Functional Annotation and Characterization of a Hypothetical Protein from Pseudoalteromonas spp. Identify Potential Biomarker: An In-silico Approach

Islam, Sk Injamamul; Mou, Moslema Jahan; Sanjida, Saloa; Mahfuj, Sarower

doi:10.4194/afs57

Cited by 3 publications

(1 citation statement)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, antibody aggregation can be caused by improper disul de bond formation or exchange, hence disul de bonding is crucial for protein characterization in the biopharmaceutical manufacturing process (Zhang et al, 2011). CYSPRED predicted two bonding states and one non-bonding state of the predicted tertiary model of HP33 indicates the quality of the model (Islam, Mou, et al, 2022a). In addition, DIANA predicted three bonded cystine sequences in different locations of the protein (Table -3).…”

Section: Analysis Of Protein-protein Interactions and Protein Disul D...mentioning

confidence: 99%

Homo-oligomer models prediction, functional characterization, and Ab initio docking analysis of hypothetical protein HP33 from Vibrio harveyi strain

Islam

Sanjida

Mou

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

It is reported that antigenicity of a unique hypothetical protein named HP33 of Vibrio harveyi Y6 strain causes scale drop and muscle necrosis disease (SDMND) in Lates calcarifer. This distinct protein was found from only V. harveyi SDMND and is responsible for 40-50% mortality. Despite these devastating complications, there is still no cure or vaccine for the disease. As a result, the current work sought to elucidate the roles of HP33 protein. The sequence similarity was searched across the available bioinformatics databases to find the homologous protein. This hypothetical protein is known to be an unstable, nonpolar, and outer membrane protein based on its subcellular localization and physicochemical properties. Functional annotation tools predicted our target protein has only a single domain. The random coil was found to be predominant in the secondary structure. Quality evaluation methods were used to predict and confirm the secondary and tertiary structure. After YASARA energy minimization, the 3D structure became more stable, which was confirmed by many quality assessment methods. Additionally, the active site and interacting proteins were examined. An important biological activity of the HP is that it contains single functional domains that may be responsible for representing a biosynthetic gene cluster. In addition, protein-ligand docking analysis showed two possible drug molecules against HP33 pathogenesis. Finally, the homo-oligomers models prediction and ab-initio docking results will provide good insights for further immunological study which might be of significant relevance to future V. harveyi genetics research.

show abstract

Section: Analysis Of Protein-protein Interactions and Protein Disul D...mentioning

confidence: 99%

Homo-oligomer models prediction, functional characterization, and Ab initio docking analysis of hypothetical protein HP33 from Vibrio harveyi strain

Islam

Sanjida

Mou

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Structural, functional, molecular docking analysis of a hypothetical protein from Talaromyces marneffei and its molecular dynamic simulation: an in-silico approach

Munna,

Islam,

Shanta

et al. 2024

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

Ligand-based Virtual Screening, Quantum Mechanics Calculations, and Normal Mode Analysis of Phytochemical Compounds Targeting Toll‐Interacting Protein (Tollip) Against Bacterial Diseases

Islam

Singh

Sonia

et al. 2023

View full text Add to dashboard Cite

The Labeo rohita (Rohu) Toll interacting protein (Tollip) is ubiquitously expressed in the kidneys, gills, spleen, liver, and blood. Tollip in L. rohita has higher eukaryotic structural features and is produced in response to bacterial infections. Several bacterial diseases, such as Aeromonas hydrophila and Vibrio spp, have been reported in the internal organs of L. rohita. The consequences of these bacterial infections can be 100% mortality of fish. There are currently no medicines or vaccines available to prevent or treat infections caused by the involvement of this protein. During bacterial infections, it was discovered that Tollip plays an essential function as a negative regulator of the MyD88-dependent TLR signalling pathway. Therefore, the study aimed to evaluate the inhibitory potentiality of the Allium sativum compound against Tollip. A. sativum has been reported to show potential antibacterial activity against numerous microbial pathogens. Still, activity against the Tollip-promoted pathogens has not yet been reported. In silico virtual screen and molecular docking methods were used in this study to calculate the binding affinity of 48 drug compounds of A. sativum against the receptor Tollip. The docking and normal mode analysis methods predict 2 (PubChem CID: 122130381 and CID 12303662) inhibitory compounds that bind strongly with the Tollip with a binding affinity of -9.2 and -8.8 kcal/mol, respectively. The ADMET properties of the compounds also verified the drug resemblance features of the two compounds of A. sativum. Furthermore, to evaluate the efficacy of these two potential inhibitors, more in-vitro testing is required.

show abstract

Functional Annotation and Characterization of a Hypothetical Protein from Pseudoalteromonas spp. Identify Potential Biomarker: An In-silico Approach

Cited by 3 publications

References 39 publications

Homo-oligomer models prediction, functional characterization, and Ab initio docking analysis of hypothetical protein HP33 from Vibrio harveyi strain

Homo-oligomer models prediction, functional characterization, and Ab initio docking analysis of hypothetical protein HP33 from Vibrio harveyi strain

Structural, functional, molecular docking analysis of a hypothetical protein from Talaromyces marneffei and its molecular dynamic simulation: an in-silico approach

Ligand-based Virtual Screening, Quantum Mechanics Calculations, and Normal Mode Analysis of Phytochemical Compounds Targeting Toll‐Interacting Protein (Tollip) Against Bacterial Diseases

Contact Info

Product

Resources

About