Structural and Functional Annotation and Molecular Docking Analysis of a Hypothetical Protein from Neisseria gonorrhoeae: An In-Silico Approach

Abstract

Background. Worldwide, Neisseria gonorrhoeae-related sexually transmitted infections (STIs) continue to be of significant public health concern. This obligate-human pathogen has developed a number of defenses against both innate and adaptive immune responses during infection, some of which are mediated by the pathogen’s proteins. Hence, the uncharacterized proteins of N. gonorrhoeae can be annotated to get insight into the unique functions of this organism related to its pathogenicity and to find a more efficient therapeutic target. Methods. In this study, a hypothetical protein (HP) of N. gonorrhoeae was chosen for analysis and an in-silico approach was used to explore various properties such as physicochemical characteristics, subcellular localization, secondary structure, 3D structures, and functional annotation of that HP. Finally, a molecular docking analysis was performed to design an epitope-based vaccine against that HP. Results. This study has identified the potential role of the chosen HP of N. gonorrhoeae in plasmid transfer, cell cycle control, cell division, and chromosome partitioning. Acidic nature, thermal stability, cytoplasmic localization of the protein, and some of its other physicochemical properties have also been identified through this study. Molecular docking analysis has demonstrated that one of the T cell epitopes of the protein has a significant binding affinity with the human leukocyte antigen HLA-B ∗ 15 : 01. Conclusions. The in-silico characterization of this protein will help us understand molecular mechanism of action of N. gonorrhoeae and get an insight into novel therapeutic identification processes. This research will, therefore, enhance our knowledge to find new medications to tackle this potential threat to humankind.

Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study

“…When the amino acid sequence is available, homology modeling is an efficient method for predicting protein structure [ 51 ]. It has been previously reported in several studies that the 3D structure of a protein and its functional activity are closely linked [ 52 , 53 ]. Hence, the 3D structure was predicted using the trRosetta server for homology modeling.…”

“…Allergenicity, however, is another significant obstacle to the development of vaccinations. The majority of immunizations produce immunoglobulin E and type 2 helper T (Th2) cells, which stimulate an unwanted allergic immune response [ 53 , 55 ]. Finally, the design of potential vaccines must ensure that they cause the production of IFN- γ following immunization [ 56 ].…”

“…The development of computational tools and databases has paved the path to vaccine creation. The conventional methods for vaccine creation which are very time-consuming and costly are now being replaced by more straightforward and cost-effective computational methods [ 53 ]. In this study, a computer-based immunoinformatics approach was employed to construct an epitope-based vaccine against the cell surface binding protein of reemerging mPox virus.…”

“…Allergenicity, however, is another significant obstacle to the development of vaccinations. The majority of immunizations produce immunoglobulin E and type 2 helper T (Th2) cells, which stimulate an unwanted allergic immune response [53,55].…”

Excavation of Biomarker Candidates for the Diagnosis of Talaromyces marneffei Infection via Genome-Wide Prediction and Functional Annotation of Secreted Proteins

“…marneffei is still mysterious since the function and localization remain unclear for >70% proteins encoded by standard genome ATCC18224 (10,707 proteins in total) . With growing amounts of whole-genome sequencing data, in-depth functional investigations of proteins have been conducted in various microorganisms, − which brought up massive proteins waiting for annotation, which were termed as hypothetical or uncharacterized proteins (HPs or UPs) . Encouragingly, a panel of bioinformatic platforms in rapid development thus provided the capability of discovery, prediction, and annotation for protein function and localization.…”