scholarly journals Possible Prophylactic and Therapeutic Foods for Prevention and Management of COVID-19- An Updated Review

2020 ◽  
Vol 8 (3) ◽  
pp. 682-689
Author(s):  
Sumia Mohammad Enani
Keyword(s):  
Immune Response ◽  
Severe Acute Respiratory Syndrome ◽  
Effective Treatment ◽  
Three Dimensional ◽  
Short Review ◽  
Dimensional Structure ◽  
Antiviral Action ◽  
High Similarity ◽  
Health Complications ◽  
Therapeutic Food

Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has resulted in an outbreak that is spreading globally. In the absence of a vaccine or effective treatment, improving the body's immune response to combat the virus, or, at least alleviate its health complications, becomes imperative. Potential prophylactic and therapeutic food interventions using black seed, garlic, honey, wasabi and high vit C foods have been proposed in various studies on previous coronaviruses, SARS-CoV and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Due to the high similarity in the three dimensional structure between SARS-CoV-2 and SARS-CoV, studies that reported antiviral action of certain foods against various viruses including SARS-CoV and MERS-CoV have been discussed in this short review.

scholarly journals In Silico Characterization of Surface Glycoprotein [QHD43416] of Severe Acute Respiratory Syndrome-Coronavirus 2

2020 ◽  
Vol 3 (2) ◽  
pp. 32-36
Author(s):  
Rajneesh Prajapat ◽  
◽  
Suman Jain ◽  
Manish K Vaishnav ◽  
Sonal Sogani ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Three Dimensional ◽  
Surface Glycoprotein ◽  
Dimensional Structure ◽  
Model Quality ◽  
Core Section ◽  
Novel Coronavirus ◽  
And Function ◽  
Tools And Techniques

The novel coronavirus (SARS-CoV-2) reported from Wuhan, China, that spread rapidly and cause severe acute respiratory syndrome. The disease associated with infection of SARS-CoV-2 that is referred as COVID-19 (Coronavirus Disease 2019). In the present study, the surface glycoprotein [QHD43416] of SARS-CoV-2 was characterized for structure analysis and validation to provide information about its three-dimensional structure by using in silico tools and techniques. The surface glycoprotein [QHD43416] sequence of SARS-CoV-2 was retrieved from NCBI and its PDB file was designed by using phyre2 server. The RAMPAGE and UCLA-DOE (Verify 3D) was used for analysis and validation of structure model of protein. The model quality estimation based on the ProSA. Alignment of surface glycoprotein [QHD43416], revealed homology (72% identity) with spike protein of bat coronavirus [BM48-31/BGR/2008]. The model corresponding to probability conformation with 90.5% residue of core section, 9.1 % of allowed section and 0.4 % residue of outer section in φ-ψ plot, that specifies accuracy of prediction model. The Verify 3D results shows that 59.53% residues have average 3D-1D score >= 0.2 this determines compatibility of 3D model with its amino acid sequence (1D). ProSA Z-score -11.19 represents the good quality of the model. The structure and function of coronavirus surface glycoprotein could be predicted by in silico modeling studies. The protein model will be further used for designing of vaccine / drug development against coronavirus infection.

scholarly journals The innate immune response in fetal lung mesenchymal cells targets VEGFR2 expression and activity

2017 ◽  
Vol 312 (6) ◽  
pp. L861-L872 ◽  
Author(s):  
Rachel M. Medal ◽  
Amanda M. Im ◽  
Yasutoshi Yamamoto ◽  
Omar Lakhdari ◽  
Timothy S. Blackwell ◽  
...  
Keyword(s):  
Immune Response ◽  
Innate Immune Response ◽  
Three Dimensional ◽  
Transcriptional Response ◽  
Fetal Lung ◽  
Mesenchymal Cells ◽  
Innate Immune ◽  
Dimensional Structure ◽  
Mouse Lung ◽  
Vegf Receptor

In preterm infants, soluble inflammatory mediators target lung mesenchymal cells, disrupting airway and alveolar morphogenesis. However, how mesenchymal cells respond directly to microbial stimuli remains poorly characterized. Our objective was to measure the genome-wide innate immune response in fetal lung mesenchymal cells exposed to the bacterial endotoxin lipopolysaccharide (LPS). With the use of Affymetrix MoGene 1.0st arrays, we showed that LPS induced expression of unique innate immune transcripts heavily weighted toward CC and CXC family chemokines. The transcriptional response was different between cells from E11, E15, and E18 mouse lungs. In all cells tested, LPS inhibited expression of a small core group of genes including the VEGF receptor Vegfr2. Although best characterized in vascular endothelial populations, we demonstrated here that fetal mouse lung mesenchymal cells express Vegfr2 and respond to VEGF-A stimulation. In mesenchymal cells, VEGF-A increased cell migration, activated the ERK/AKT pathway, and promoted FOXO3A nuclear exclusion. With the use of an experimental coculture model of epithelial-mesenchymal interactions, we also showed that VEGFR2 inhibition prevented formation of three-dimensional structures. Both LPS and tyrosine kinase inhibition reduced three-dimensional structure formation. Our data suggest a novel mechanism for inflammation-mediated defects in lung development involving reduced VEGF signaling in lung mesenchyme.

scholarly journals Nuclear Magnetic Resonance Structure Shows that the Severe Acute Respiratory Syndrome Coronavirus-Unique Domain Contains a Macrodomain Fold

2008 ◽  
Vol 83 (4) ◽  
pp. 1823-1836 ◽  
Author(s):  
Amarnath Chatterjee ◽  
Margaret A. Johnson ◽  
Pedro Serrano ◽  
Bill Pedrini ◽  
Jeremiah S. Joseph ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Severe Acute Respiratory Syndrome ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Resonance Structure ◽  
Nuclear Magnetic Resonance Structure ◽  
Three Dimensional Structure ◽  
Unique Domain ◽  
Nuclear Magnetic

ABSTRACT The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for “middle of the SARS-unique domain”) in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

scholarly journals Three-dimensional structure of fimbriae determines specificity of immune response.

1985 ◽  
Vol 50 (2) ◽  
pp. 517-522 ◽  
Author(s):  
H Karch ◽  
H Leying ◽  
P Goroncy-Bermes ◽  
H P Kroll ◽  
W Opferkuch
Keyword(s):  
Immune Response ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure

scholarly journals Biosynthesis of the Tricyclic Aromatic Type II Polyketide Rishirilide: New Potential Third Ring Oxygenation after Three Cyclization Steps

2021 ◽  
Author(s):  
Ahmad Alali ◽  
Lin Zhang ◽  
Jianyu Li ◽  
Chijian Zuo ◽  
Dimah Wassouf ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Three Dimensional ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Flavin Reductase ◽  
High Similarity ◽  
Dynamic Simulations ◽  
High Sequence Similarity ◽  
The Past ◽  
Biosynthetic Studies

AbstractRishirilides are a group of PKS II secondary metabolites produced by Streptomyces bottropensis Gö C4/4. Biosynthetic studies in the past have elucidated early and late steps of rishirilide biosynthesis. This work is aiming to solve the remaining steps in the rishirilide biosynthesis. Inactivation of the cyclase gene rslC3 in Streptomyces bottropensis resulted in an interruption of rishirilide production. Instead, accumulation of the tricyclic aromatic galvaquinones was observed. Similar results were observed after deletion of rslO4. Closer inspection into RslO4 crystal structure in addition to site-directed mutagenesis and molecular dynamic simulations revealed that RslO4 might be responsible for quinone formation on the third ring. The RslO1 three-dimensional structure shows a high similarity to FMN-dependent luciferase-like monooxygenases such as the epoxy-forming MsnO8 which acts with the flavin reductase MsnO3 in mensacarcin biosynthesis in the same strain. The high sequence similarity between RslO2 and MsnO3 suggests that RslO2 provides RslO1 with reduced FMN to form an epoxide that serves as substrate for RslO5.

scholarly journals ConA-Like Lectins: High Similarity Proteins as Models to Study Structure/Biological Activities Relationships

2018 ◽  
Vol 20 (1) ◽  
pp. 30 ◽  
Author(s):  
Benildo Cavada ◽  
Vanir Pinto-Junior ◽  
Vinicius Osterne ◽  
Kyria Nascimento
Keyword(s):  
Biological Activity ◽  
Structural Properties ◽  
Concanavalin A ◽  
Biological Activities ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Carbohydrate Specificity ◽  
High Similarity ◽  
Antitumor Activities ◽  
Reversible Binding

Lectins are a widely studied group of proteins capable of specific and reversible binding to carbohydrates. Undoubtedly, the best characterized are those extracted from plants of the Leguminosae family. Inside this group of proteins, those from the Diocleinae subtribe have attracted attention, in particular Concanavalin A (ConA), the best-studied lectin of the group. Diocleinae lectins, also called ConA-like lectins, present a high similarity of sequence and three-dimensional structure and are known to present inflammatory, vasoactive, antibiotic, immunomodulatory and antitumor activities, among others. This high similarity of lectins inside the ConA-like group makes it possible to use them to study structure/biological activity relationships by the variability of both carbohydrate specificity and biological activities results. It is in this context the following review aims to summarize the most recent data on the biochemical and structural properties, as well as biological activities, of ConA-like lectins and the use of these lectins as models to study structure/biological activity relationships.

scholarly journals Structural Genomics of the Severe Acute Respiratory Syndrome Coronavirus: Nuclear Magnetic Resonance Structure of the Protein nsP7

2005 ◽  
Vol 79 (20) ◽  
pp. 12905-12913 ◽  
Author(s):  
Wolfgang Peti ◽  
Margaret A. Johnson ◽  
Torsten Herrmann ◽  
Benjamin W. Neuman ◽  
Michael J. Buchmeier ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Terminal Segment ◽  
Dimensional Structure ◽  
Resonance Structure ◽  
Nuclear Magnetic Resonance Structure ◽  
Protein Protein Interactions ◽  
Surface Charge Distribution ◽  
Α Helix

ABSTRACT Here, we report the three-dimensional structure of severe acute respiratory syndrome coronavirus (SARS-CoV) nsP7, a component of the SARS-CoV replicase polyprotein. The coronavirus replicase carries out regulatory tasks involved in the maintenance, transcription, and replication of the coronavirus genome. nsP7 was found to assume a compact architecture in solution, which is comprised primarily of helical secondary structures. Three helices (α2 to α4) form a flat up-down-up antiparallel α-helix sheet. The N-terminal segment of residues 1 to 22, containing two turns of α-helix and one turn of 310-helix, is packed across the surface of α2 and α3 in the helix sheet, with the α-helical region oriented at a 60° angle relative to α2 and α3. The surface charge distribution is pronouncedly asymmetrical, with the flat surface of the helical sheet showing a large negatively charged region adjacent to a large hydrophobic patch and the opposite side containing a positively charged groove that extends along the helix α1. Each of these three areas is thus implicated as a potential site for protein-protein interactions.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Three-Dimensional Reconstruction Using Stereo Pairs from Serial Thick Sections

1977 ◽  
Vol 35 ◽  
pp. 562-563
Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Thin Sections ◽  
3 Dimensional ◽  
Transmission Electron ◽  
Freeze Dried ◽  
Dimensional Reconstruction ◽  
Stereo Imagery ◽  
Whole Mounts

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.

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