• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.911-916
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• 2012

Ion selectivity in a simple cyclic peptide nanotube, composed of four cyclo[-(D-Ala-Glu-D-Ala-Gln)$_2-$] units, is investigated by calculating the PMF profiles of $Na^+$, $K^+$, and $Cl^-$ ions permeating through the peptide nanotube in water. The final PMF profiles of the ions obtained from the umbrella sampling (US) method show an excellent agreement with those from the thermodynamic integration (TI) method. The PMF profiles of $Na^+$ and $K^+$ display free energy wells while the PMF curve of $Cl^-$ features free energy barriers, indicating the selectivity of the cyclic peptide nanotube to cations. Decomposition of the total mean force into the contribution from each component in the system is also accomplished by using the TI method. The mean force decomposition profiles of $Na^+$ and $K^+$ demonstrate that the dehydration free energy barriers by water molecules near the channel entrance and inside the channel are completely compensated for by attractive electrostatic interactions between the cations and carbonyl oxygens in the nanotube. In the case of $Cl^-$, the dehydration free energy barriers are not eliminated by an interaction between the anion and the peptide nanotube, leading to the high free energy barriers in the PMF profile. Calculations of the coordination numbers of the ions with oxygen atoms pertaining to either water molecules or carbonyl groups in the peptide nanotube reveal that the stabilization of the cations in the midplane regions of the nanotube arises from the favorable interaction of the cations with the negatively charged carbonyl oxygens.

• Journal of Microbiology and Biotechnology
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• v.15 no.5
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• pp.1054-1059
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• 2005

An extracellular protease was identified from Bacillus subtilis KCCM 10257 by N-terminal sequencing and mass spectral analysis. The molecular mass of the extracellular protease was estimated to be 28 kDa by SDS-PAGE. Sequencing of the N-terminal of the protease revealed the sequence of A(G,S,R)QXVPYG(A)V(P,L)SQ. The N-terminal sequence exhibited close similarity to the sequence of other proteases from Bacillus sp. A mass list of the monoisotopic peaks in the MALDI-TOF spectrum was searched after peptide fragmentation of the protease. Six peptide sequences exhibiting monoisotopic masses of 1,276.61, 1,513.67, 1,652.81, 1,661.83, 1,252.61, and 1,033.46 were observed from the fragmented protease. These monisotopic masses corresponded to the lytic enzyme L27 from Bacillus subtilis 168, and the Mowse score was found to be 75. A doubly charged Top product (MS) at a m/z of 517.3 exhibiting a molecular mass of 1034.6 was further analyzed by de novo sequencing using a PE Sciex QSTAR Hybrid Quadropole-TOF (MS/MS) mass spectrometer. MS/MS spectra of the Top product (MS) at a m/z of 517.3 obtained from the fragmented peptide mixture of protease with Q-star contained the b-ion series of 114.2, 171.2, 286.2, 357.2, 504.2, 667.4, 830.1, and 887.1 and y-ion series of 147.5, 204.2, 367.2, 530.3, 677.4, 748.4, 863.4, and 920.5. The sequence of analyzed peptide ion was identified as LGDAFYYG from the b- and y-ion series by de novo sequencing and corresponded to the results from the MALDI-TOF spectrum. From these results the extracellular protease from Bacillus subtilis KCCM 10257 was successfully identified with the lytic enzyme L27 from Bacillus subtilis 168.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.770-774
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• 2014

The bond dissociation energy (BDE) of the chemical bond between the carbon and oxygen atoms of a simple TEMPO-derivative is calculated by employing the density functional theory, the $2^{nd}$ order M${\phi}$ller-Plesset (MP2) perturbation theory, and complete basis set (CBS) methods. We find that BDE of the positive ion of the TEMPO-derivative is larger at least by 7 kcal/mol than that of the negative ion, which implies that the dissociation reaction rate of the positive ion should be slower than that of the negative ion. Such theoretical predictions are contrary to the results of our previous experiments (Anal. Chem. 2013, 85, 7044), in which the larger energy was required for negative o-TEMPO-Bz-C(O)-peptides to undergo the dissociation reactions than for the positive ones. By comparing our theoretical results to those of the experiments, we conclude that the dissociation reaction of o-TEMPO-Bz-C(O)-peptide should occur in a complicated fashion with a charge, either positive or negative, probably being located on the amino acid residues of the peptide.

• Journal of Pharmaceutical Investigation
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• v.26 no.1
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• pp.43-53
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• 1996

The objective of this study was to determine whether 4-phenylazobezyloxycarbonyl-Pro-Leu-Gly-Pro-D-Arg (Pz-peptide), an enhancer of hydrophilic solute permeability in the intestine, could elevate the paracellular permeability of hydrophilic drugs across cornea and conjunctiva in the rabbit. The in-vitro penetration of hydrophilic drugs (mannitol, atenolol) and lipophilic drug (propranolol) across the rabbit cornea and conjunctiva was studied either in the presence or absence of 3 mM Pz-peptide. Drug penetration was evaluated using the modified Ussing chamber. The conjunctiva was more permeable than the cornea to all drugs. Pz-peptide showed enhanced effects on the drug transport across cornea and conjunctiva in a concentration dependent manner. Effects or ion transport inhibitor on the mannitol penetration were then investigated. Mannitol penetration was not changed by serosal addition of $100\;{\mu}M$ ouabain, suggesting that $Na^+/K^+$ ion tranporter was not involved in the Pz-peptide induced elevation of paracellular drug permeability. Furthermore, effects of Pz-peptide and EDTA on the transport of atenolol and propranolol into the ocular tissues or blood circulation after its administration into both eyes were investigated. EDTA showed enhanced effect on propranolol transport into the ocular tissues, but Pz-peptide did not show significant difference. Systemic absorption of propranolol by the addition of EDTA or Pz-peptide was not changed. On the other hand, EDTA and Pz-peptide elavated the atenolol transport into the ocular tissues. The transport of atenolol into the blood circulation was also enhanced by the addition of EDTA, but no effect was observed by the addition of Pz-peptide. The above findings suggest that Pz-peptide would be used as an paracellular pathway enahncer of hydrophilic drugs into the eye, without affecting the systemic absortion of topically applied opthalmic drugs.

• Fisheries and Aquatic Sciences
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• v.13 no.1
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• pp.84-87
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• 2010

A peptide that inhibits HIV-1 protease was isolated from a hydrolysate of oyster (Crassostrea gigas) proteins digested with thermolysin. The peptide was using membrane filtration, gel permeation chromatography, ion exchange chromatography, and reverse-phase high performance liquid chromatography. Amino acid sequence of the peptide was determined to be Val-Phe-Glu-Leu. Chemically synthesized Val-Phe-Glu-Leu showed an $IC_{50}$ value of 106 ${\mu}M$.

• Journal of the Korean Chemical Society
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• v.39 no.5
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• pp.371-378
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• 1995

The triazacrown compound, 1,7-dioxa-4,10,13-triazacyclopentadecane trihydrobromide salt (Na3O2-3HBr) was synthesized. And this compound was used to synthesize the new ion exchanger, which combined with Merrifield peptide resin. This new ion exchanger had a capacity of 3.2 meq/g dry resin. And the distribution coefficients of alkali and alkaline earth metal ions on this ion exchanger in the various concentrations of hydrochloric acid were determined. The ion exchange behaviors of alkali and alkaline earth metal ions in the various hydrochloric acid concentrations are, also, discussed.

• Bulletin of the Korean Chemical Society
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• v.31 no.1
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• pp.92-99
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• 2010

Photoexcitation of a precursor ion inside a cell floated at high voltage installed in a tandem time-of-flight (TOF) mass spectrometer provides triple tandem mass spectrometric information and allows kinetic and mechanistic studies. In this work, the factors affecting, or downgrading, the performance of the technique were identified. Ion-optical and computational analyses showed that an optimum instrument could be designed by utilizing a reflectron with linear-plus-quadratic potential inside. Theoretical predictions were confirmed by tests with instruments built with different ion-optical layout. With optimized instruments, masses of intermediate ions in the consecutive dissociation of a precursor ion could be determined with the maximum error of $\pm5$ Da. We also observed excellent agreement in dynamical parameters (critical energy and entropy) for the dissociation of a model peptide ion determined by instruments with different ion-optical layout operated under optimum conditions. This suggests that these parameters can be determined reliably by the kinetic method developed previously when properly designed and operated tandem TOF instruments are used.

• Journal of Chitin and Chitosan
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• v.23 no.4
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• pp.220-227
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• 2018

Amyloid plaque is a product of aggregation of ${\beta}$-amyloid peptide ($A{\beta}$) and is an important factor in the pathogenesis of Alzheimer's Disease (AD). $A{\beta}$ is a major component of amyloid plaque and vascular deposits in the AD brain. The enzyme ${\beta}$-secretase is required for the production of $A{\beta}$; thus, prevention of the formation of $A{\beta}$ through the inhibition of ${\beta}$-secretase is a major focus in the study of the treatment of AD. In this study, we investigated ${\beta}$-secretase inhibitory activity of an Arctoscopus japonicus peptide. An Alcalase hydrolysate had the highest ${\beta}$-secretase inhibitory activity. A ${\beta}$-secretase inhibitory activity peptide was separated using ion exchange column chromatography (carboxy-methyl: CM, quaternary methyl ammonium: QMA) and reverse phase high performance liquid chromatography (RP-HPLC) on a C18 column. The $IC_{50}$ value of the purified peptide was $248.2{\pm}1.73{\mu}g/mL$. The ${\beta}$-secretase inhibitory peptide was identified as a six amino acid residue of Gly-Pro-Val-Gly-Ala-Pro (MW: 497.27 Da). In cell viability experiments, the final purified fraction, the carboxy-methyl ion exchange column fraction (CM-F1) showed no significant cytotoxic effect in SH-SY5Y cells at concentrations below $100{\mu}g/mL$ in 24 h. The results of this study suggest that peptides separated from Arctoscopus japonicus may be beneficial as ${\beta}$-secretase inhibitor compounds in functional foods.

• Bulletin of the Korean Chemical Society
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• v.34 no.6
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• pp.1903-1905
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• 2013

• Preventive Nutrition and Food Science
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• v.15 no.4
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• pp.282-286
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• 2010

To isolate a calcium-binding peptide from chlorella protein hydrolysates, chlorella protein was extracted and hydrolyzed using Flavourzyme, a commercial protease. The degree of hydrolysis and calcium-binding capacity were determined using trinitrobenzenesulfonic acid and orthophenanthroline methods, respectively. The enzymatic hydrolysis of chlorella protein for 6 hr was sufficient for the preparation of chlorella protein hydrolysates. The hydrolysates of chlorella protein were then ultra-filtered under 5 kDa as molecular weight. The membrane-filtered solution was fractionated using ion exchange, reverse phase, normal phase chromatography, and fast protein liquid chromatography to identify a calcium-binding peptide. The purified calcium-binding peptide had a calcium binding activity of 0.166 mM and was determined to be 700.48 Da as molecular weight, and partially identified as a peptide containing Asn-Ser-Gly-Cys based on liquid chromatography/electrospray ionization tandem mass spectrum.