• BMB Reports
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• v.39 no.5
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• pp.595-606
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• 2006

Metallothioneins are a group of low molecular mass and cysteine-rich metal-binding proteins, ubiquitously found in most living organisms. They play an important role in maintaining intracellular metal homeostasis, eliminating metal toxification and protecting against intracellular oxidative damages. Analysis of complete rice genome sequences revealed eleven genes encoding putative metallothionein (OsMT), indicating that OsMTs constitute a small gene family in rice. Expression profiling revealed that each member of the OsMT gene family differs not only in sequence but also in their tissue expression patterns, suggesting that these isoforms may have different functions they perform in specific tissues. On the basis of OsMT structural and phylogenetic analysis, the OsMT family was classified as two classes and class I was subdivided into four types. Additionally, in this paper we also present a complete overview of this family, describing the gene structure, genome localization, upstream regulatory element, and exon/intron organization of each member in order to provide valuable insight into this OsMT gene family.

• Journal of Microbiology and Biotechnology
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• v.23 no.11
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• pp.1529-1535
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• 2013

Tuberculosis is a worldwide epidemic disease caused by Mycobacterium tuberculosis, with an estimated one-third of the human population currently affected. Treatment of this disease with aminoglycoside antibiotics has become less effective owing to antibiotic resistance. Recent determination of the crystal structure of the M. tuberculosis Rv3168 protein suggests a structure similar to that of Enterococcus faecalis APH(3')-IIIa, and that this protein may be an aminoglycoside phosphotransferase. To determine whether Rv3168 confers antibiotic resistance against kanamycin, we performed dose-response antibiotic resistance experiments using kanamycin. Expression of the Rv3168 protein in Escherichia coli conferred antibiotic resistance against $100{\mu}M$ kanamycin, a concentration that effected cell growth arrest in the parental E. coli strain and an E. coli strain expressing the $Rv3168^{D249A}$ mutant, in which the catalytic Asp249 residue was mutated to alanine. Furthermore, we detected phosphotransferase activity of Rv3168 against kanamycin as a substrate. Moreover, docking simulation of kanamycin into the Rv3168 structure suggests that kanamycin fits well into the substrate binding pocket of the protein, and that the phosphorylation-hydroxyl-group of kanamycin was located at a position similar to that in E. faecalis APH(3')-IIIa. On the basis of these results, we suggest that the Rv3168 mediates kanamycin resistance in M. tuberculosis, likely through phosphotransferase targeting of kanamycin.

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2002.08a
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• pp.90-90
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• 2002

Syndecans, transmembrane heparan sulfate proteoglycans, are coreceptors with integrin in cell adhesion process. It forms a ternary signaling complex with protein kinase C and phosphatidylinositol 4,5 bisphosphate (PIP2) for integrin signaling. NMR data indicates that cytoplasmic domain of syndecan-4 (4L) undergoes a conformational transition in the presence of PIP2, forming oligomeric conformation. The structure based on NMR data demonstrated that syndecan-4L itself forms a compact intertwined symmetric dimer with an unusual clamp shape for residues Leu$^{186}$ -Ala$^{195}$ . The molecular surface of the syndecan-4L dimer is highly positively charged. In addition, no inter-subunit NOEs in membrane proximal amino acid resides (Cl region) has been observed, demonstrating that the Cl region is mostly unstructured in syndecan-4L dimmer. However, the complex structure in the presence of PIP2 induced a high order multimeric conformation in solution. In addition, phosphorylation of cytoplasmic domain induces conformational change of syndecan-4, resulting inhibition of PKC signaling. The NMR structural data strongly suggest that PIP2 promotes oligomerization of syndecan-4 cytoplasmic domain for PKC activation and further induces structural reorganization of syndecan for mediating signaling network in cell adhesion procedure.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.9
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• pp.1381-1388
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• 2019

Objective: The aims of this study were to reveal the magnitude of the differences in protein structures at a cellular level as well as protein utilization and availability among soybean meal (SBM), canola meal (CM), and rapeseed meal (RSM) as feedstocks in China. Methods: Experiments were designed to compare the three different types of feedstocks in terms of: i) protein chemical profiles; ii) protein fractions partitioned according to Cornell Net Carbohydrate and Protein System; iii) protein molecular structures and protein second structures; iv) special protein compounds-amino acid (AA); v) total digestible protein and energy values; vi) in situ rumen protein degradability and intestinal digestibility. The protein second structures were measured using FT/IR molecular spectroscopy technique. A summary chemical approach in National Research Council (NRC) model was applied to analyze truly digestible protein. Results: The results showed significant differences in both protein nutritional profiles and protein structure parameters in terms of ${\alpha}-helix$, ${\beta}-sheet$ spectral intensity and their ratio, and amide I, amide II spectral intensity and their ratio among SBM, CM, and RSM. SBM had higher crude protein (CP) and AA content than CM and RSM. For dry matter (DM), SBM, and CM had a higher DM content compared with RSM (p<0.05), whereas no statistical significance was found between SBM and CM (p = 0.28). Effective degradability of CP and DM did not demonstrate significant differences among the three groups (p>0.05). Intestinal digestibility of rumen undegradable protein measured by three-step in vitro method showed that there was significant difference (p = 0.05) among SBM, CM, and RSM, which SBM was the highest and RSM was the lowest with CM in between. NRC modeling results showed that digestible CP content in SBM was significantly higher than that of CM and RSM (p<0.05). Conclusion: This study suggested that SBM and CM contained similar protein value and availability for dairy cattle, while RSM had the lowest protein quality and utilization.

• Molecules and Cells
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• v.43 no.9
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• pp.804-812
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• 2020

In cells, proteins form macromolecular complexes to execute their own unique roles in biological processes. Conventional structural biology methods adopt a bottom-up approach starting from defined sets of proteins to investigate the structures and interactions of protein complexes. However, this approach does not reflect the diverse and complex landscape of endogenous molecular architectures. Here, we introduce a top-down approach called Electron Microscopy screening for endogenous Protein ArchitectureS (EMPAS) to investigate the diverse and complex landscape of endogenous macromolecular architectures in an unbiased manner. By applying EMPAS, we discovered a spiral architecture and identified it as AdhE. Furthermore, we performed screening to examine endogenous molecular architectures of human embryonic stem cells (hESCs), mouse brains, cyanobacteria and plant leaves, revealing their diverse repertoires of molecular architectures. This study suggests that EMPAS may serve as a tool to investigate the molecular architectures of endogenous macromolecular proteins.

• Journal of Microbiology and Biotechnology
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• v.8 no.6
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• pp.663-668
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• 1998

Several neurodegenerative diseases such as Huntington's disease, dentatorubralpallidoluysian atrophy, spinobulbar muscular atrophy, Machado-Joseph disease, and spinocerebellar ataxias type 1 are associated with the aggregation of expanded glutamine repeats within their proteins. Generally, in clinically affected individuals, the expansion of the polyglutamine sequences is beyond 40 residues. To address the length of polyglutamine that forms aggregation, we have constructed plasmids encoding glutathione S-transferase (GST) Machado-Joseph disease gene fusion proteins containing polyglutamine and investigated the formation of aggregates in E. coli. Surprisingly, even $(Gin)_8$, in the normal range as well as $(Gin)_{65}$ in the pathogenic range enhanced the formation of insoluble protein aggregates, whereas $(Ser)_8$, and $(Aia)_8$, did not form aggregates. Our results indicate that the formation of protein aggregates in GST-polyglutamine proteins is specifically mediated by the polyglutamine repeat sequence within their protein structure. Our study may contribute to the understanding of the molecular mechanism of the formation of protein aggregates in neurodegenerative disorders and the development of preventative strategies.

• Genomics & Informatics
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• v.10 no.2
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• pp.128-132
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• 2012

To learn the differences between the structure-activity relationship and molecular vibration-activity relationship in the ligand-receptor interaction of the histamine receptor, 47 ligands of the histamine receptor were analyzed by structural similarity and molecular vibrational frequency patterns. The radial tree that was produced by clustering analysis of molecular vibrational frequency patterns shows its potential for the functional classification of histamine receptor ligands.

• Proceedings of the Zoological Society Korea Conference
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• 2003.08a
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• pp.194.3-194
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• 2003

No Abstract, See Full Text

• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.743-750
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• 2016

Mus musculus (Rodentia: Muridae) has generally been infected with a rodent hookworm Nippostrongylus brasiliensis. In this report, we present morphological and molecular identification of N. brasiliensis by light and scanning electron microscopy and PCR amplification of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene and the protein sequences encoded by cox1 gene, respectively. Despite the use of N. brasiliensis in many biochemistry studies from India, their taxonomic identification was not fully understood, especially at the species level, and no molecular data is available in GenBank from India. Sequence analysis of cox1 gene in this study revealed that the present specimen showed close identity with the same species available in GenBank, confirming that the species is N. brasiliensis. This study represents the first record of molecular identification of N. brasiliensis from India and the protein structure to better understand the comparative phylogenetic characteristics.

• BMB Reports
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• v.33 no.1
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• pp.1-36
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• 2000

Acetohydroxyacid synthase (EC 4.1.3.18) catalyses the first reaction in the pathway for synthesis of the branched-chain amino acids. The enzyme is inhibited by several commercial herbicides and has been subjected to detailed study over the last 20 to 30 years. Here we review the progress that has been made in understanding its structure, regulation, mechanism, and inhibition.