• Journal of Microbiology and Biotechnology
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• 제9권1호
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• pp.62-69
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• 1999

In order to investigate the critical amino acid residues involved in the catalytic activities of $\beta$-cyclodextrin glucanotransferase ($\beta$-CGTase) excreted by Bacillus firmus var. alkalophilus, the amino acid residues in $\beta$-CGTase were modified by various site-specific amino acid modifying reagents. The cyclizing and amylolytic activities of $\beta$-CGTase were all seriously reduced after treatment with Woodward's reagent K (WRK) modifying aspartic/glutamic acid, N-bromosuccinimde (NBS) modifying tryptophan, and diethylpyrocarbonate (DEPC) modifying histidine residues. The roles of tryptophan and histidine residues in $\beta$-CGTase were further investigated by measuring the protection effect of various substrates during chemical modification, comparing protein mobility in native and affinity polyacrylamide gel electrophoresis containing soluble starch, and comparing the $K_m$ and $V_{max}$ values of native and modified enzymes. Tryptophan residues were identified as affecting substrate-binding ability rather than influencing catalytic activities. On the other hand, histidine residues influenced catalytic ability rather than substrate-binding ability, plus histidine modification had an effect on shifting the optimum pH and pH stability.

• 한국자기공명학회논문지
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• 제28권2호
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• pp.6-9
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• 2024

HscA is a Hsp70-type chaperone protein that plays an essential role to mediate the iron-sulfur (Fe-S) cluster biogenesis mechanism in Escherichia coli. Like other Hsp70 chaperones, HscA is composed of two domains: the nucleotide binding domain (NBD), which can hydrolyze ATP and use its chemical energy to facilitate the Fe-S cluster transfer process, and the substrate binding domain (SBD), which directly interacts with the substrate, IscU, the scaffold protein of an Fe-S cluster. In the present work, we prepared the isolated SBD construct of HscA (HscA(SBD)) and conducted the solution-state nuclear magnetic resonance (NMR) experiments to have its backbone chemical shift assignment information. Due to low spectral quality of HscA(SBD), we obtained all the NMR data from the sample containing the peptide LPPVKIHC, the HscA-interaction motif of IscU, from which the chemical shift assignment could be done successfully. We expect that this information provides an important basis to execute detailed structural characterization of HscA and appreciate its interaction with IscU.

• Bulletin of the Korean Chemical Society
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• 제32권4호
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• pp.1133-1137
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• 2011

Ordered array of gold nanoparticles (Au NPs) over ITO glass was investigated in terms of ITO pretreatment, particle size, and diamines with different chain length. Owing to the indium-tin-oxide (ITO) layer coated on the glass, the substrate surface has a limited number of hydroxyl groups which can produce functionalized amine groups for Au binding, which resulted in the loosely-packed array of Au NPs on the ITO surface. Diamine ligand as a molecular linker was introduced to enhance the lateral binding of adjacent Au NPs immobilized on the amine-functionalized ITO glass, consequently leading to the densely-packed array of Au NPs over the ITO substrate. The molecular bridging effect was strengthened with the increase of chain length of diamines: C-12 > C-8. The packing density of small Au NPs (< 40 nm) was significantly increased with the increase of C-8 diamine, but large Au NPs (> 60 nm) did not produce densely-packed array on the ITO glass even for the dosage of C-12 diamine.

• 대한화학회지
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• 제14권2호
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• pp.161-168
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• 1970

In order to obtain the more effective evidence, supporting the hypothesis which have been previously described by former report that pepsin (EC 3.4. 4.1) forms a hydrophobic bond with the nonpolar side chain of its substrate, the inhibitory effect of carboxylic acids(from formic acid to iso-butyric acid) on the activity of pepsin to the synthetic dipeptide, N-Carbobenzoxy-L-glutamyl-L-tyrosine, was discussed. The kinetic study showed that the inhibition by carboxylic acids was competitive. The Kidecreased with increasing size of the inhibitor molecule. The $-{\Delta}F^{\circ}$increased linearly with increasing number of carbon atoms in the hydrocarbon chain of the inhibitor. It was confirmed that the hydrophobic bond between more than one side chain of amino acid residues(phenylalanine) in the binding region of the active center of pepsin and the side chain of amino acid residues in the substrate was formed as the first step of its enzymic mechanism. The inhibitory effect of carboxylic acids was due to the competition of the hydrocarbon group of the carboxylic acids with the side chain of the substrate for the hydrophobic binding site(the side chain of phenylalanine) of the pepsin.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2002년도 제9회 학술 발표회 프로그램과 논문초록
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• pp.18-18
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• 2002

Nitrogenase, comprised of the MoFe and Fe proteins, catalyzes the reduction of dinitrogen to ammonia at ambient temperature and pressure. The MoFe protein contains two metal centers, the P-cluster (Fe8S7-8) and the FeMo-cofactor (Fe7S9：homocitrate), the substrate binding site. Despite the availability of the crystal structure of the MoFe protein, suprisingly little is known about the molecular details of catalysis at the active site, and no small-molecule substrate or inhibitor had ever been shown to directly interact with a protein-bound cluster of the functioning enzyme, until our electron-nuclear double resonance(ENDOR) study of CO-inhibited nitrogenase.(omitted)

• Journal of Microbiology and Biotechnology
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• 제23권12호
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• pp.1699-1707
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• 2013

During the fermentative production of 1,3-propanediol under high substrate concentrations, accumulation of intracellular 3-hydroxypropionaldehyde will cause premature cessation of cell growth and glycerol consumption. Discovery of oxidoreductases that can convert 3-hydroxypropionaldehyde to 1,3-propanediol using NADPH as cofactor could serve as a solution to this problem. In this paper, the yqhD gene from Klebsiella pneumoniae DSM2026, which was found encoding an aldehyde reductase (KpAR), was cloned and characterized. KpAR showed broad substrate specificity under physiological direction, whereas no catalytic activity was detected in the oxidation direction, and both NADPH and NADH can be utilized as cofactors. The cofactor binding mechanism was then investigated employing homology modeling and molecular dynamics simulations. Hydrogen-bond analysis showed that the hydrogen-bond interactions between KpAR and NADPH are much stronger than that for NADH. Free-energy decomposition dedicated that residues Gly37 to Val41 contribute most to the cofactor preference through polar interactions. In conclusion, this work provides a novel aldehyde reductase that has potential applications in the development of novel genetically engineered strains in the 1,3-propanediol industry, and gives a better understanding of the mechanisms involved in cofactor binding.

• Biomolecules & Therapeutics
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• 제32권4호
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• pp.474-480
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• 2024

Streptomyces avermitilis genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid compounds. The recombinant CYP107P2 protein was expressed in Escherichia coli and the purified enzyme exhibited a typical P450 spectrum upon CO-binding in its reduced state. Type-I substrate-binding spectral titrations were observed with various terpenoid compounds, including α-pinene, β-pinene, α-terpinyl acetate, and (+)-3-carene. The calculated binding affinities (Kd) ranged from 15.9 to 50.8 µM. The X-ray crystal structure of CYP107P2 was determined at 1.99 Å resolution, with a well-conserved overall P450 folding conformation. The terpenoid compound docking models illustrated that the structural interaction between monoterpenes and CYP107P2, with the distance between heme and terpenes ranging from 3.4 to 5.4 Å, indicates potential substrate binding for P450 enzyme. This study suggests that CYP107P2 is a Streptomyces P450 enzyme capable of catalyzing terpenes as substrates, signifying noteworthy advancements in comprehending a novel P450 enzyme's involvement in terpene reactions.

• Toxicological Research
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• 제23권1호
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• pp.1-9
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• 2007

Transporters are membrane proteins that mediate the transfer of substrate across the cellular membrane. In this overview, the characteristics and the toxicological relevance were discussed for various types of transporters. For drug transporters, the overview focused on ATP-binding cassette transporters and solute carrier family 21A/22A member transporters. Except for OCTN transporters and OATP transporters, drug transporters tend to have broad substrate specificity, suggesting drug-drug interaction at the level of transport processes (e.g., interaction between methotrexate and non-steroidal anti-inflammatory agents) is likely. For metal transporters, transporters for zinc, copper and multiple metals were discussed in this overview. These metal transporters have comparatively narrow substrate specificity, except for multiple metal transporters, suggesting that inter-substrate interaction at the level of transport is less likely. In contrast, the expressions of the transporters are often regulated by their substrates, suggesting cellular adaptation mechanism exists for these transporters. The drug-drug interactions in drug transporters and the cellular adaptation mechanisms for metal transporters are likely to lead to alterations in pharmacokinetics and cellular metal homeostasis, which may be linked to the development of toxicity. Therefore, the transporter-mediated alterations may have toxicological relevance.

• BMB Reports
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• 제44권6호
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• pp.375-380
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• 2011

Bacillus licheniformis SK-1 naturally produces chitinase 72 (CHI72) with two truncation derivatives at the C-terminus, one with deletion of the chitin binding domain (ChBD), and the other with deletions of both fibronectin type III domain (FnIIID) and ChBD. We constructed deletions mutants of CHI72 with deletion of ChBD (CHI72${\Delta}$ChBD) and deletions of both FnIIID and ChBD (CHI72${\Delta}$FnIIID${\Delta}$ChBD), and studied their activity on soluble, amorphous and crystalline substrates. Interestingly, when equivalent amount of specific activity of each enzyme on soluble substrate was used, the product yield from CHI72-${\Delta}$ChBD and CHI72${\Delta}$FnIIID${\Delta}$ChBD on colloidal chitin was 2.5 and 1.6 fold higher than CHI72, respectively. In contrast, the product yield from CHI72${\Delta}$ChBD and CHI72${\Delta}$FnIIID-${\Delta}$ChBD on ${\beta}$-chitin reduced to 0.7 and 0.5 fold of CHI72, respectively. These results suggest that CHI72 can modulate its substrate specificities through truncations of the functional domains at the C-terminus, producing a mixture of enzymes with elevated efficiency of hydrolysis.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2005년도 International Meeting of the Microbiological Society of Korea
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• pp.101-104
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• 2005