scholarly journals Identification of Receptor Binding Proteins in Flagellotropic Agrobacterium Phage 7-7-1

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1267
Author(s):  
Floricel Gonzalez ◽  
Birgit E. Scharf
Keyword(s):  
Cell Growth ◽  
Receptor Binding ◽  
In Silico ◽  
Binding Proteins ◽  
Homology Modelling ◽  
Structure And Function ◽  
Host Cells ◽  
Future Studies ◽  
Bacterial Flagella ◽  
And Function

The rapid discovery of new and diverse bacteriophages has driven the innovation of approaches aimed at detailing interactions with their bacterial hosts. Previous studies on receptor binding proteins (RBPs) mainly relied on their identification in silico and are based on similarities to well-characterized systems. Thus, novel phage RBPs unlike those currently annotated in genomic and proteomic databases remain largely undiscovered. In this study, we employed a screen to identify RBPs in flagellotropic Agrobacterium phage 7-7-1. Flagellotropic phages utilize bacterial flagella as receptors. The screen identified three candidate RBPs, Gp4, Gp102, and Gp44. Homology modelling predicted that Gp4 is a trimeric, tail associated protein with a central β-barrel, while the structure and function of Gp102 and Gp44 are less obvious. Studies with purified Gp41-247 confirmed its ability to bind and interact with host cells, highlighting the robustness of the RBP screen. We also discovered that Gp41-247 inhibits the growth of host cells in a motility and lipopolysaccharide (LPS) dependent fashion. Hence, our results suggest interactions between Gp41-247, rotating flagellar filaments and host glycans to inhibit host cell growth, which presents an impactful and intriguing focus for future studies.

Structure prediction of SPAK C-terminal domain and analysis of its binding to RFXV/I motifs by homology modelling, docking, and molecular dynamics simulation studies

2020 ◽  
Vol 16 ◽  
Author(s):  
Mubarak A. Alamri ◽  
Ahmed D. Alafnan ◽  
Obaid Afzal ◽  
Alhumaidi B. Alabbas ◽  
Safar M. Alqahtani
Keyword(s):  
Molecular Dynamic ◽  
Dynamic Stability ◽  
Md Simulation ◽  
Homology Modelling ◽  
Antihypertensive Agents ◽  
Structure And Function ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Terminal Domain ◽  
And Function

Background: The STE20/SPS1-related proline/alanine-rich kinase (SPAK) is a component of WNKSPAK/OSR1 signaling pathway that plays an essential role in blood pressure regulation. The function of SPAK is mediated by its highly conserved C-terminal domain (CTD) that interacts with RFXV/I motifs of upstream activators, WNK kinases, and downstream substrate, cation-chloride cotransporters. Objective: To determine and validate the three-dimensional structure of the CTD of SPAK and to study and analyze its interaction with the RFXV/I motifs. Methods: A homology model of SPAK CTD was generated and validated through multiple approaches. The model was based on utilizing the OSR1 protein kinase as a template. This model was subjected to 100 ns molecular dynamic (MD) simulation to evaluate its dynamic stability. The final equilibrated model was used to dock the RFQV-peptide derived from WNK4 into the primary pocket that was determined based on the homology sequence between human SPAK and OSR1 CTDs. The mechanism of interaction, conformational rearrangement and dynamic stability of the binding of RFQV-peptide to SPAK CTD were characterized by molecular docking and molecular dynamic simulation. Results: The MD simulation suggested that the binding of RFQV induces a large conformational change due to the distribution of salt bridge within the loop regions. These results may help in understanding the relation between the structure and function of SPAK CTD and to support drug design of potential SPAK kinase inhibitors as antihypertensive agents. Conclusion: This study provides deep insight into SPAK CTD structure and function relationship.

scholarly journals Structure and function insights garnered from in silico modeling of the thrombospondin type-1 domain-containing 7A antigen

2018 ◽  
Vol 87 (2) ◽  
pp. 136-145 ◽  
Author(s):  
Shana V. Stoddard ◽  
Colin L. Welsh ◽  
Maggie M. Palopoli ◽  
Serena D. Stoddard ◽  
Mounika P. Aramandla ◽  
...  
Keyword(s):  
In Silico ◽  
Structure And Function ◽  
In Silico Modeling ◽  
And Function

In silico study of the structure and function of Streptococcus mutans plasmidic proteins

2017 ◽  
Vol 13 (2) ◽  
Author(s):  
Silvia Caprari ◽  
Giovanni Minervini ◽  
Valentina Brandi ◽  
Fabio Polticelli
Keyword(s):  
Streptococcus Mutans ◽  
In Silico ◽  
Structure And Function ◽  
Positive Bacterium ◽  
Gram Positive ◽  
In Silico Study ◽  
And Function

AbstractThe Gram-positive bacterium

scholarly journals Novel deleterious nsSNPs within MEFV gene that could be used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using bioinformatics analysis

2018 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Tebyan A Abdelhameed ◽  
Fatima A. Abdelrhman ◽  
Soada Ahmed Osman ◽  
Mohamed A. Hassan
Keyword(s):  
Familial Mediterranean Fever ◽  
In Silico ◽  
Mediterranean Basin ◽  
Mefv Gene ◽  
Structure And Function ◽  
Diagnostic Markers ◽  
Novel Mutations ◽  
Bioinformatics Tools ◽  
Mediterranean Fever ◽  
And Function

AbstractBackgroundFamilial Mediterranean Fever (FMF) is the most common auto inflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin, we aimed to identify the pathogenic SNPs in MEFV by computational analysis software.MethodsWe carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function.Result23 novel mutations out of 857 nsSNPs that are found to be deleterious effect on the MEFV structure and function.ConclusionThis is the first in silico analysis in MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

scholarly journals Regulation of synaptic structure and function by palmitoylated AMPA receptor binding protein

2010 ◽  
Vol 43 (4) ◽  
pp. 341-352 ◽  
Author(s):  
Charu Misra ◽  
Sophie Restituito ◽  
Jainne Ferreira ◽  
Gerald A. Rameau ◽  
Jie Fu ◽  
...  
Keyword(s):  
Ampa Receptor ◽  
Receptor Binding ◽  
Binding Protein ◽  
Structure And Function ◽  
Synaptic Structure ◽  
Ampa Receptor Binding Protein ◽  
And Function ◽  
Receptor Binding Protein
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