Structural Phylogeny of Different Allergens May Reveal Common Epitopic Footprint

2021 ◽  
Vol 28 ◽  
Author(s):  
Anubhab Laha ◽  
Rajib Bandopadhyay ◽  
Anindya Sundar Panja
Keyword(s):  
Structural Analysis ◽  
In Silico ◽  
Protein Sequences ◽  
Food Allergens ◽  
Significant Relationships ◽  
Structural Identity ◽  
In Silico Study

Background: The incidence of allergy is increasing at an alarming rate for the last few decades. Objective: Our present study is focused on finding out the structurally homologous motifs present in different proteinaceous allergens Methods: Significant number of protein sequences and their corresponding structures of various pollen, fungal, bacterial, and food allergens were retrieved, and the sequence and structural identity were analyzed. Results: Intra- and inter-sequence and their structural analysis of the proteinaceous allergens, resulted in no significant relationships among them. A few, but not negligible number of high structural similarities were observed within different groups of allergens from fungus, angiosperms, and animals (Aves and Mammalia). Conclusion: Our in silico study on thirty-six different allergens showed a significant level of structural similarities among themselves, regardless of their sequences.

Characterization of Tannase Protein Sequences of Bacteria and Fungi: An In Silico Study

2012 ◽  
Vol 31 (4) ◽  
pp. 306-327 ◽  
Author(s):  
Amrita Banerjee ◽  
Arijit Jana ◽  
Bikash R. Pati ◽  
Keshab C. Mondal ◽  
Pradeep K. Das Mohapatra
Keyword(s):  
In Silico ◽  
Protein Sequences ◽  
In Silico Study ◽  
Bacteria And Fungi

scholarly journals Characteristics of hemolysins from pathogenic bacteria in tropical aquaculture: an in-silico study

2021 ◽  
Vol 890 (1) ◽  
pp. 012017
Author(s):  
Dewi Syahidah
Keyword(s):  
Blood Cells ◽  
In Silico ◽  
Pathogenic Bacteria ◽  
Protein Sequences ◽  
Host Cells ◽  
Bacterial Isolates ◽  
Damage Cell ◽  
In Silico Study ◽  
Tropical Aquaculture

Abstract Some species of known pathogenic bacteria isolates in tropical aquaculture produces hemolysin. Hemolysin can be identified based on its ability to break down red blood cells in vitro. Some hemolysin is a pore-shaped poison that can damage cell membranes and kill host cells. The character of the 13 sequences of hemolysin protein in several pathogenic bacterial isolates in tropical aquaculture was analysed using the NCBI protein bioinformatics database. The phylogenetic tree was generated, and the analysis was conducted using the base character method (Maximum Parsimony) of Mega 6.06 software. The result showed that there are two big family of hemolysin from the known pathogenic bacteria. The closest characteristics of protein sequences were hemolysin of Streptococcus agalacticae and of S. iniae.

In Silico Study of Structural and Geometrical Requirements of Natural Sesquiterpene Lactones with Trypanocidal Activity

2013 ◽  
Vol 13 (10) ◽  
pp. 1407-1414 ◽  
Author(s):  
L. Fabian ◽  
V. Sulsen ◽  
F. Frank ◽  
S. Cazorla ◽  
E. Malchiodi ◽  
...  
Keyword(s):  
In Silico ◽  
Sesquiterpene Lactones ◽  
Trypanocidal Activity ◽  
In Silico Study

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

In Silico Study of Ethylene Biosynthesis: Seeking New Effectors of ACC Synthase and ACC Oxidase

2016 ◽  
Vol 11 (3) ◽  
pp. 346-356
Author(s):  
Nada Ayadi ◽  
Sarra Aloui ◽  
Rabeb Shaiek ◽  
Oussama Rokbani ◽  
Faten Raboud ◽  
...  
Keyword(s):  
In Silico ◽  
Acc Oxidase ◽  
Acc Synthase ◽  
Ethylene Biosynthesis ◽  
In Silico Study

In Silico Identification of a Potent Arsenic Based Approved Drug Darinaparsin against SARS-CoV-2: Inhibitor of RNA Dependent RNA polymerase (RdRp) and Essential Proteases

2020 ◽  
Vol 20 ◽  
Author(s):  
Trinath Chowdhury ◽  
Gourisankar Roymahapatra ◽  
Santi M. Mandal
Keyword(s):  
Rna Polymerase ◽  
Viral Entry ◽  
In Silico ◽  
Rna Dependent Rna Polymerase ◽  
Replication Complex ◽  
In Silico Study ◽  
Life Threatening ◽  
In Vivo Analysis ◽  
3Cl Protease

Background: COVID-19 is a life threatening novel corona viral infection to our civilization and spreading rapidly. Terrific efforts are generous by the researchers to search for a drug to control SARS-CoV-2. Methods: Here, a series of arsenical derivatives were optimized and analyzed with in silico study to search the inhibitor of RNA dependent RNA polymerase (RdRp), the major replication factor of SARS-CoV-2. All the optimized derivatives were blindly docked with RdRp of SARS-CoV-2 using iGEMDOCK v2.1. Results: Based on the lower idock score in the catalytic pocket of RdRp, darinaparsin (-82.52 kcal/mol) revealed most effective among them. Darinaparsin strongly binds with both Nsp9 replicase protein (-8.77 kcal/mol) and Nsp15 endoribonuclease (-8.3 kcal/mol) of SARS-CoV-2 as confirmed from the AutoDock analysis. During infection, the ssRNA of SARS-CoV2 is translated into large polyproteins forming viral replication complex by specific proteases like 3CL protease and papain protease. This is also another target to control the virus infection where darinaparsin also perform the inhibitory role to proteases of 3CL protease (-7.69 kcal/mol) and papain protease (-8.43 kcal/mol). Conclusion: In host cell, the furin protease serves as a gateway to the viral entry and darinaparsin docked with furin protease which revealed a strong binding affinity. Thus, screening of potential arsenic drugs would help in providing the fast invitro to in-vivo analysis towards development of therapeutics against SARS-CoV-2.

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