scholarly journals Predictive structure and protein-ligand interface of novel lectin from rice bean (Vigna umbellata)

2021 ◽  
Author(s):  
Ankur Tripathi ◽  
Vipin Hallan ◽  
Ritu Raj ◽  
Rajan Katoch
Keyword(s):  
Sequence Similarity ◽  
3D Structure ◽  
Md Simulations ◽  
The Novel ◽  
Quality Model ◽  
Rice Bean ◽  
Vigna Umbellata ◽  
Defense Protein ◽  
Hydrophobic Nature ◽  
Legume Lectins

Abstract Lectins are an important group of multivalent glycoproteins having the property of selectively recognizing and precipitating glycoconjugates. Although lectins have been reported from diverse biological sources, legume lectins is the best-characterized family of plant lectins. We have successfully cloned and sequenced the RbL ORF of 843bp from immature rice bean seeds (Vigna umbellata). We report the results of in silico analysis of novel lectin precursor of 280 amino acids from rice bean. BlastP analysis revealed more than 90% sequence similarity of RbL protein with Vigna angularis lectin and Vigna aconitifolia lectin. ProtParam analysis revealed acidic, stable and hydrophobic nature of RbL protein. Template based 3D structure of RbL protein was modeled using I-TASSER tool and validated as good quality model. Structural analysis revealed the presence of β-sandwich (Jelly roll fold or lectin fold) in modeled RbL structure. RbL protein was functionally annotated as a plant defense protein. Molecular docking was performed to analyze interactions of RbL protein with predicted ligands (N-acetyl-D-glucosamine β-galactose, Lactose and Adenine) and two selected ligands (Glucose and Mannose). Molecular dynamics (MD) simulations of RbL-ligand complexes confirmed robust hydrogen bonding interactions between ligands and RbL protein. The novel information generated in the study would be useful in exploring RbL protein for different biomedical and biotechnological applications.

scholarly journals Characterization of the SARS-CoV-2 coronavirus X4-like accessory protein

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Olanrewaju Ayodeji Durojaye ◽  
Nkwachukwu Oziamara Okoro ◽  
Arome Solomon Odiba
Keyword(s):  
Rapid Development ◽  
Protein A ◽  
The Novel ◽  
Quality Model ◽  
A Value ◽  
Model Protein ◽  
Novel Coronavirus ◽  
Global Threat

Abstract Background The novel coronavirus SARS-CoV-2 is currently a global threat to health and economies. Therapeutics and vaccines are in rapid development; however, none of these therapeutics are considered as absolute cure, and the potential to mutate makes it necessary to find therapeutics that target a highly conserved regions of the viral structure. Results In this study, we characterized an essential but poorly understood coronavirus accessory X4 protein, a core and stable component of the SARS-CoV family. Sequence analysis shows a conserved ~ 90% identity between the SARS-CoV-2 and previously characterized X4 protein in the database. QMEAN Z score of the model protein shows a value of around 0.5, within the acceptable range 0–1. A MolProbity score of 2.96 was obtained for the model protein and indicates a good quality model. The model has Ramachandran values of φ = − 57o and ψ = − 47o for α-helices and values of φ = − 130o and ψ = + 140o for twisted sheets. Conclusions The protein data obtained from this study provides robust information for further in vitro and in vivo experiment, targeted at devising therapeutics against the virus. Phylogenetic analysis further supports previous evidence that the SARS-CoV-2 is positioned with the SL-CoVZC45, BtRs-BetaCoV/YN2018B and the RS4231 Bat SARS-like corona viruses.

scholarly journals Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan

2010 ◽  
Vol 60 (3) ◽  
pp. 603-609 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova
Keyword(s):  
Sea Of Japan ◽  
Sequence Similarity ◽  
Fatty Acid Analysis ◽  
Phenotypic Characterization ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
The Novel ◽  
Bacterial Strains ◽  
Separate Branch

Two bacterial strains, KMM 3891T and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink–reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C17 : 1 ω6c, C17 : 0, C16 : 0 and C16 : 1 ω7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891T was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891T and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891T and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891T (=NRIC 0753T =JCM 15738T).

scholarly journals Rubritalea halochordaticola sp. nov., a carotenoid-producing verrucomicrobial species isolated from a marine chordate

2011 ◽  
Vol 61 (7) ◽  
pp. 1515-1520 ◽  
Author(s):  
Jaewoo Yoon ◽  
Satoru Matsuda ◽  
Kyoko Adachi ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Sea Squirt ◽  
Cell Biomass ◽  
Taxonomic Approach

A Gram-negative-staining, obligately aerobic, non-motile, rod-shaped and chemoheterotrophic bacterium, designated strain MN1-1006T, was isolated from an ascidian (sea squirt) sample, and was studied using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the new isolate shared approximately 93–99% sequence similarity with recognized species of the genus Rubritalea within the phylum ‘Verrucomicrobia’. DNA–DNA hybridization values between strain MN1-1006T and Rubritalea squalenifaciens HOact23T and Rubritalea sabuli YM29-052T were 57% and 14.5%, respectively. Strain MN1-1006T produced carotenoid compounds that rendered the cell biomass a reddish pink colour. The strain also contained squalene. The cell-wall peptidoglycan of the novel strain contained muramic acid and meso-diaminopimelic acid. The DNA G+C content of strain MN1-1006T was 51.4 mol%. The major cellular fatty acids were iso-C14:0, iso-C16:0 and anteiso-C15:0. The major isoprenoid quinone was MK-9. On the basis of these data, it was concluded that strain MN1-1006T represents a novel species of the genus Rubritalea, for which the name Rubritalea halochordaticola sp. nov. is proposed. The type strain is MN1-1006T ( = KCTC 23186T = NBRC 107102T).

scholarly journals Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

2006 ◽  
Vol 56 (7) ◽  
pp. 1531-1534 ◽  
Author(s):  
Reiji Tanaka ◽  
Satoshi Kawaichi ◽  
Hiroshi Nishimura ◽  
Yoshihiko Sako
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Optimum Ph ◽  
Kagoshima Prefecture ◽  
Bacterium Strain

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52–78 °C (optimum, 70 °C), pH 5–8 (optimum, pH 7) and 0–4.5 % NaCl (optimum, 1.0 %). The novel isolate was a strictly aerobic heterotroph that utilized complex proteinaceous substrates as well as a variety of carboxylic acids and amino acids. The G+C content of the genomic DNA was 70.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain KW1T is closely related to Thermaerobacter subterraneus C21T (98.4 % sequence similarity). However, the DNA–DNA hybridization value for strain KW1T and T. subterraneus ATCC BAA-137T was below 46 %. On the basis of the molecular and physiological traits of strain KW1T, it represents a novel species of the genus Thermaerobacter, for which the name Thermaerobacter litoralis sp. nov. is proposed. The type strain is KW1T (=JCM 13210T=DSM 17372T).

scholarly journals Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shallow Marine Hydrothermal System ◽  
Type Strains

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

scholarly journals Salinicoccus luteus sp. nov., isolated from a desert soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1901-1905 ◽  
Author(s):  
Yu-Qin Zhang ◽  
Li-Yan Yu ◽  
Hong-Yu Liu ◽  
Yue-Qin Zhang ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Desert Soil ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Moderately Halophilic Bacterium

A moderately halophilic bacterium, strain YIM 70202T, was isolated from a desert soil sample collected from Egypt and was subjected to a taxonomic investigation. In a phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70202T was affiliated to the Salinicoccus clade, showing 94.5–96.8 % 16S rRNA gene sequence similarity to the recognized species of the genus Salinicoccus, in which Salinicoccus roseus CCM 3516T was the nearest neighbour. The DNA–DNA relatedness value of the novel isolate with S. roseus CCM 3516T was 12.7 %. The novel isolate grew at temperatures between 4 and 45 °C and at pH values ranging from 7.0 to 11.0, with an optimum of 30 °C and pH 8.0–9.0, respectively. Strain YIM 70202T grew optimally in the presence of 10 % NaCl (w/v) and growth was observed at NaCl concentrations in the range 1–25 % (w/v). Chemotaxonomic data revealed that strain YIM 70202T contained MK-6 as the predominant respiratory quinone, possessed l-Lys–Gly5 as the cell-wall peptidoglycan, had phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid as the polar lipids and contained i-C15 : 0 and ai-C15 : 0 as the predominant fatty acids. The DNA G+C content was 49.7 mol%. The biochemical and chemotaxonomic properties demonstrate that strain YIM 70202T represents a novel species of the genus Salinicoccus. The name Salinicoccus luteus sp. nov. is proposed with strain YIM 70202T (=CGMCC 1.6511T=KCTC 3941T) as the type strain.

scholarly journals Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

2019 ◽  
Vol 476 (5) ◽  
pp. 809-826
Author(s):  
Karthik V. Rajasekar ◽  
Shuangxi Ji ◽  
Rachel J. Coulthard ◽  
Jon P. Ride ◽  
Gillian L. Reynolds ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Analytical Ultracentrifugation ◽  
De Novo ◽  
Learning Algorithm ◽  
Sequence Similarity ◽  
Homology Modelling ◽  
3D Structure ◽  
Large Family ◽  
Secreted Proteins ◽  
Self Incompatibility

Abstract SPH (self-incompatibility protein homologue) proteins are a large family of small, disulfide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy (Papaver rhoeas), but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of Escherichia coli, we expressed one member of this family, SPH15 from Arabidopsis thaliana, as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a β-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins: human transthyretin, bacterial TssJ and pneumolysin, with no discernible sequence similarity. The NMR-derived structure was compared with a de novo model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred de novo method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from P. rhoeas, which have only 15–18% sequence homology to SPH15. The DeepCDPred method gave models with lower discreet optimised protein energy scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes.

Morpho-physiological and nutritional characterization of rice bean (Vigna umbellata)

2011 ◽  
Vol 59 (2) ◽  
pp. 125-136 ◽  
Author(s):  
R. Katoch
Keyword(s):  
Crude Protein ◽  
Nutritive Value ◽  
Total Phenolics ◽  
Crude Fibre ◽  
Nutritional Factors ◽  
Rice Bean ◽  
Vigna Umbellata ◽  
Superior Genotypes ◽  
Limiting Amino Acids

Rice bean, a lesser known pulse, has excellent nutritive value. The seed yield of the crop is higher as compared to other pulses of the Vigna family. In the present study thirty diverse rice bean genotypes were evaluated for nutritional and morpho-physiological characteristics for selecting overall superior genotypes. Variations were observed for crude protein (16.1–19.12%), carbohydrates (59.28–76.89%), ascorbic acid (0.19–0.80 mg/100 g), crude fibre (4.23-6.0%), limiting amino acids, namely tryptophan (0.85–2.42 g/16 g N) and methionine (0.52–0.67 g/16 g N), and ether extract (0.57–2.13%). Anti-nutritional factors, such as total phenolics, total tannins, condensed tannins, hydrolysable tannins and α-amylase inhibitor, also varied to a considerable extent. The cumulative grading of the genotypes based upon nutritional and morpho-physiological attributes revealed that the genotypes JCR-76, IC-137200, IC-140796 and IC-137189 were nutritionally superior genotypes for consumption.

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