• Journal of Microbiology and Biotechnology
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• 제26권12호
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• pp.2184-2191
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• 2016

The time-consuming and high-cost preparation of soluble peptide-major histocompatibility complexes (pMHC) currently limits their wide uses in monitoring antigen-specific T cells. The single-chain trimer (SCT) of peptide-${\beta}2m$-MHC class I heavy chain was developed as an alternative strategy, but its gene fusion is hindered in many cases owing to the incompatibility between the multiple restriction enzymes and the restriction endonuclease sites of plasmid vectors. In this study, overlap extension PCR and one-step cloning were adopted to overcome this restriction. The SCT gene of the $OVA_{257-264}$ peptide-$(GS_4)_3-{\beta}2m-(GS_4)_4-H-2K^b$ heavy chain was constructed and inserted into plasmid pET28a by overlap extension PCR and one-step cloning, without the requirement of restriction enzymes. The SCT protein was expressed in Escherichia coli, and then purified and refolded. The resulting $H-2K^b/OVA_{257-264}$ complex showed the correct structural conformation and capability to bind with $OVA_{257-264}$-specific T-cell receptor. The overlap extension PCR and one-step cloning ensure the construction of single-chain MHC class I molecules associated with random epitopes, and will facilitate the preparation of soluble pMHC multimers.

• 한국자기공명학회논문지
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• 제10권2호
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• pp.163-174
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• 2006

Luteinizing Hormone Releasing Hormone(LHRH) is a decapeptide neurotransmitter known to be regulated by metal ions in the hyperthalamus. Zn-binding LHRH complex was systhesized, and zinc-LHRH complex was studied to understand what kinds of structural modifications would be critical in the LHRH releasing mechanism. Both nonexchangeable and exchangeable $^1H-NMR$ signal assignments were accomplished by pH-dependent and COSY NMR experiments. In addition, $^1H-NMR$ chemical shift changes of a-proton and peptide NH NMR signals at different pH condition, and $^1H-NMR$ signal differences between metal free and metallo-LHRH complex was monitored. NMR signals exhibit that primary metal-binding sites are nitrogens donor of imidazole ring and Arg, and peptide oxygen of Pro-His in the sequence. Structure obtained in this study has a cyclic conformation which is similar to that of energy minimized, and exhibits a specific a-helical turn with residue numbers $(2{\sim}7)$ out of 10 amino acids.

• BMB Reports
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• 제39권3호
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• pp.284-291
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• 2006

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the $\beta$-strand1 to the $\alpha$-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of $\alpha$-, $\beta$-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a $\beta$-toxin that competes with the depressant insect toxins for binding to $Na^+$ channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded $\beta$-sheet and a stretch of $\alpha$-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1996년도 정기총회 및 학술발표회
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• pp.10-10
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• 1996

High-resolution solution conformation of a novel conotoxin, [Pro 7,13] $\alpha$A-conotoxin $P_{IVA}$, GCCGSYPNAACHPCSCKDROSYCGQ-N $H_2$, has been determined by two-dimensional $^1$H nmr methods in combination with distance geometry calculation to rmsd values of 0.90 $\AA$ and 1.16 $\AA$ for the backbone and heavy atoms, respectively. Total of 324 NOE-derived interproton distance restraints including 33 long-range NOE restraints a well as 11 $\Phi$ and 7 $\chi$$^1$ torsion angle restraints were used for computation of structures. (omitted)d)

• 한국자기공명학회논문지
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• 제12권1호
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• pp.40-50
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• 2008

Ghrelin is a unique peptide hormone that releases growth factor and it stimulates appetite. It comes from pre pro-ghrelin by the post translational modification process and its innate functions are known as food up-take and the growth hormone regulation. Therefore, the structural information of ghrelin precursor is of importance in understanding it function. From our results, we found that the solution structure of ghrelin is mostly random coil conformation at neutral pH value and the structural population changes with pH environments. Data from circular dichroism in different TFE concentrations revealed that the secondary structure changes from random coil to a-helix and the isodichroic point is observed at 202nm, implying that two equilibrium states exist between random coil and helical structure.

• Bulletin of the Korean Chemical Society
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• 제22권5호
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• pp.507-513
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• 2001

Histones, nuclear proteins that interact with DNA to form nucleosomes, are essential for both the regulation of transcription and the packaging of DNA within chromosomes. The N-terminal domain of histone H4 which contains four acetylation sites at lysines, may play a separate role in chromatin structure from the remainder of the H4 chain. NMR data suggest that H4NTP peptide does have relating disordered structure at physiological pH, however, it has a defined structure at lower pH conditions. The solution structure calculated from NMR data shows a well structured region comprising residues of Val21-Asp24. In addition, our results suggest that the H4NTP prefers an extended backbone conformation at acetylation sites, however, it (especially Lys 12 ) became more defined structures after acetylation for its optimum function.

• Advances in nano research
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• 제15권2호
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• pp.105-111
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• 2023

Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin αvβ3 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.

• Bulletin of the Korean Chemical Society
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• 제29권8호
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• pp.1505-1509
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• 2008

Comparative molecular simulations were performed to establish molecular interaction and inhibitory effect of flavonoid myricetin on formation of amyloid fibris. For computational comparison, the conformational stability of myricetin with amyloid $\beta$ -peptide (A$\beta$ ) and $\beta$ -amyloid fibrils (fA$\beta$) were traced with multiple molecular dynamics simulations (MD) using the CHARMM program from Monte Carlo docked structures. Simulations showed that the inhibition by myricetin involves binding of the flavonoid to fA$\beta$ rather than A$\beta$ . Even in MD simulations over 5 ns at 300 K, myricetin/fA$\beta$ complex remained stable in compact conformation for multiple trajectories. In contrast, myricetin/A$\beta$ complex mostly turned into the dissociated conformation during the MD simulations at 300 K. These multiple MD simulations provide a theoretical basis for the higher inhibitory effect of myricetin on fibrillogenesis of fA$\beta$ relative to A$\beta$ . Significant binding between myricetin and fA$\beta$ observed from the computational simulations clearly reflects the previous experimental results in which only fA$\beta$ had bound to the myricetin molecules.

• BMB Reports
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• 제29권4호
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• pp.286-293
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• 1996

Association of antigenic peptide with class I MHC is believed to be crucial for maintaining stable conformation of class I molecules. T2 cells that are defective in TAP gene function mainly express class I molecules with an unstable conformation due to little or no association with antigenic peptides, whereas T1 cells that are normal in TAP gene function mainly express the stable form of class I molecules. In this work, attempts were made to determine the molecular stability of stable and unstable class I molecules. Dissociation of HLA-A2 molecules on T1 and T2 cells was monitored by flow cytometry using anti-HLA-A2 antibody after the cells were treated with brefeldin A to shut down the transport of newly-assembled HLA-A2. Estimated dissociation rate constants for the stable and unstable forms of HLA-A2 were 0.076 $h^{-1}$ and 0.66 $h^{-1}$, respectively. It appeared that both T1 and T2 cells express stable and unstable class I complex, but with different ratios of the two forms. Furthermore, $interferon-{\gamma}$ treatment of T1 cells appeared to induce the expression of both the stable and unstable class I molecules. These results demonstrate that class I MHC molecules can be divided into two groups in terms of structural stability and that they exist on the cell surface in both forms in a certain ratio.

• Archives of Pharmacal Research
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• 제25권6호
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• pp.801-806
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• 2002

Cyclicpeptides are important targets in peptide synthesis because of their interesting biological properties. Constraining highly flexible linear peptides by cyclization is one of the mostly widely used approaches to define the bioactive conformation of peptides. Cyclic peptides often have increased receptor affinity and metabolic stability over their linear counterparts. We carried out virtual screening experiment via docking in order to understand the interaction between HLE-Human Leukocyte Elastase and ligand peptide and to identify the sequence that can be a target in various ligand peptides. We made cyclic peptides as a target base on Metlle-Phe sequence having affinity for ligand and receptor active site docking. There are three ways to cyclize certain sequences of amino acids such as Met-lie-Phe-Gly-Ile. First is head-to-tail cyclization method, linking between N-terminal and C-terminal. Second method utilizes amino acid side chain such as thiol functional group in Cys, making a thioether bond. The last one includes an application of resin-substituted amino acids in solid phase reaction. Among the three methods, solid phase reaction showed the greatest yield. Macrocyclization of Fmoc-Met-Ile-Phe-Gly-Ile-OBn after cleavage of Fmoc protection in solution phase was carried out to give macrocyclic compound 5 in about 7% yield. In the contrast with solution phase reaction, solid phase reaction for macrocyclization of Met-Ile-Phe-Gly-Ile-Asp-Tentagel in normal concentrated condition gave macrocyclic compound 7 in more than 35% yield.