• Journal of Electrochemical Science and Technology
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• v.10 no.3
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• pp.284-293
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• 2019

Herein, we report an electrode surface with a hierarchical assembly of wild-type M13 virus nanofibers (M13) to nucleate the AuPt alloy nanostructures by electrodeposition. M13 was pulled on the electrode surface to produce a virus film, and then a layer of sol-gel matrix (SSG) was wrapped over the surface to protect the film, thereby a bio-template was constructed. Blending of metal binding domains of M13 and amine groups of the SSG of the bio-template were effectively nucleate and directed the growth of nanostructures (NSs) such as Au, Pt and AuPt alloy onto the modified electrode surface by electrodeposition. An electrocatalytic activity of the modified electrode toward methanol oxidation in alkaline medium was investigated and found an enhanced mass activity ($534mA/mg_{Pt}$) relative to its controlled experiments. This bio-templated growth of NSs with precise composition could expedite the intention of new alloy materials with tuneable properties and will have efficacy in green energy, catalytic, and energy storage applications.

• International Journal of Computer Science & Network Security
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• v.21 no.1
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• pp.207-213
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• 2021

Networks in Mobile ad hoc contain distribution and do not have a predefined structure which practically means that network modes can play the role of being clients or servers. The routing protocols used in mobile Ad-hoc networks (MANETs) are characterized by limited bandwidth, mobility, limited power supply, and routing protocols. Hybrid routing protocols solve the delay problem of reactive routing protocols and the routing overhead of proactive routing protocols. The Ant Colony Optimization (ACO) algorithm is used to solve other real-life problems such as the travelling salesman problem, capacity planning, and the vehicle routing challenge. Bio-inspired methods have probed lethal in helping to solve the problem domains in these networks. Hybrid routing protocols combine the distance vector routing protocol (DVRP) and the link-state routing protocol (LSRP) to solve the routing problem.

• Bulletin of the Korean Chemical Society
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• v.33 no.9
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• pp.2907-2909
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• 2012

A disintegrin and metalloprotease with thrombospondin domains (ADAMTS) are a member of peptidase and involved in processing of von Willebrand factor as well as cleavage of aggrecan, versican, brevican and neurocan. Among 19 subfamilies of human ADAMTS, ADAMTS-4 is a zinc-binding metalloprotease and is a famous therapeutic target for arthritis. It has been reported that a flavonoid luteolin shows inhibitory activity against ADMATS-4. In this study, we verified that luteolin is a potent inhibitor of ADAMTS-4 and probed the molecular basis of its action. On the basis of a docking study, we proposed a binding model between luteolin and ADAMTS-4 in which 3',4'-dihydroxyl groups in luteolin formed hydrogen bonding with ADMATS-4 and these interactions are important for its inhibitory activity against ADAMTS-4.

• Molecules and Cells
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• v.39 no.11
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• pp.814-820
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• 2016

FtsZ, a tubulin homologue, is an essential protein of the Z-ring assembly in bacterial cell division. It consists of two domains, the N-terminal and C-terminal core domains, and has a conserved C-terminal tail region. Lateral interactions between FtsZ protofilaments and several Z-ring associated proteins (Zaps) are necessary for modulating Z-ring formation. ZapD, one of the positive regulators of Z-ring assembly, directly binds to the C-terminal tail of FtsZ and promotes stable Z-ring formation during cytokinesis. To gain structural and functional insights into how ZapD interacts with the C-terminal tail of FtsZ, we solved two crystal structures of ZapD proteins from Salmonella typhimurium (StZapD) and Escherichia coli (EcZapD) at a 2.6 and $3.1{\AA}$ resolution, respectively. Several conserved residues are clustered on the concave sides of the StZapD and EcZapD dimers, the suggested FtsZ binding site. Modeled structures of EcZapD-EcFtsZ and subsequent binding studies using bio-layer interferometry also identified the EcFtsZ binding site on EcZapD. The structural insights and the results of bio-layer interferometry assays suggest that the two FtsZ binding sites of ZapD dimer might be responsible for the binding of ZapD dimer to two protofilaments to hold them together.

• Journal of Microbiology and Biotechnology
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• v.16 no.6
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• pp.933-938
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• 2006

Decaprenyl diphosphate synthase (DPS) is the key enzyme for the production of coenzyme $Q_{10}$ ($CoQ_{10}$). A dps gene from Sinorhizobium meliioti KCCM 11232 (IFO 14782) was isolated by PCR and then cloned in Escherichia coli. DNA sequencing analysis revealed an open reading frame of 1,017 bp encoding a 338-amino-acid protein. The protein was identical at the 98% level to the putative octaprenyl diphosphate synthase (IspB) of S. meliloti 1021. The deduced amino acid sequence included the DDxxD domains conserved in the majority of the prenyl diphosphate synthases. Heterologous expression in E. coli BL21 (DE3) was carried out, and the $CoQ_{10}$ produced was then analyzed by HPLC. E. coli BL21 (DE3) harboring the dps gene from S. melioti produced CoQ$_{10}$ in addition to endogenous coenzyme Q$_8$ (CoQ$_8$), whereas wild-type E. coli BL21 (DE3) host did not have the ability of producing CoQ$_{10}$. The results suggest that the putative dps from S. meliloti KCTC 2353 encoded the DPS.

• Journal of Microbiology and Biotechnology
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• v.24 no.12
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• pp.1636-1643
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• 2014

3-Hydroxybutyryl-CoA dehydrogenase is an enzyme that catalyzes the second step in the biosynthesis of n-butanol from acetyl-CoA, in which acetoacetyl-CoA is reduced to 3-hydroxybutyryl-CoA. To understand the molecular mechanisms of n-butanol biosynthesis, we determined the crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Clostridium butyricum (CbHBD). The monomer structure of CbHBD exhibits a two-domain topology, with N- and C-terminal domains, and the dimerization of the enzyme was mostly constituted at the C-terminal domain. The mode of cofactor binding to CbHBD was elucidated by determining the crystal structure of the enzyme in complex with $NAD^+$. We also determined the enzyme's structure in complex with its acetoacetyl-CoA substrate, revealing that the adenosine diphosphate moiety was not highly stabilized compared with the remainder of the acetoacetyl-CoA molecule. Using this structural information, we performed a series of site-directed mutagenesis experiments on the enzyme, such as changing residues located near the substrate-binding site, and finally developed a highly efficient CbHBD K50A/K54A/L232Y triple mutant enzyme that exhibited approximately 5-fold higher enzyme activity than did the wild type. The increased enzyme activity of the mutant was confirmed by enzyme kinetic measurements. The highly efficient mutant enzyme should be useful for increasing the production rate of n-butanol.

• Molecules and Cells
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• v.38 no.9
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• pp.781-788
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• 2015

Mutations of MYO15A are generally known to cause severe to profound hearing loss throughout all frequencies. Here, we found two novel MYO15A mutations, c.3871C>T (p.L1291F) and c.5835T>G (p.Y1945X) in an affected individual carrying congenital profound sensorineural hearing loss (SNHL) through targeted resequencing of 134 known deafness genes. The variant, p.L1291F and p.Y1945X, resided in the myosin motor and IQ2 domains, respectively. The p.L1291F variant was predicted to affect the structure of the actin-binding site from three-dimensional protein modeling, thereby interfering with the correct interaction between actin and myosin. From the literature analysis, mutations in the N-terminal domain were more frequently associated with residual hearing at low frequencies than mutations in the other regions of this gene. Therefore we suggest a hypothetical genotype-phenotype correlation whereby MYO15A mutations that affect domains other than the N-terminal domain, lead to profound SNHL throughout all frequencies and mutations that affect the N-terminal domain, result in residual hearing at low frequencies. This genotype-phenotype correlation suggests that preservation of residual hearing during auditory rehabilitation like cochlear implantation should be intended for those who carry mutations in the N-terminal domain and that individuals with mutations elsewhere in MYO15A require early cochlear implantation to timely initiate speech development.

• Journal of Integrative Natural Science
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• v.6 no.3
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• pp.163-169
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• 2013

The chemokine receptor CCR1 a GPCR super family protein contains seven transmembrane domains. It plays an important role in rheumatoid arthritis, organ transplant rejection, Alzheimer's disease and also causes inflammation. Because of its role in disease processes, antagonism of CCR1 became an attractive therapeutic target. In the current study, we have taken a novel series of recently reported CCR1 antagonist of 1-(4-Phenylpiperazin-1-yl_-2-(1H-Pyrazol-1-yl) ethanone derivatives and performed a HQSAR analysis. The model was developed with Atom (A) and bond (B) parameters and with different set of atom counts to improve the model. The results of HQSAR showed good predictive ability in terms of $r^2$ (0.904) and $q^2$ (0.590) with 0.710 as standard error of prediction and 0.344 as standard error of estimate. The contribution map depicted the atom contribution in inhibitory effect. Compound-14 which was reported to be a highly active compound showed positive atom contribution in three R groups ($R^3$. $R^{5a}$ and $R^{2b}$) in inhibitory effect, which could be the reason why this compound is highly active compound whereas, the lowest active compound-6 showed negative contribution to inhibitory effect.

• Fisheries and Aquatic Sciences
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• v.18 no.2
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• pp.173-181
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• 2015

We identified the $Na^+-K^+-2Cl^-$ cotransporter 2 (NKCC2) cDNA isoform from starry flounder, Platichthys stellate. The NKCC2 cDNA encoded a polypeptide of 1,043 amino acids representing 12 putative transmembrane domains based on the bioinformatic topology prediction. In addition, starry flounder NKCC2 possessed highly conserved residues within transmembrane domain 4, known as an essential site for its function. End-point reverse transcription-polymerase chain reaction analysis revealed that the NKCC2 transcript was moderately expressed only in the anterior and posterior intestines and the rectum. The NKCC2 mRNA level in the rectum, but not in other segments, was significantly induced 3 days post Streptococcus parauberis challenge, indicating that excess salt may be transported into the rectum. Taken together, our data indicate that an S. parauberis infection could tip the intestinal fluid balance in favor of fluid accumulation, indicating that bacterial pathogens can interfere with intestinal osmotic balance and normal mucosal immune homeostasis.

• Journal of Microbiology and Biotechnology
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• v.26 no.2
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• pp.226-232
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• 2016

Dihydrodipicolinate reductase is an enzyme that converts dihydrodipicolinate to tetrahydrodipicolinate using an NAD(P)H cofactor in L-lysine biosynthesis. To increase the understanding of the molecular mechanisms of lysine biosynthesis, we determined the crystal structure of dihydrodipicolinate reductase from Corynebacterium glutamicum (CgDapB). CgDapB functions as a tetramer, and each protomer is composed of two domains, an Nterminal domain and a C-terminal domain. The N-terminal domain mainly contributes to nucleotide binding, whereas the C-terminal domain is involved in substrate binding. We elucidated the mode of cofactor binding to CgDapB by determining the crystal structure of the enzyme in complex with NADP⁺ and found that CgDapB utilizes both NADH and NADPH as cofactors. Moreover, we determined the substrate binding mode of the enzyme based on the coordination mode of two sulfate ions in our structure. Compared with Mycobacterium tuberculosis DapB in complex with its cofactor and inhibitor, we propose that the domain movement for active site constitution occurs when both cofactor and substrate bind to the enzyme.