scholarly journals Applying In Silico Approaches for Designing a Chimeric InaV/N-DFPase Protein and Evaluating its Binding with Diisopropyl-Fluorophosphate

2019 ◽  
Vol 75 ◽  
pp. 41-51
Author(s):  
Hossein Allahyari ◽  
Ali Karami ◽  
Hamid Tebyanian ◽  
Hamid Reza Nouri ◽  
Samaneh Khodi ◽  
...  
Keyword(s):  
Cell Surface ◽  
Pseudomonas Syringae ◽  
In Silico ◽  
Chimeric Protein ◽  
Minimum Free Energy ◽  
Amino Acid Residues ◽  
Ice Nucleation Protein ◽  
Tertiary Structures ◽  
Rna Molecules ◽  
Diisopropyl Fluorophosphate

The N-terminal domain of the ice-nucleation protein InaV (InaV-N) ofPseudomonas syringaewas applied to display the DFPase on the cell surface.In silicotechniques were used to generate a model in order to examine the possibility of DFPase exhibition on the cell surface. The secondary and tertiary structures of a chimeric protein were determined and then, the predicted model was subjected to several repeated cycles of stereochemical evaluation and energy minimization. The homology-modeled structure of the InaV/N-DFPase protein was docked to DFP. The optimizedinaV/N-dfpasegene was translated to 519 amino acids. The minimum free energy of the best-predicted secondary structures was formed by RNA molecules (-215.45 kcal/mol). SOPMA analysis results showed that the main helix peak corresponded to the anchor fragment. Validation of the 3D model indicated that 86.1% of amino acid residues were incorporated into the favored regions. The moldock score was 360.22 for DFP. Results of this study indicated that according toin silicoanalysis, all of these findings were effective in targeting DFPase.

scholarly journals Cell surface anchorage and ligand-binding domains of the Saccharomyces cerevisiae cell adhesion protein alpha-agglutinin, a member of the immunoglobulin superfamily.

1993 ◽  
Vol 13 (4) ◽  
pp. 2554-2563 ◽  
Author(s):  
D Wojciechowicz ◽  
C F Lu ◽  
J Kurjan ◽  
P N Lipke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Adhesion ◽  
Amino Acid ◽  
Cell Surface ◽  
Consensus Sequence ◽  
Binding Domain ◽  
Immunoglobulin Superfamily ◽  
Cell Contact ◽  
Amino Acid Residues ◽  
Adhesion Proteins

alpha-Agglutinin is a cell adhesion glycoprotein expressed on the cell wall of Saccharomyces cerevisiae alpha cells. Binding of alpha-agglutinin to its ligand a-agglutinin, expressed by a cells, mediates cell-cell contact during mating. Analysis of truncations of the 650-amino-acid alpha-agglutinin structural gene AG alpha 1 delineated functional domains of alpha-agglutinin. Removal of the C-terminal hydrophobic sequence allowed efficient secretion of the protein and loss of cell surface attachment. This cell surface anchorage domain was necessary for linkage to a glycosyl phosphatidylinositol anchor. A construct expressing the N-terminal 350 amino acid residues retained full a-agglutinin-binding activity, localizing the binding domain to the N-terminal portion of alpha-agglutinin. A 278-residue N-terminal peptide was inactive; therefore, the binding domain includes residues between 278 and 350. The segment of alpha-agglutinin between amino acid residues 217 and 308 showed significant structural and sequence similarity to a consensus sequence for immunoglobulin superfamily variable-type domains. The similarity of the alpha-agglutinin-binding domain to mammalian cell adhesion proteins suggests that this structure is a highly conserved feature of adhesion proteins in diverse eukaryotes.

scholarly journals BAK1 Is Not a Target of the Pseudomonas syringae Effector AvrPto

2011 ◽  
Vol 24 (1) ◽  
pp. 100-107 ◽  
Author(s):  
Tingting Xiang ◽  
Na Zong ◽  
Jie Zhang ◽  
Jinfeng Chen ◽  
Mingsheng Chen ◽  
...  
Keyword(s):  
Cell Surface ◽  
Immune Responses ◽  
Pseudomonas Syringae ◽  
Plant Cell ◽  
Crucial Role ◽  
Pathogenic Bacteria ◽  
Effector Proteins ◽  
Receptor Like Kinase ◽  
Receptor Kinases ◽  
New Evidence

Plant cell surface-localized receptor kinases such as FLS2, EFR, and CERK1 play a crucial role in detecting invading pathogenic bacteria. Upon stimulation by bacterium-derived ligands, FLS2 and EFR interact with BAK1, a receptor-like kinase, to activate immune responses. A number of Pseudomonas syringae effector proteins are known to block immune responses mediated by these receptors. Previous reports suggested that both FLS2 and BAK1 could be targeted by the P. syringae effector AvrPto to inhibit plant defenses. Here, we provide new evidence further supporting that FLS2 but not BAK1 is targeted by AvrPto in plants. The AvrPto-FLS2 interaction prevented the phosphorylation of BIK1, a downstream component of the FLS2 pathway.

scholarly journals Effects of atmospheric conditions on ice nucleation activity of <i>Pseudomonas</i>

2012 ◽  
Vol 12 (22) ◽  
pp. 10667-10677 ◽  
Author(s):  
E. Attard ◽  
H. Yang ◽  
A.-M. Delort ◽  
P. Amato ◽  
U. Pöschl ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Pseudomonas Syringae ◽  
Ice Nucleation ◽  
Acidic Ph ◽  
Bacterial Cells ◽  
Atmospheric Conditions ◽  
Ice Nucleation Protein ◽  
Ice Melt ◽  
Nucleation Activity ◽  
Ice Nucleation Activity

Abstract. Although ice nuclei from bacterial origin are known to be efficient at the highest temperatures known for ice catalysts, quantitative data are still needed to assess their role in cloud processes. Here we studied the effects of three typical cloud conditions (i) acidic pH (ii) NO2 and O3 exposure and (iii) UV-A exposure on the ice nucleation activity (INA) of four Pseudomonas strains. Three of the Pseudomonas syringae strains were isolated from cloud water and the phyllosphere and Pseudomonas fluorescens strain CGina-01 was isolated from Antarctic glacier ice melt. Among the three conditions tested, acidic pH caused the most significant effects on INA likely due to denaturation of the ice nucleation protein complex. Exposure to NO2 and O3 gases had no significant or only weak effects on the INA of two P. syringae strains whereas the INA of P. fluorescens CGina-01 was significantly affected. The INA of the third P. syringae strain showed variable responses to NO2 and O3 exposure. These differences in the INA of different Pseudomonas suggest that the response to atmospheric conditions could be strain-specific. After UV-A exposure, a substantial loss of viability of all four strains was observed whereas their INA decreased only slightly. This corroborates the notion that under certain conditions dead bacterial cells can maintain their INA. Overall, the negative effects of the three environmental factors on INA were more significant at the warmer temperatures. Our results suggest that in clouds where temperatures are near 0 °C, the importance of bacterial ice nucleation in precipitation processes could be reduced by some environmental factors.

scholarly journals In Silico Potential of Turmeric (Cucurma longa) as Antibacterial Agent for Salmonella typhi

BIOEDUKASI ◽  
2018 ◽  
pp. 103
Author(s):  
Boni Herdiawan ◽  
Dwi Rulitasari ◽  
Ella Triana Aprilianty ◽  
Huzaimatul Khalisah ◽  
Nur Fatichah Choirudiniyah ◽  
...  
Keyword(s):  
Typhoid Fever ◽  
In Silico ◽  
Antibacterial Agent ◽  
Bacterial Resistance ◽  
Curcuma Longa ◽  
Salmonella Typhi ◽  
Amino Acid Residues ◽  
Tropical Country ◽  
Receptor Proteins ◽  
Docking Method

Indonesia is a tropical country that has a variety of endemic infectious diseases, one of these diseases is typhoid fever. Salmonella typhi is a bacterium that causes typhoid fever. Antibiotic treatment is often used but fails due to bacterial resistance to antibiotics. An alternative treatment is required to gradually substitute synthetic antibiotic. One of this potential is given by turmeric (Curcuma longa).The purpose of this research was to know the potential of turmeric as in silico antibacterial agent for Salmonella typhi using docking method. Docking result showed that the five compounds produced different values ​​on the affinity and rmsd binding parameters. The highest affinity binding value was the Ciprofloxacin compound, the lowest was Bisdemethoxycurcumin compound. The highest rmsd value was Demethoxycurcumin, while the lowest was Xanthorrhizol, and the result revealed that all compounds have bioaffinity properties. Based on the results, three compounds derived from turmeric (demethoxycurcumin, bisdemethoxy curcumin and xanthorrizol) are still not effectively used as antibacterial agent for Salmonella typhi due to the absence of equality of amino acid residues between alternative compounds turmeric with compounds which has been clinically tested as a drug and ineffective use of receptor proteins that result in less optimal alternative compounds.   Keywords: Turmeric, Antibacterial, Salmonella typhi, In Silico

scholarly journals Identification and in silico characterization of hemocyanin γ-type subunit protein in Vibrio harveyi infected freshwater prawn, Macrobrachium rosenbergii

2021 ◽  
Vol 42 (1) ◽  
pp. 14-23
Author(s):  
B.B. Patnaik ◽  
◽  
S. Baliarsingh ◽  
S. Sahoo ◽  
J.M. Chung ◽  
...  
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Vibrio Harveyi ◽  
Macrobrachium Rosenbergii ◽  
Full Length ◽  
Freshwater Prawn ◽  
Amino Acid Residues ◽  
Subunit Protein ◽  
In Silico Tools

Aim: Identification of full-length ORF of hemocyanin subunit-1 (Mr_HC_1) from the hepatopancreas transcriptome of freshwater prawn, Macrobrachium rosenbergii infected with Vibrio harveyi and characterization of its sequence and structure by in silico tools and softwares. Methodology: Illumina HiSeq and de novo assembled unigenes were scanned against PANM-DB to screen Mr_HC_1. FGENESH gene prediction and SMART programs were used to predict the ORF region. Subsequently, Clustal X2 and MEGA in-silico tools were used to understand the sequence relatedness and evolutionary status of Mr_HC_1. Structural prediction was performed by SWISS-MODEL and Ramachandran plot modeling programs Results: The full-length ORF was 1983 bp in length encoding a polypeptide of 661 amino acid residues. Mr_HC_1 showed a putative signal peptide of 21 amino acid residues at the N-terminus and three hemocyanin domains. Homology analysis of Mr_HC_1 amino acid sequence confirms maximum identity to M. nipponense hemocyanin subunit-1 (Mn_HC_1). Phylogenetic analysis showed that Mr_HC_1 is more closely related to the hemocyanin γ-type subunit of freshwater shrimps. Homology modeling of Mr_HC_1 showed homo-hexameric protein containing 12 copper ions. With a QMEAN score of -3.33 and model-template sequence identity of 59.15%, the predicted model of Mr_HC_1 is convincing Interpretation: This study characterizes the hemocyanin γ-type subunit protein of freshwater prawn, M. rosenbergii for future studies on host defense mechanisms.

Detection of local ATP release from activated platelets using cell surface-attached firefly luciferase

1999 ◽  
Vol 276 (1) ◽  
pp. C267-C278 ◽  
Author(s):  
Reza Beigi ◽  
Eiry Kobatake ◽  
Masuo Aizawa ◽  
George R. Dubyak
Keyword(s):  
Cell Surface ◽  
Affinity Purification ◽  
Protein A ◽  
Atp Release ◽  
Chimeric Protein ◽  
Firefly Luciferase ◽  
Live Cells ◽  
Adherent Cell ◽  
Local Concentration ◽  
Activated Platelets

We have developed a method for measuring the local concentration of ATP at the extracellular surface of live cells. This method relies on the specific attachment to the cell surface of a chimeric protein that consists of the IgG-binding domain of Staphylococcus aureus protein A fused in-frame with the complete sequence for firefly luciferase (proA-luc). Expression of proA-luc in Escherichia coli and its one-step affinity purification are straightforward. Attachment to cells is demonstrated to be specific and antibody dependent using several suspended and adherent cell types. Light production by cell surface-attached luciferase is continuous, linearly related to ATP concentration, and sufficient to provide nanomolar sensitivity. The spatial resolution of this method enables the observation of strictly local changes in extracellular ATP during its secretion from activated platelets. Furthermore, the activity of cell-attached luciferase is relatively refractory to the inclusion of nucleotidases in the medium, arguing for its effectiveness in cell systems possessing potent ecto-ATPases.

The FHA domain mediates phosphoprotein interactions

2000 ◽  
Vol 113 (23) ◽  
pp. 4143-4149 ◽  
Author(s):  
J. Li ◽  
G.I. Lee ◽  
S.R. Van Doren ◽  
J.C. Walker
Keyword(s):  
Sequence Similarity ◽  
Sequence Motif ◽  
Amino Acid Residues ◽  
Fha Domain ◽  
Tertiary Structures ◽  
Cellular Processes ◽  
Forkhead Transcription Factors ◽  
Binding Domains ◽  
Cycle Arrest ◽  
Protein Kinase Signaling

The forkhead-associated (FHA) domain is a phosphopeptide-binding domain first identified in a group of forkhead transcription factors but is present in a wide variety of proteins from both prokaryotes and eukaryotes. In yeast and human, many proteins containing an FHA domain are found in the nucleus and involved in DNA repair, cell cycle arrest, or pre-mRNA processing. In plants, the FHA domain is part of a protein that is localized to the plasma membrane and participates in the regulation of receptor-like protein kinase signaling pathways. Recent studies show that a functional FHA domain consists of 120–140 amino acid residues, which is significantly larger than the sequence motif first described. Although FHA domains do not exhibit extensive sequence similarity, they share similar secondary and tertiary structures, featuring a sandwich of two anti-parallel (beta)-sheets. One intriguing finding is that FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine, distinguishing them from other well-studied phosphoprotein-binding domains. The diversity of proteins containing FHA domains and potential differences in binding specificities suggest the FHA domain is involved in coordinating diverse cellular processes.

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