• Microbiology and Biotechnology Letters
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• v.35 no.4
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• pp.278-284
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• 2007

A novel screening strategy for salt-resistant antimicrobial peptides from a M13 peptide library was developed. Fusion of MSI-344, a magainin derivative and indolicidin to pIII coat proteins did not significantly affect viability of the recombinant phages, which indicated that the pIII could neutralize toxicity of the antimicrobial peptides and therefore it is possible to construct antimicrobial peptide library in Escherichia coli. On the basis of the conserved sequence of ${\alpha}$-helical antimicrobial peptides, a semi-combinatorial peptide library was constructed in which the peptides were displayed by pIII. To remove hemolytic activity from the library, the phages bound to red blood cells were removed, and the subtracted phage library was screened for binding to target bacteria Pseudomonas aeruginosa and Staphylococcus aureus under high salt concentrations. The screened peptides showed relatively low antimicrobial activity against the target bacteria. However, antimicrobial activities of the screened peptides P06 and S18 were not affected by the cation concentrations of 150 mM $Na^+$, 2 mM $Mg^{2+}$ and 2 mM $Ca^{2+}$ without significant hemolytic activity. This screening strategy that is based on binding capacity to target cells provides new potential to develop salt-tolerant antimicrobial peptides.

• BMB Reports
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• v.42 no.11
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• pp.737-742
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• 2009

Hypoxia-inducible factor-$1{\alpha}/{\beta}$ (HIF-$1{\alpha}/{\beta}$) is a heterodimeric transcriptional activator that mediates gene expression in response to hypoxia. HIF-$1{\alpha}$ has been noted as an effective therapeutic target for ischemic diseases such as myocardiac infarction, stroke and cancer. By using a yeast two-hybrid system and a random peptide library, we found a 16-mer peptide named F29 that directly interacts with the bHLH-PAS domain of HIF-$1{\alpha}$. We found that F29 facilitates the interaction of the HIF-$1{\alpha/\beta}$ heterodimer with its target DNA sequence, hypoxia-responsive element (HRE). The transient transfection of an F29-expressing plasmid increases the expression of both an HRE-driven luciferase gene and the endogenous HIF-1 target gene, vascular endothelial growth factor (VEGF). Taken together, we conclude that F29 increases the DNA-binding ability of HIF-$1{\alpha}$, leading to increased expression of its target gene VEGF. Our results suggest that F29 can be a lead compound that directly targets HIF-$1{\alpha}$ and increases its activity.

• Molecules and Cells
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• v.21 no.2
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• pp.244-250
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• 2006

Gangliosides are receptors for various peptides and proteins including neuropeptides, ${\beta}$-amyloid proteins, and prions. Recently, the role of gangliosides in mucosal immunization has attracted attention due to the emerging interest in oral vaccination. Ganglioside GM1 exists in abundance on the surface of the M cells of Peyer's patch, a well-known mucosal immunity induction site. In the present study we identified a peptide ligand for GM1 and tested whether it played a role in immune induction. GM1-binding peptides were selected from a phage-displayed dodecapeptide library and one peptide motif, GWKERLSSWNRF, was fused to the C-terminus of enhanced green fluorescent protein (EGFP). The fusion protein, but not EGFP fused with a control peptide, was concentrated around Peyer's patch after incubation in the lumen of the intestine ex vivo. Furthermore, oral feeding of the fusion protein but not control EGFP induced mucosal and systemic immune responses against EGFP resembling Th2-type immune responses.

• IMMUNE NETWORK
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• v.3 no.3
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• pp.219-226
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• 2003

Background: Phage display is the most widely used technique among display methods to produce monoclonal antibody fragment with a specific binding activity. Having a large library for efficient antibody display/selection is quite laborious process to have more than $10^9$ members of transformants. To overcome these limitations, several in vitro selection approaches have been reported. Ribosome display that links phenotypes, proteins, directly to genotype, mRNA, is one of the in vitro display methods. Ribosome display can reach the size of scFv library up to $10^{14}$ molecules and it can be further diversified during PCR steps. To select the high affinity scFv from one pot library, we established ribosome display technique by modifying the previously reported eukaryotic translation system. Methods: To establish the antibody selection system by ribosome display, we used 3D8, anti-DNA antibody. A 3D8 scFv was synthesized in vitro by an in vitro transcription-translation system. The translated 3D8 scFv and the encoding 3D8 mRNA are connected to the ribosome. These scFv-ribosome-mRNA complexes were selected by binding to their specific antigens. The eluted mRNAs from the complexes are reverse transcribed and re-amplified by PCR. To apply this system, antibody library from immunized mouse with terminal protein (TP)-peptide of hepatitis B virus DNA polymerase TP domain was also used. This TP-peptide encompasses the 57~80 amino acid residues of TP. These mRNA/ribosome/scFv complexes by our system were panned three times against TP-peptide. The enrichment of antibody from library was determined by radioimmunoassay. Results: We specifically selected 3D8, anti-DNA antibody, against ssDNA as a model system. The selected 3D8 RNAs sequences from translation complexes were recovered by RT-PCR. By applying this model system, we enriched TP-peptide-specific scFv pools through three cycles of panning from immunized library. Conclusion: We show that our translating ribosome complexes are well maintained and we can enrich the TP-specific scFv pools. This system can be applied to select specific antibody from an antibody library.

• The Korean Journal of Physiology and Pharmacology
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• v.28 no.5
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• pp.457-467
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• 2024

Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phage-displayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.

• Journal of Life Science
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• v.13 no.4
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• pp.541-550
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• 2003

E2 glycoprotein of hepatitis C virus (HCV) comprises a surface of viral particle together with E1 glycoprotein, and is thought to be involved in the attachment of HCV viral particle to receptor (s) on the permissible cells including hepatocytes, B cells, T cells, and monocytes. We constructed a phage library expressing cellular proteins of hepatocytes on the phage surface, which turned out to be 8.8${\times}$$10^5$ cfu of diversity and carried inserts in 95% of library. We screened both cDNA phage library and 12-mer peptide library to identify the cellular proteins binding to E2 protein. Some intracellular proteins including tensin and membrane band 4.1 which are involved in signal transduction of survival and cytoskeleton organization, were selected from cDNA phage library through several rounds of panning and screening. On the contrary, membrane proteins such as CCR7, CKR-L2, and insulin-like growth factor-1 receptor were identified through screening of peptide library. Phages expressing peptides corresponding to those membrane proteins were bound to E2 protein specifically as determined by neutralization of binding assay. Since it is well known that HCV can infect T cells as well as hepatocytes, we examined to see if E2 protein can bind to CCR7, a member of C-protein coupled receptor family expressed on T cells, using CCR7 transfected tells. Human CCR7 cDNA was cloned into pcDNA3.1(-) vector and transfected into human embryonic kidney cell, 293T, and expressed on the surface of the cell as shown by flow cytometer. Binding assay of E2 protein using CCR7 transfected cells indicated that E2 protein bound to CCR7 by dose-dependent mode, giving rise to the possibility that CCR7 might be a putative cellular receptor for HCV.

• Bulletin of the Korean Chemical Society
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• v.32 no.9
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• pp.3425-3428
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• 2011

Apolipoprotein A-I (Apo A-I) is a major component for high density lipoproteins (HDL). A number of mimetic peptides of Apo A-I were screened from the phase-displayed random peptide library by utilizing monoclonal antibodies (A12). Mimetic peptide for A12 epitope against Apo A-I was selected as CPFARLPVEHHDVVGL (pA1). From the BLAST search, the mimetic peptide pA1 had 40% homology with Apo A-I. As a result of the structural determination of this mimotope using homo/hetero nuclear 2D-NMR techniques and NMR-based distance geometry (DG)/molecular dynamic (MD) computations, DG structure had low penalty value of 0.3-0.7 ${\AA}^2$ and the total RMSD was 0.6-1.6 ${\AA}$. The mimotope pA1 exhibited characteristic conformation including a ${\beta}$-turn from Pro[7] to His[11].

• Journal of Microbiology and Biotechnology
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• v.19 no.8
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• pp.792-802
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• 2009

Antimicrobial peptides (AMPs) are considered to be a promising alternative to conventional antibiotics for future generations. We identified four novel hexapeptides with antimicrobial activity: KCM11 (TWWRWW-$NH_2$), KCM12 (KWRWlW-$NH_2$), KCM21 (KWWWRW-$NH_2$), and KRS22 (WRWFIH-$NH_2$), through positional scanning of a synthetic peptide combinatorial library (PS-SCL). The ability of these peptides to inhibit the growth of a variety of bacteria and unicellular fungi was evaluated. KCM11 and KRS22 preferentially inhibited the normal growth of fungal strains, whereas KCM12 and KCM21 were more active against bacterial strains. Bactericidal activity was addressed in a clear zone assay against phytopathogenic bacteria, including Pectobacterium spp., Xanthomonas spp., Pseudomonas spp., etc. KCM21 showed the highest activity and was effective against a wide range of target organisms. Application of KCM21 with inoculation of Pectobacterium carotovorum subsp. carotovorum on detached cabbage leaves resulted in an immune phenotype or a significant reduction in symptom development, depending on the peptide concentration. Cytotoxicity of the four hexapeptides was evaluated in mouse and human epithelial cell lines using an MTT test. The results revealed a lack of cytotoxic effects.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3703-3706
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• 2010

Biomolecules specific to explosives can be exploited as chemical sensors. Peptides specific to immobilized dinitrotoluene (DNT) were identified using a phage display library. A derivative of DNT that contained an extended amine group, 4-(2,4-dinitrophenyl)butan-1-amine, was synthesized and immobilized using a self-assembled monolayer surface on gold. Filamentous M13 phages displaying random sequences of 12-mer peptides specific to the immobilized DNT-derivate were isolated from the M13 phage library by biopanning. A common peptide sequence was identified from the isolated phages and the synthesized peptides showed selective binding to DNT. When the peptide was immobilized on a quartz crystal microbalance (QCM) chip, it showed a binding signal to DNT, while toluene barely showed significant binding to the QCM chip. These results demonstrate that peptides screened by biopanning against immobilized DNT can be useful for quick and accurate detection of DNT.

• KSBB Journal
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• v.28 no.3
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• pp.185-190
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• 2013

For the selection of peptide specifically binding to $Pb^{2+}$, the biopanning with the commercially available Ph.D.-7 phage displayed heptapeptide library was carried out against $Pb^{2+}$ immobilized on a metal-chelating IDA (iminodiacetic acid) resin. After four rounds of screening against $Pb^{2+}$-IDA including negative selections against charged bead with metal ions other than $Pb^{2+}$ and uncharged bead, several candidate lead-binding phage peptides were initially determined based on the order of frequency from the screened phage clones. Of the selected phage peptide sequences, the peptide of the highest frequency, CysSerIleArgThrLeuHisGlnCys (CSIRTLHQC) also exhibited the strongest affinity for $Pb^{2+}$ in binding assays for individual phage clones. However, there was not a significant difference in $Pb^{2+}$ affinity between selected peptides when using synthetic heptapeptides corresponding to the displayed peptide sequences of phage clones.