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Garlic sprouts can provide data on functional and food processing materials. This study compared the leaves, bulbs, and roots of garlic sprouts grown on smart farms during two growth periods (20 and 25 days). In addition, data for garlic bulbs grown in open fields were presented as reference materials. All garlic sprouts’ total free sugar content decreased as the growth period increased. All plant parts’ total organic acid content decreased as the growth period progressed, except for the root section. Potassium, phosphorus, and sulfur content increased during growth in all parts of the garlic sprouts. Alliin content decreased in all parts of the plant over time, whereas thiosulfinate content increased in the roots but decreased in the leaves and bulbs. Total polyphenol content increased in all parts of the plant during the growth period, except for the bulb, whereas the flavonoid content did not change significantly over time. The 2,2-diphenyl-1-picrylhydrazy (DPPH) and 2,2′-azinobis (3-ethylben-zothiazoline 6-sulfonate) (ABTS) free radical scavenging activities, as well as the superoxide dismutase (SOD)-like activity of garlic sprouts were 37.45-65.47%, 59.12-89.81%, and 89.52-98.59%, respectively. These activities tend to decrease during the growth period. Here, we showed that garlic sprouts have higher levels of functional substances and physiological activities than general garlic sprouts. It was also determined that a growth period of 20 days was suitable for garlic sprouts. Data for research on functional and food-processing materials can be obtained by analyzing garlic sprouts produced by smart farms.

The aim of this study was to improve the quality and functionality of Korean soy sauce made with onion juice. At the end of fermentation, the titratable acidity of the soy sauce containing 100% onion juice was the highest at 2.90%. The salt (NaCl) content was highest and lowest in the samples without and with onion juice supplementation, respectively. The protein content ranged from 11.09-12.50%. The sensory evaluation revealed that the soy sauce sample containing 70% onion juice had the highest scove at 5.0-5.8 levels in terms of sweetness, salty taste, delicate flavor, and overall preference. Quercetin content was 1.73 mg/100 g and 1.68 mg/100 g in soy sauce containing 70% and 100% onion juice, respectively. However, quercetin was not detected in the soy sauce without onion juice supplementation. Total polyphenol and flavonoid contents, as well as antioxidant activity, increased proportionally to the amount of onion juice added. Overall, it was confirmed that the addition of onion juice improved the quality and functionality of Korean soy sauce.

This study aimed to select natural materials with antibacterial activity against Streptococcus mutans (S. mutans) KCCM 40105 and determine their most efficient extraction conditions. The antibacterial activity was stable under various treatment conditions. Of the 17 material groups, extracts of Sophora flavescens (SF) and Schisandra chinensis (SC) showed antibacterial activity against the S. mutans strain. Measuring the antibacterial activity based on ethanol concentration revealed that the 30% ethanol extracts of SF and SC showed the highest antibacterial activity as observed by the inhibition zones of 10.69 and 14.49 mm, respectively. The minimum inhibitory concentrations of the 30% ethanol extracts of SF and SC against the S. mutans strain were 2.0 and 5.0 mg/mL, respectively. Heat stability was confirmed; however, the 30% ethanol extract of SC was inactive at pH values ≥6.0. The antibacterial activity of the 30% ethanol extract of SF and SC treated with nine enzymes was the same at 10 ppm and 100 ppm. However, the activity tended to decrease marginally in the 1,000 ppm concentration treatment group.

This study aimed to improve the physiological activity and processing properties of ginseng sprouts. We first determined the effect of extraction and fermentation conditions on the antioxidant activity of ginseng sprouts. The optimal extraction conditions were 2 h at 80°C, with water as a solvent. The fermentation strains used were Lactobacillus delbrueckii subsp. bulgaricus KCTC 3635 and Enterococcus faecalis KCTC 3206. We then analyzed the changes in the reducing sugar and alcohol content. In fermented samples, the reducing sugar content was lower and the alcohol content was higher than those in control sample. The cell counts of lactic acid bacteria were higher in the fermented samples than those in the control sample. Fermented samples contained more ginsenoside than the extract samples, and ginsenoside was not detected in the control sample. The total polyphenol and total flavonoid contents were relatively high in the fermented samples, particularly in the sample fermented by E. faecalis. Finally, sensory evaluation revealed that the Yakju prepared using ginseng sprouts fermented by lactic acid bacteria was preferable to other drinks control and ginseng sprouts extracted sample. Overall, it was confirme that the addition of fermented ginseng improved the physiological activity and palatability of yakju, there by improving the quality of yakju.

Soybean mosaic virus (SMV) is a member of the genus Potyvirus in the family Potyviridae. Legume crops are often infected by SMV. SMV has not been naturally isolated from sword bean (Canavalia gladiata) in South Korea. In July 2021, 30 samples of sword bean were collected at the field located in Hwasun and Muan, Jeonnam, Korea to investigate viruses infecting sword bean. The samples exhibited symptoms typical of viral infection such as mosaic pattern and, mottling of leaves. Reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) techniques were employed to identify the agent of viral infection in sword bean samples. Total RNA was extracted from the samples using the Easy-SpinTM Total RNA Extraction Kit (Intron, Seongnam, Korea). Out of the 30 samples, seven were found to be infected by the SMV. RT-PCR was performed using RT-PCR Premix (GeNet Bio, Daejeon, Korea) with SMV-specific primer set, forward primer (SM-N40, 5′-CATATCAGTTTGTTGGGCA-3′) and the reverse primer (SM-C20, 5′-TGCCTATACCCTCAACAT-3′), yielding a product of 492 bp (Lim et al., 2014). RT-LAMP was performed using RT-LAMP Premix (EIKEN Chemical, Tokyo, Japan) with SMV-specific primer set, the forward primer (SML-F3, 5′-GACGATGAACAGATGGGC-3′, SML-FIP, 5′-GCATCTGGAGATGTGCTTTTGTGGTTATGAATGGTTTCATGG-3′) and reverse primer (SML-B3, 5′-TCTCAGAGTTGGTTTTGCA-3′, SML-BIP, 5′-GCGTGTGGGTGATGATGGATTTTTTCGACAATGGGTTTCAGC-3′) for diagnosis of viral infection (Lee et al., 2015). The full coat protein genes of seven isolates were amplified using RT-PCR to determine their nucleotide sequence. The standard nucleotide BLAST (blastn suite) showed that the seven isolates had approximately 98.2–100% homology with SMV isolates (FJ640966, MT603833, MW079200, and MK561002) in NCBI GenBank. The sequences of seven isolates were deposited in the GenBank database under the accession numbers: OP046403–9. For the pathogenicity assay of the isolate, the crude saps from SMV-infected samples were mechanically inoculated into sword bean. Fourteen days after inoculation, the mosaic symptoms were observed on the upper leaves of sword bean. As a result of the RT-PCR diagnosis in the upper leaves, SMV was reconfirmed in sword bean. This is the first report of natural SMV infection in sword bean. As sword beans are increasingly consumed for teas, transmitted seeds are resulting in a decrease in pod production and quality. It is necessary to develop efficient methods of seed processing and management strategies to control SMV infection in sword bean.

In this study, the quality characteristics of kombucha according to the mixing ratio of green tea extract and yuzu juice during fermentation were compared. The pH of the kombucha decreased as the amount of yuzu juice increased. The titratable acidity increased in a juice-concentration dependent manner during fermentation. The reducing sugar content was 1.68% in kombucha made with a mixture of 70% green tea extract and 30% yuzu juice on the 20th day of fermentation, showing the lowest reducing sugar content. The alcohol content did not change until the 10th day of fermentation and increased slightly thereafter. The number of lactic acid bacteria and the quantity of yeast were the highest in the samples of kombucha made with a mixture of 70% green tea extract and 30% yuzu juice. The total polyphenol content was 40.79 mg TAE/mL in the kombucha made with this combination and this also showed the highest total flavonoid content of 37.15 mg QE/mL. In addition, the sensory evaluation results showed the highest preference in all the measured parameters for kombucha made with a mixture of 70% green tea extract and 30% yuzu juice.

CRISPR-Cas systems are adaptive immune systems in bacteria and archaea that provide resistance against phages and other mobile genetic elements. To fight against CRISPR-Cas systems, phages and archaeal viruses encode anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas systems. The expression of acr genes is controlled by anti-CRISPR-associated (Aca) proteins encoded within acr-aca operons. AcrIF24 is a recently identified Acr that inhibits the type I-F CRISPR-Cas system. Interestingly, AcrIF24 was predicted to be a dual-function Acr and Aca. Here, we elucidated the crystal structure of AcrIF24 from Pseudomonas aeruginosa and identified its operator sequence within the regulated acr-aca operon promoter. The structure of AcrIF24 has a novel domain composition, with wing, head and body domains. The body domain is responsible for recognition of promoter DNA for Aca regulatory activity. We also revealed that AcrIF24 directly bound to type I-F Cascade, specifically to Cas7 via its head domain as part of its Acr mechanism. Our results provide new molecular insights into the mechanism of a dual functional Acr-Aca protein.

In this study, natural materials with antibacterial activity against the Streptococcus mutans KCCM 40105 strain were selected, and the most efficient extraction conditions were observed. The active substance was stable under various treatment conditions. Of the 10 food materials groups, only Prunus mume fruit showed antibacterial activity against S. mutans strains. The antimicrobial activity by the various extraction solvents was 18.66 mm (clear zone diameter) in the ethanol extract and 20.18 mm in the water extract. Measurements of the antibacterial activity according to the mixing ratio of the two solvents revealed the 30% ethanol extract to have the highest activity (20.49 mm). Measurements of the minimum inhibitory concentration (MIC) showed activity at a concentration of 3.0 mg/mL. The stability to heat was observed, but the extract was not active at pH 6.0 or higher. The antimicrobial activity of the 30% ethanol extract of P. mume treated with enzymes was the same with both 10 ppm and 100 ppm of the nine enzymes. On the other hand, the activity tended to decrease slightly at 1,000 ppm. The activity of the catazyme enzyme and hydrogen peroxide treatment decreased at the treatment concentration of 100 ppm.

A simple technology to manufacture ‘Nuruk’ with pigmented rice and ‘Yakju’ with improved quality and functionality was developed. Yakju (designated WY and PY, respectively) was prepared with white rice flour Nuruk (WN) and pigmented rice flour Nuruk (PN), and their qualities were compared. The enzyme activities of Nuruk revealed that PN had higher β-amylase activity (1,186.67 Saccharogenic acitivty, SP/g) and higher protease activity (378.90 tyrosine mg/min) than WN. During 11 days of fermentation, the pH of PY was steady in the range of 4.77-4.58, whereas the pH (4.82) of WY decreased to 3.90 on day 3 of fermentation and then increased to similar pH of PY until the fermentation was completed. The titratable acidities of PY and WY increased to 0.40-0.48%. The ethanol content of PY and WY increased to 13.43% ad 13.23%, respectively, on day 5, after then PY showed higher ethanol content than WY until day 11 of fermentation. The organic acid content of PY (1,225.87 mg%) was higher than that of WY (1,021.69 mg%). The antioxidant activities of PY were twice as high as those of WY, and the total polyphenolics and total flavonoid contents of PY were also higher (35.96 mg% and 19.01 mg%, respectively) than those of WY (16.29 mg% and 6.36 mg%, respectively). Sensory scores on color, flavor and taste, and overall preference were higher in PY than in WY.

Immunity-related GTPase B10 (IRGB10) belongs to the interferon (IFN)-inducible GTPases, a family of proteins critical to host defense. It is induced by IFNs after pathogen infection, and plays a role in liberating pathogenic ligands for the activation of the inflammasome by directly disrupting the pathogen membrane. Although IRGB10 has been intensively studied owing to its functional importance in the cell-autonomous immune response, the molecular mechanism of IRGB10-mediated microbial membrane disruption is still unclear. In this study, we report the structure of mouse IRGB10. Our structural study showed that IRGB10 bound to GDP forms an inactive head-to-head dimer. Further structural analysis and comparisons indicated that IRGB10 might change its conformation to activate its membrane-binding and disruptive functions. Based on this observation, we propose a model of the working mechanism of IRGB10 during pathogen membrane disruption., Ha et al. present a crystal structure of mouse IRGB10, a mouse interferon-inducible GTPase that mediates bacteriolysis in cell autonomous immunity. With further mutagenesis studies, they show that IRGB10 bound to GDP forms an inactive head-to-head dimer, which changes its conformation to activate its membrane-binding and disruptive functions.

In this study, pigmented rice flour ‘Nuruk’ was prepared using various fungal strains to improve the quality of Korean traditional ‘Kochujang’, and the quality characteristics during the aging of ‘Kochujang’ made with the ‘Nuruk’ were confirmed. The pH of ‘Nuruk’ was highest using Aspergillus oryzae pigmented rice flour ‘Nuruk’ (N2) at 5.83, and the highest acidity was Aspergillus niger pigmented rice flour ‘Nuruk’ (N3) at 2.69. The crude ash content was 1.10-1.14% from the ‘Nuruk’ made with pigmented rice flour, which was higher than the 0.42% from ‘Nuruk’ made with white rice flour. The pH of ‘Kochujang’ decreased gradually from 0 to 90 days as aging progressed. The titratable acidity was 2.76-3.71%, which increased with increasing aging period. During the aging of ‘Kochujang’, the water content increased by 2-3%. The reducing sugar content decreased from 0.33 to 3.25% after 60 days of aging and increased to 3.85 to 4.94% at the end of aging. Regarding the color values, the ‘Kochujang’ made with white rice flour ‘Nuruk’ showed higher overall L, a, and b values than the ‘Kochujang’ made with pigmented rice flour ‘Nuruk’. A sensory evaluation of six kinds of ‘Kochujang’ revealed the ‘Kochujang’ made with N2 ‘Nuruk’ to have the highest preference in all evaluation items.

This study aimed to isolate and identify antibacterial compounds from Schisandra chinensis (S. chinensis) that are effective against the Streptococcus mutans KCCM 40105 strain. First, S. chinensis was extracted using varying concentrations of ethanol, and the resulting antibacterial activity was evaluated. The 30% ethanol extract of S. chinensis showed high activity. The fractionation and antibacterial activity of a 30% ethanol extract from S. chinensis were examined using five different solvents. Upon investigation of the antibacterial activity of the solvent fraction, the water and butanol fractions showed high activity, and no significant difference was found. Therefore, the butanol fraction was chosen for material exploration using silica gel column chromatography. A total of 24 fractions were obtained from the butanol portion using silica gel chromatography. The fraction with the highest antibacterial activity was Fr 7. From Fr 7, thirty-three sub-fractions were isolated, and sub-fraction 17 showed the highest level of antibacterial activity. A total of five peaks were obtained through the pure separation of sub-fraction 17 using HPLC. Peak 2 was identified as a substance exhibiting a high level of antibacterial activity. Based on the results of UV spectrometry, 13C-NMR, 1H-NMR, LC-MS, and HPLC analyses, the compound corresponding to peak number 2 was identified as tartaric acid.

In this study, we examined the quality of Tenebrio molitor L. that ingested yuzu supplemented feed at four feed compositions: C120 (120 g Chinese cabbage), C80+Y40 (80 g Chinese cabbage+40 g yuzu peel), C40+Y80 (40 g Chinese cabbage+80 g yuzu peel) and Y120 (120 g yuzu peel). Tenebrio molitor L. was fed for 90 d at a rate according to age, after which the moisture, crude protein, crude fat, and crude ash contents of the samples were determined to be 0.49-0.50%, 52.58-53.90%, 30.76-32.34%, and 3.32-3.45%, respectively. Color values, namely yellowness (b) and redness (a), were observed to decrease with increasing yuzu ingestion, and the C80+Y40 sample exhibited the highest lightness (L=36.28). The K and Mg contents were observed to increase with increasing yuzu content, and Pb and As were not detected in any Tenebrio molitor L. sample that ingested the yuzu supplemented feed. The free amino acid (serine and alanine) contents also increased with increasing yuzu content, while the histidine and arginine contents were observed to decrease with increasing yuzu ingestion. Naringin and hesperidin were detected at 1.77 mg% and 1.63 mg% in sample Y120, respectively, while trace amounts were detected in samples C80+Y40 and C40+Y80, but none were detected in the control. The total polyphenol and flavonoid contents increased with increasing level of yuzu ingestion, and were highest in sample Y120 (123.11 mg% and 5.69 mg%, respectively).

An easy and simple method of producing Nuruk using rice was developed. In addition, the quality characteristics of the prepared Nuruk were evaluated for Makgeolli production. A comparison of the enzyme activities between A. kawachii rice Koji (RK) and non-steamed rice flour Nuruk according to the fungal strain revealed the β-amylase activity of A. oryzae rice flour Nuruk (AON) to be the highest at 3697.85 SP/g. The α-amylase activity and protease activity were highest at 111.67 A.U and 33.23 tyrosine mg/min of P. candidum rice flour Nuruk (PCN), respectively. The ethanol contents of the four samples were similar at 16.1-16.4%. The sensory evaluation result showed that Makgeolli made with PCN had the highest preference score of 5.78 and showed a significant difference in overall preference. Moreover, Makgeolli made with PCN showed a higher preference than of Makgeolli made with RK. The titratable acidity and reducing sugar content of Makgeolli made with PCN were 0.48% and 4.14%, respectively, which were higher than those of Makgeolli made with RK. The ethanol content of Makgeolli made with PCN was 15.10%, which showed a 12.80% higher ethanol production yield than that of Makgeolli made with RK. Therefore the PCN produced in this study will be effective for Makgeolli production.

In this study, milk samples were fermented following the addition of Ligularia fischeri extracts. The aqueous extracts were obtained from L. fischer grown in the open field (OL) or in a greenhouse (GL). The quality related properties, and antioxidant activity of the fermented milk were evaluated, and the effects of storage on the fermented samples were assessed. The time required for the fermented milk to reach pH 4.6 was approximately four hours in all samples. The titratable acidity of the samples was in the range of 0.5-1%. The number of lactic acid bacteria in the fermented milks made with L. fischeri GL extract was slightly higher than it was in milks samples fermented with L. fischeri OL extract. The Hunter Lab color (L) and redness (a) values of the samples were lower after fermentation, but their yellowness (b) increased with increasing amounts of L. fischeri extracts. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity in milk fermented with 0.5%, 1%, 3%, and 8% L. fischeri OL extracts was higher than that in milk fermented with corresponding amounts of L. fischeri GL extract. However, the difference was not significant. DPPH activity in milk fermented with 5% L. fischeri GL extract was higher than it was in milk fermented with 5% L. fischeri OL extract. The pattern of 2,2’-azinobis-(3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS˙+) scavenging activity in the samples was similar to that observed during the DPPH assay. The pH and, titratable acidity, of the fermented samples were not significantly affected by storage, and the number of lactic acid bacteria in the stored and freshly fermented samples was similar.

This study was conducted to enhance the utilization of Ligularia fischeri as a food ingredient. The effects of the location of cultivation and the harvest time on the components were examined. The crude fats and proteins in greenhouse samples (GL) were 2% higher than those in open field samples (OL). The fat content was found to increase from 4.31% to 5.27% as the harvest time was delayed. The Na contents were more than two times higher in GL than in OL. Moreover, the amount of free sugars in leaves differed slightly according to the harvest time but decreased overall as the harvest time was delayed. The total polyphenols increased from 202.53 to 389.16 mg% in OL and 293.57 to 439.40 mg% in GL as the harvest time was delayed. The levels of total flavonoids in OL and GL ranged from 105.58 to 202.79 mg% and 135.84 to 216.96 mg%, respectively. These increased from 0.3 to 2 times upon delaying the harvest time. The samples were also analyzed for the presence of five catechin compounds, namely, (-)-epigallocatechin (EGC), (+)-catechin (CE), (-)-epigallocatechin gallate (EGCG), (-)-epicatechin gallate (ECG), and (-)-gallocatechin gallate (GCG). EGC and CE were detected in both OL and GL, while EGCG, ECG, and GCG were detected only in OL at low concentrations. The 4-Ο-caffeoylquinic acid content in GL was higher than that in OL, except in the early stages of harvesting.

Vaccines and therapeutics are urgently needed for the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we screen human monoclonal antibodies (mAb) targeting the receptor binding domain (RBD) of the viral spike protein via antibody library constructed from peripheral blood mononuclear cells of a convalescent patient. The CT-P59 mAb potently neutralizes SARS-CoV-2 isolates including the D614G variant without antibody-dependent enhancement effect. Complex crystal structure of CT-P59 Fab/RBD shows that CT-P59 blocks interaction regions of RBD for angiotensin converting enzyme 2 (ACE2) receptor with an orientation that is notably different from previously reported RBD-targeting mAbs. Furthermore, therapeutic effects of CT-P59 are evaluated in three animal models (ferret, hamster, and rhesus monkey), demonstrating a substantial reduction in viral titer along with alleviation of clinical symptoms. Therefore, CT-P59 may be a promising therapeutic candidate for COVID-19., Therapies and vaccines for COVID-19, caused by the SARS-CoV-2 viral pandemic, are urgently needed. Here the authors establish and screen an antibody library from a convalescent COVID-19 patient to isolate a neutralizing antibody with the ability to reduce viral titer and alleviate symptoms in ferret, hamster, and rhesus monkey infection models.

Significance Cell death-inducing DFF45-like effector (CIDE) domains, initially identified in apoptotic nucleases, form a highly conserved family with diverse functions ranging from cell death to lipid homeostasis and synaptic regulation. Through structural determination of two CIDE family proteins, Drep2 and Drep4, we found that CIDE domains can form helical oligomers. Our results reveal that such higher-order structures not only are conserved in the CIDE family, but also are critically important for both DNA fragmentation and lipid droplet fusion. Therefore, our findings identify the CIDE domain as a scaffolding component for higher-order structure assembly. Our results expand the importance of higher-order structures from the established field of immune signaling to broader biological functions.

This study was carried out to investigate the quality characteristics of fermented milk containing Rhus verniciflua seed (RVS) extracts (0.0%, 0.1%, 0.3% and 0.5%) and antioxidant activity of RVS extracts. The proximate composition of RVS was moisture (4.76%), crude ash (1.40%), crude fat (5.33%) and crude protein (11.10%). A total polyphenol content of 70% ethanol extract of RVS (554±2.64 mg/g) was higher than that of RVS water extract (145±3.47 mg/g). 70% ethanol extract (1103±6.42 mg/g) of RVS showed higher content in the total flavonoids (37±2.30 mg/g) and activities on DPPH free radical scavenging (73.23%) and ABTS free radical scavenging (83.47%) when compared with water extracted of RVS. The quality characteristics, such as pH, titratable acidity, and the number of lactic acid producing bacteria were not remarkably different between the fermented milk samples subjected to treatments with and without the addition of RVS extracts.

Caspase recruitment domain (CARD)-only proteins (COPs), regulate apoptosis, inflammation, and innate immunity. They inhibit the assembly of NOD-like receptor complexes such as the inflammasome and NODosome, which are molecular complexes critical for caspase-1 activation. COPs are known to interact with either caspase-1 CARD or RIP2 CARD via a CARD-CARD interaction, and inhibit caspase-1 activation or further downstream signaling. In addition to the human COPs, Pseudo-ICE, INCA, and ICEBERG, several viruses also contain viral COPs that help them escape the host immune system. To elucidate the molecular mechanism of host immunity inhibition by viral COPs, we solved the structure of a viral COP for the first time. Our structure showed that viral COP forms a structural transformation-mediated dimer, which is unique and has not been reported in any structural study of a CARD domain. Based on the current structure, and the previously solved structures of other death domain superfamily members, we propose that structural transformation-mediated dimerization might be a new strategy for dimer assembly in the death domain superfamily.

β-Lactam antibiotics that inhibit penicillin-binding proteins (PBPs) have been widely used in the treatment of bacterial infections. However, the molecular basis underlying the different inhibitory potencies of β-lactams against specific PBPs is not fully understood. Here, we present the crystal structures of penicillin-binding protein D2 (PBPD2) from Listeria monocytogenes, a Gram-positive foodborne bacterial pathogen that causes listeriosis in humans. The acylated structures in complex with four antibiotics (penicillin G, ampicillin, cefotaxime, and cefuroxime) revealed that the β-lactam core structures were recognized by a common set of residues; however, the R1 side chains of each antibiotic participate in different interactions with PBPD2. In addition, the structural complementarities between the side chains of β-lactams and the enzyme were found to be highly correlated with the relative reactivities of penam or cephem antibiotics against PBPD2. Our study provides the structural basis for the inhibition of PBPD2 by clinically important β-lactam antibiotics that are commonly used in listeriosis treatment. Our findings imply that the modification of β-lactam side chains based on structural complementarity could be useful for the development of potent inhibitors against β-lactam-resistant PBPs.

This study was performed to improve the availability of reed and quality of traditional Yakju by using roasted reed. The pH of sprout Yakju was 3.43, whereas the pHs of other Yakjus were 3.57. No remarkable differences were observed in contents of total titratable acids and reducing sugars. Color changes were measured by Hunter’s color value; L value decreased, whereas redness (+a) and yellowness (+b) increased during fermentation. Ethanol content of Yakjus prepared with sprout and root were 15.30% and 15.28%, respectively, which were lower than that of control Yakju (15.31%). However, there were obvious differences of ethanol contents in three types of Yakjus. The major free sugar and organic acid were glucose and lactic acid, respectively. The total polyphenol contents of sprout Yakju (4.26 mg%) and root Yakju (4.21 mg%) were much higher than that of control Yakju (2.56 mg%). The DPPH (1,1-diphenyl-2-picryl- hydrazyl) free radical scavenging activities of sprout Yakju and root Yakju were higher than those of control Yakju. Yakju prepared from 0.3% addition of sprout showed the highest score in overall preference from the sensory test.

Tumor necrosis factor receptor-associated factor 1 (TRAF1) is a multifunctional adaptor protein involved in important processes of cellular signaling, including innate immunity and apoptosis. TRAF family member-associated NF-kappaB activator (TANK) has been identified as a competitive intracellular inhibitor of TRAF2 function. Although TRAF recognition by various receptors has been studied extensively in the field of TRAF-mediated biology, molecular and functional details of TANK recognition and interaction with TRAF1 have not been studied. In this study, we report the crystal structure of the TRAF1/TANK peptide complex. Quantitative interaction experiments showed that TANK peptide interacts with both TRAF1 and TRAF2 with similar affinity in a micromolar range. Our structural study also reveals that TANK binds TRAF1 using a minor minimal consensus motif for TRAF binding, Px(Q/E)xT. Database Coordinate and structural factor were deposited in the Protein Data Bank under PDB ID code 5H10.

The synaptonemal complex protein 1 (SYCP1) is the main structural element of transverse filaments (TFs) of the synaptonemal complex (SC), which is a meiosis-specific complex structure formed at the synapse of homologue chromosomes to hold them together. The N-terminal domain of SYCP1 is known to be located within the central elements (CEs), whereas the C-terminal domain is located toward lateral elements (LEs). SYCP1 is a well-known meiosis marker that is also known to be a prognostic marker in the early stage of several cancers including breast, gliomas, and ovarian cancers. The structure of SC, especially the TF structure formed mainly by SYCP1, remains unclear without any structural information. To elucidate a molecular basis of SC formation and function, we first solved the crystal structure of C-terminal coiled-coil domain of SYCP1. The coiled-coil domain of SYCP1 forms asymmetric, anti-parallel dimers in solution.

Ketosteroid isomerase (3-oxosteroid Δ(5)-Δ(4)-isomerase, KSI) from Pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of Δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. The active site of KSI is formed by several hydrophobic residues and three catalytic residues (Tyr14, Asp38, and Asp99). In this study, we investigated the role of a hydrophobic Met112 residue near the active site in the catalysis, steroid binding, and stability of KSI. Replacing Met112 with alanine (yields M112A) or leucine (M112L) decreased the kcat by 20- and 4-fold, respectively. Compared with the wild type (WT), M112A and M112L KSIs showed increased KD values for equilenin, an intermediate analogue; these changes suggest that loss of packing at position 112 might lead to unfavorable steroid binding, thereby resulting in decreased catalytic activity. Furthermore, M112A and M112L mutations reduced melting temperature (Tm) by 6.4°C and 2.5°C, respectively. These changes suggest that favorable packing in the core is important for the maintenance of stability in KSI. The M112K mutation decreased kcat by 2000-fold, compared with the WT. In M112K KSI structure, a new salt bridge was formed between Asp38 and Lys112. This bridge could change the electrostatic potential of Asp38, and thereby contribute to the decreased catalytic activity. The M112K mutation also decreased the stability by reducing Tm by 4.1°C. Our data suggest that the Met112 residue may contribute to the catalytic activity and stability of KSI by providing favorable hydrophobic environments and compact packing in the catalytic core.

TNF-receptor associated factor (TRAF) proteins are key adaptor molecules containing E3 ubiquitin ligase activity that play a critical role in immune cell signaling. TRAF1 is a unique family of TRAF lacking the N-terminal RING finger domain. TRAF1 is an important scaffold protein that participates in TNFR2 signaling in T cells as a negative or positive regulator via direct interaction with TRAF2, which has recently been identified as a pro-apoptotic regulator in neuronal cell death. Here, we report the first crystal structure of the TRAF1 TRAF domain containing both the TRAF-N coiled-coil domain and the TRAF-C domain. Our structure reveals both similarities and differences with other TRAF family members, which may be functionally relevant to TRAFs. We also found that the TRAF-N coiled-coil domain of TRAF1 is critical for the trimer formation and stability of the protein. Finally, we found that conserved surface residues on the TRAF1 TRAF domain that might be binding hot spots that are critical for interaction with signaling molecules.

Apoptosis repressor with caspase recruiting domain (ARC) is a multifunctional inhibitor of apoptosis that is unusually over-expressed or activated in various cancers and in the state of the pulmonary hypertension. Therefore, ARC might be an optimal target for therapeutic intervention. Human ARC is composed of two distinct domains, N-terminal caspase recruiting domain (CARD) and C-terminal P/E (proline and glutamic acid) rich domain. ARC inhibits the extrinsic apoptosis pathway by interfering with DISC formation. ARC CARD directly interacts with the death domains (DDs) of Fas and FADD, as well as with the death effector domains (DEDs) of procaspase-8. Here, we report the first crystal structure of the CARD domain of ARC at a resolution of 2.4 Å. Our structure was a dimer with novel homo-dimerization interfaces that might be critical to its inhibitory function. Interestingly, ARC did not exhibit a typical death domain fold. The sixth helix (H6), which was detected at the typical death domain fold, was not detected in the structure of ARC, indicating that H6 may be dispensable for the function of the death domain superfamily.