidates for immunologic intervention against dental caries. In this study, we cloned the genes for GTFb, GTFc, GTFd from S. mutans GS-5 and did the nucleotide sequence analysis. And the recombinant proteins of GTFd and N-terminus of GTFd were expressed. Intact GTF which we get from this experiment can be used for antibody production specific for any GTF activity domain through animal experiment.