• BMB Reports
• /
• 제40권3호
• /
• pp.315-324
• /
• 2007

The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.

• Bulletin of the Korean Chemical Society
• /
• 제33권10호
• /
• pp.3233-3240
• /
• 2012

We demonstrated the combined applications of online protein digestion using trypsin immobilized enzyme reactor (IMER) and dual tandem mass spectrometry with collisionally activated dissociation (CAD) and electron transfer dissociation (ETD) for tryptic peptides eluted through the trypsin-IMER. For the trypsin-IMER, the organic and inorganic hybrid monolithic material was used. By employing the trypsin-IMER, the long digestion time could be saved with little or no sacrifice of the digestion efficiency, which was demonstrated for standard protein samples. For three model proteins (cytochrome c, carbonic anhydrase, and bovine serum albumin), the tryptic peptides digested by the IMER were analyzed using LC-MS/MS with the dual application of CAD and ETD. As previously shown by others, the dual application of CAD and ETD increased the sequence coverage in comparison with CAD application only. In particular, ETD was very useful for the analysis of highly-protontated peptide cations, e.g., ${\geq}3+$. The combination approach provided the advantages of both trypsin-IMER and CAD/ETD dual tandem mass spectrometry applications, which are rapid digestion (i.e., 10 min), good digestion efficiency, online coupling of trypsin-IMER and liquid chromatography, and high sequence coverage.

• Food Science and Biotechnology
• /
• 제18권2호
• /
• pp.494-499
• /
• 2009

To improve phenylalanine ammonia lyase (E.C.4.3.1.5-PAL) activity in recombinant Escherichia coli, Some approaches for improving phenylalanine ammonia lyase (PAL) activity in recombinant E. coli were developed following preliminary studies by means of response surface method. The results shown that permeabilization with combination of Triton X-100, cetyl trimethyl ammonium bromide (CTAB), and acetone enriched cellular recombinant PAL activity significantly, which improved over 10-fold as compared with the control (untreat cell), as high as 181.37 U/g. The optimum values for the tested variables were Triton X-100 0.108 g/L, CTAB 0.15 g/L, and acetone 45.2%(v/v). Furthermore, a second-order model equation was suggested and then validated experimentally. It was indicated that addition of surfactants and organic solvents made the cells more permeable and therefore allowed easier access of the substrate to the enzyme and excretion of the product, which increased the rate of transport of L-phenylalanine and trans-cinnamic acids. These improved methods of PAL activity enrichment could serve as a rich enzyme source, especially in the biosynthesis of L-phenylalanine.

• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 2003년도 정기총회 및 학술발표회
• /
• pp.70-70
• /
• 2003

Active sites and substrate bindings of 1-aminoxyclopropane-1-carboxylate oxidase (MD-ACO1) catalyzing the oxidative conversion of ACC to ethylene have been determined based on site-directed mutagenesis and comparative modeling methods. Molecular modeling based on the crystal structure of Isopenicillin N synthase (IPNS) provided MD-ACO1 structure. MD-ACO1 protein folds into a compact jelly roll shape, consisting of 9 ${\alpha}$-helices, 10 ${\beta}$-strands and several long loops. The MD-ACO1/ACC/Fe(II)/Ascorbate complex conformation was determined from automated docking program, AUTODOCK. The MD-ACO1/Fell complex model was consistent with well known binding motif information (HIS177-ASP179-HIS234). The cosubstrate, ascorbate is placed between iron binding pocket and Arg244 of MD-ACO1 enzyme, supporting the critical role of Arg244 for generating reaction product. These findings are strongly supported by previous biochemical data as well as site-directed mutagenesis data. The structure of enzyme/substrate suggests the structural mechanism for the biochemical role as well as substrate specificity of MD-ACO1 enzyme.

• Bulletin of the Korean Chemical Society
• /
• 제26권6호
• /
• pp.952-958
• /
• 2005

Angiotensin-converting enzyme (ACE) is known to be primarily responsible for hypertension. Threedimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of 28 ACE inhibitors. The availability of ACE crystal structure (1UZF) provided the plausible biological orientation of inhibitors to ACE active site (C-domain). Alignment for CoMFA obtained by docking ligands to 1UZF protein using FlexX program showed better statistical model as compared to superposition of corresponding atoms. The statistical parameters indicate reasonable models for both CoMFA ($q^2$ = 0.530, $r^2$ = 0.998) and CoMSIA ($q^2$ = 0.518, $r^2$ = 0.990). The 3D-QSAR analyses provide valuable information for the design of ACE inhibitors with potent activity towards C-domain of ACE. The group substitutions involving the phenyl ring and carbon chain at the propionyl and sulfonyl moieties of captopril are essential for better activity against ACE.

• Natural Product Sciences
• /
• 제20권2호
• /
• pp.113-118
• /
• 2014

Ribes fasciculatum which belongs to Saxifragaceae has been widely used as a traditional medicine for the treatment of symptoms associated with lacquer poison. However, pharmacological studies on the R. fasciculatum are extremely limited until now. Thus, in this study, we evaluated the possible anti-inflammatory effects of ethyl acetate fraction of R. fasciculatum (ERF) using IFN-${\gamma}$/LPS-stimulated peritoneal macrophage model. We investigated the change in nitrite level in the absence or presence of ERF after LPS stimulation, and we found that ERF effectively attenuates the NO production in a dose dependent manner without notable toxicity. To determine the mechanism of the inhibitory action of ERF on NO production, we performed iNOS enzyme activity assay and Western blotting. Here we showed that both of iNOS enzyme activities and iNOS expressions were significantly down-regulated by ERF, indicating that these dual activities of ERF are responsible for ERF-mediated NO suppression. In addition, ERF inhibitied the expression of cyclooxygenase-2 (COX-2), an another key enzyme in inflammation through suppression of NF-${\kappa}B$ activation. We also tested anti-inflammatory properties of ERF not only in vitro, but in vivo using trypsin-induced paw edema model in mice. Our results revealed that the increased paw volume in response to trypsin injection was recovered by ERF supplement dose dependently.

• 멤브레인
• /
• 제19권1호
• /
• pp.72-82
• /
• 2009

A mathematical model was written for simulating the removal of phenol from wastewater in enzyme-loaded membrane reactor (EMR). The numerical simulation program was developed so as to predict the degradation of phenol through an EMR. Numerical model proves to be effective in searching for optimal operating conditions and creating an optimal microenvironment for the biocatalyst in order to optimize productivity. In this study, several dimensionless parameters such as Thiele Modulus (${\phi}^2$, dimensionless Michaelis-Menten constant ($\xi$), Peclet number (Pe) were introduced to simplify their effects on system efficiency. In particular, the study of phenol conversion at different feed compositions shows that low phenol concentrations and high Thiele Modulus values lead to higher reactant degradation.

• 한국생물공학회:학술대회논문집
• /
• 한국생물공학회 2005년도 생물공학의 동향(XVII)
• /
• pp.511-516
• /
• 2005

Sorbitan methacrylate was synthesized from sorbitan dehydrated from D-sorbitol using an immobilized lipase. To optimize the enzymatic synthesis of sorbitan methacrylate, response surface methodology was applied to determine the effects of five-level-four-factors and their reciprocal interactions on sorbitan methacrylate biosynthesis. A total of 30 individual experiments were performed, which were designed to study reaction temperature, reaction time, enzyme amount and substrate molar ratio. A statistical model predicted that the highest conversion yield of sorbitan methacrylate was 100%, at the following optimized reaction conditions: a reaction temperature of 43.06 $^{\circ}C$, a reaction time of 164.25 mins., an enzyme amount of 7.47%, and a substrate molar ratio of 3.98:1. Using these optimal factor values under experimental conditions in four independent replicates, the average conversion yield reached 98.7%${\pm}$1.2% and was well within the value predicted by the model.

• 한국염색가공학회지
• /
• 제25권4호
• /
• pp.271-278
• /
• 2013

In order to investigate the effect of gallotannin treatment to ceramide-containing fabrics on atopic skin diseases, the agglomeration of standard protein BSA and the deactivation of model enzyme were examined. The gallotannin treated on ceramide-containing fabrics precipitated the standard protein, BSA, and therefore deactivated the model enzyme by 70% at 6% treatment concentration. Wash durability should be improved after around 5 cycles of washing. Clinical test of the gallotannin-treated fabrics was carried out on mice for two test items, transepidermal water loss assay and severity score of diseased skin of mice. The results showed significant level of improvement of atopic skin diseases compared with the negative controled.

• 미생물학회지
• /
• 제52권2호
• /
• pp.226-229
• /
• 2016

먹물버섯 Coprinellus congregatus의 버섯조직이 자가분해되는 시기에 발현되는 chitinase (Chi2)는 사람에게 질병을 일으키는 Cryptococcus neoformans의 세포벽 두께를 정상 세포벽의 32% 수준까지 감소시킬 뿐만 아니라, 세포 외 섬유상 물질도 제거하였다. Chi2 처리에 의하여 사람에게 알레르기를 유발하는 Alternaria alternata의 생장은 물론 생쥐 모델에서 이 균에 의한 피부알레르기 증상도 감소시켰다.