• Molecules and Cells
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• v.26 no.3
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• pp.228-235
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• 2008

Thiol-dependent redox systems are involved in regulation of diverse biological processes, such as response to stress, signal transduction, and protein folding. The thiol-based redox control is provided by mechanistically similar, but structurally distinct families of enzymes known as thiol oxidoreductases. Many such enzymes have been characterized, but identities and functions of the entire sets of thiol oxidoreductases in organisms are not known. Extreme sequence and structural divergence makes identification of these proteins difficult. Thiol oxidoreductases contain a redox-active cysteine residue, or its functional analog selenocysteine, in their active sites. Here, we describe computational methods for in silico prediction of thiol oxidoreductases in nucleotide and protein sequence databases and identification of their redox-active cysteines. We discuss different functional categories of cysteine residues, describe methods for discrimination between catalytic and noncatalytic and between redox and non-redox cysteine residues and highlight unique properties of the redox-active cysteines based on evolutionary conservation, secondary and three-dimensional structures, and sporadic replacement of cysteines with catalytically superior selenocysteine residues.

• Macromolecular Research
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• v.12 no.4
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• pp.342-351
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• 2004

Poly(ethylene glycol) (PEG1K) and sulfonated PEG (PEG1K-SO$_3$) methacrylate (MA) copolymers have been prepared and characterized. The structures of the synthesized copolymers were confirmed by $^1$H and $^{13}$ C NMR spectroscopy and elemental analysis. The bulk characteristics of the copolymers were evaluated by viscosity and thermal analysis. The surface properties of the copolymers were investigated using dynamic contact angle measurements and electron spectroscopy for chemical analysis. The hydrophilicity of the surfaces modified with PEG1KMA or PEG1K-SO$_3$MA increased, possibly as a result of the orientation of the hydrophilic PEG1KMA/PEG1K-SO$_3$MA chains into the water phase. Platelets adhered less to the surfaces of the copolymers than they did to a polyurethane control. In addition, adhesion of platelets to the copolymer surfaces decreased upon increasing the chain density of PEG1KMA and sulfonated PEG1KMA in the copolymers. Both bacterial adhesion and protein adsorption were significantly reduced on the copolymer surfaces and their levels differ depending on the kind of surface or media.

• BMB Reports
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• v.33 no.6
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• pp.448-453
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• 2000

In yeast the key gluconeogenic enzyme, fructose-1,6-bisphosphatase (FBPase), is selectively targeted from the cytosol to the lysosome (vacuole) for degradation when glucose starved cells are replenished with glucose. The pathway for glucose induced FBPase degradation is unknown. To identify the receptor-mediated degradation pathway of FBPase, we investigated the presence of the FBPase receptor on the vacuolar membrane by cell fractionation experiments and binding assay using vid mutant (vacuolar import and degradation), which is defective in the glucose-induced degradation of FBPase. FBPase sedimented in the pellets from vid24-1 mutant after centrifugation at $15,000{\times}g$ for 15 min, suggesting that FBPase is associated with subcellular structures. Cell fractionation experiments revealed that FBPase is preferentially associated with the vacuole, but not with other organelles in vid24-1. FBPase enriched fractions that cofractionated with the vacuole were sensitive to proteinase K digestion, indicating that FBPase is peripherally associated with the vacuole. We developed an assay for the binding of FBPase to the vacuole. The assay revealed that FBPase bound to the vacuole with a Kd of $2.3{\times}10^6M$. The binding was saturable and specific. These results suggest that a receptor for FBPase degradation exists on the vacuolar membrane. It implies the existence of the receptor-mediated degradation pathway of FBPase by the lysosome.

• Journal of Dairy Science and Biotechnology
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• v.21 no.2
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• pp.138-147
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• 2003

We here analyzed and proposed the structures of the N-linked sugar chains of PAS-7 from bovine milk fat globule membrane. The N-linked sugar chains were liberated from PAS-7 by hydrazinolysis and, after modifying the reducing ends with 2-aminopyridine (PA), were separated into one neutral (7N,55%) and two acidic (7M mono-, 43%; 7D, di-, 2%) sugar chain roups. The latter were converted into neutral groups (7MN and 7DN) by sialidase digestion. The structure of each of these PA-neutral sugar chains was determined by sugar analysis, sequential exoglycosidase digestion, partial acetolysis, and 1H-NMR spectroscopy. The results show that the 10 sugar chains were of the biantennary complex type with and without fucose. The structure of 7N2A one of the major sugar chains, was proposed as; [structure: see text] A structural comparison between PAS-6 and -7 indicated that although they shared the same protein core, their sugar moiety was markedly different, involving the existence of a different pathway during the post-transcriptional modification.

• Food Science of Animal Resources
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• v.41 no.6
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• pp.983-996
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• 2021

This study explored the physicochemical, textural, and sensorial properties of a meat analog (MA) as compared to beef and pork meats. Results illustrate that MA patties had lower moisture, fat, and protein content, as well as higher ash and crude fiber than beef and pork. Likewise, MA patties had a higher pH, lightness (L^*), and redness (a^*) than either beef or pork. Pork meat exhibited the highest released water (RW) and cooking loss (CL) values, followed closely by MA with beef displaying the lowest values. Regardless of patty type, the post-cooking diameter patties were reduced significantly (p<0.05). However, the Warner-Bratzler shear force (WBSF), hardness, chewiness, and gumminess of beef were significantly higher than that of either pork or MA. The visible appearance of MA patties had more porous and loose structures before and after cooking. Consequently, based on sensory parameters, MA patties demonstrated the higher values for appearance and firmness, followed by beef and pork respectively, although the difference was not statistically significant. Therefore, the current study demonstrated that some physicochemical, textural, and sensory characteristics of beef and pork exhibited the most similarity to MA.

• Genomics & Informatics
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• v.20 no.4
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• pp.41.1-41.9
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• 2022

The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.

• The Journal of Korean Society of Virology
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• v.30 no.1
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• pp.39-49
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• 2000

The genome of Hantaan virus, the prototype of the hantavirus genus, is composed of three segmented, single stranded negative sense RNA genome. The 5' and 3' termini of the Hantaan virus RNA genome contain noncoding regions (NCRs) that are highly conserved and complementary to form panhandle structures. There are some reports that these NCRs seems to control gene expression and viral replication in influenza virus and vesicular stomatitis virus. In this study, we examined whether NCRs in Hantaan virus playa role in expression of the viral nucleocapsid protein (Np) and foreign (luciferase) gene. The 5' and/or 3' NCR-deleted mutants were constructed and analysed. The Np expression of 5' NCR-deleted clone was similar to that of the clone containing full S genome. In the case of 3' NCR-deleted clone, it showed 40% reduction. To investigate the role of NCR in foreign gene expression, the clones which are replaced ORF of Hantaan viral Np gene with that of luciferase gene were constructed. The results were similar to those of the experiments using Np gene. These results suggest that 3' NCR is more important than 5' NCR in protein expression. To find out a critical region of 3' NCR in protein expression, several clones with a deleted part of 3' NCR were constructed and analyzed. The deletion of the conserved region in 3' NCR showed $20{\sim}30%$ decrease in Np expression. However there were no change in luciferase activities between clones with or without non-conserved region of 3' NCR. These results suggest that the 3' NCR of Hantaan virus S genome, especially conserved region in 3' NCR, plays an important role in the expression of Hantaan viral Np and foreign genes.

• Journal of the Korea Society of Computer and Information
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• v.27 no.8
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• pp.49-59
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• 2022

In this paper, we designed a new enzyme function prediction model PSCREM based on a study that compared and evaluated CNN and LSTM/GRU models, which are the most widely used deep learning models in the field of predicting functions and structures using protein sequences in 2020, under the same conditions. Sequence evolution information was used to preserve detailed patterns which would miss in CNN convolution, and the relationship information between amino acids with functional significance was extracted through overlapping RNNs. It was referenced to feature map production. The RNN family of algorithms used in small CNN-RNN models are LSTM algorithms and GRU algorithms, which are usually stacked two to three times over 100 units, but in this paper, small RNNs consisting of 10 and 20 units are overlapped. The model used the PSSM profile, which is transformed from protein sequence data. The experiment proved 86.4% the performance for the problem of predicting the main classes of enzyme number, and it was confirmed that the performance was 84.4% accurate up to the sub-sub classes of enzyme number. Thus, PSCREM better identifies unique patterns related to protein function through overlapped RNN, and Overlapped RNN is proposed as a novel methodology for protein function and structure prediction extraction.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2187-2191
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• 2015

Background: Protrusive structures formed by migrating and invading cells are termed lamellipodia, filopodia, invadopodia and podosomes. Lamellipodia and filopodia appear on the leading edges of migrating cells and function to command the direction of the migrating cells. Invadopodia and podosomes are special F-actin-rich matrix-degrading structures that arise on the ventral surface of the cell membrane. Invadopodia are found in a variety of carcinomatous cells including squamous cell carcinoma of head and neck region whereas podosomes are found in normal highly motile cells of mesenchymal and myelomonocytic lineage. Invadopodia-associated protein markers consisted of 129 proteins belonging to different functional classes including WASP, NWASP, cortactin, Src kinase, Arp 2/3 complex, MT1-MMP and F-actin. To date, our current understanding on the role(s) of these regulators of actin dynamics in tumors of the orofacial region indicates that upregulation of these proteins promotes invasion and metastasis in oral squamous cell carcinoma, is associated with poor/worst prognostic outcome in laryngeal cancers, contributes to the persistent growth and metastasis characteristics of salivary gland adenoid cystic carcinoma, is a significant predictor of increased cancer risk in oral mucosal premalignant lesions and enhances local invasiveness in jawbone ameloblastomas.

• Applied Microscopy
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• v.1 no.1
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• pp.11-17
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• 1969

Conidio spores of Aspergillus niger (strain No. NRRL 330) cultured on potato dextrose agar media were studied by electron microscopy, using the thin sectioning techniques. Conidio spores to be sectioned were fixed by triple methods with $K_2Cr_2O_7$, Glutaraldehyde and $OsO_4$. After dehydrated with alcohol, the specimens were embedded in metacrylate and epon resin media, and thinly sectioned by Porter-Blum MT-2. After sectioned these specimens were negative-stained with uranyl acetate and observed. by Hitachi HS-6 electron microscope. The results of this experiment were summarized as follows. 1. The structures of spore ,wall system seem to be formed 4 layers; exosporium, basal layer, spore coat and unit cell membrane. The protuberance of spore surface that was looked like hair appears to be protrusived from the basal layer. 2. The 3 layers of unit cell membrane was constituted outer layer membrane, inner layer membrane and inter-mediate light layer. 3. The structures of intra cytoplasmic membrane appear as spiral form which was consisted of 3 layers membrane system; outer membrane, inner membrane, and intermediate layer, which has pits. 4. The cement substance of spore coat and cortex may be changed quantitatively by physiological state in cell. 5. In some cases, we observed that the ribosome was transformed into poly ribosome group, and the storage materials and the protein crystals were changed variously. It. has been suggested that the morphological change of some cytoplasmic materials may be caused by some specialized function of the physiological stage.