Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination

Abstract

Stenotrophomonas maltophilia is a multidrug-resistant bacterium with no precise clinical treatment. This bacterium can be a vital cause for death and different organ failures in immune-compromised, immune-competent, and long-time hospitalized patients. Extensive quorum sensing capability has become a challenge to develop new drugs against this pathogen. Moreover, the organism possesses about 789 proteins which function, structure, and pathogenesis remain obscured. In this piece of work, we tried to enlighten the aforementioned sectors using highly reliable bioinformatics tools validated by the scientific community. At first, the whole proteome sequence of the organism was retrieved and stored. Then we separated the hypothetical proteins and searched for the conserved domain with a high confidence level and multi-server validation, which resulted in 24 such proteins. Furthermore, all of their physical and chemical characterizations were performed, such as theoretical isoelectric point, molecular weight, GRAVY value, and many more. Besides, the subcellular localization, protein-protein interactions, functional motifs, 3D structures, antigenicity, and virulence factors were also evaluated. As an extension of this work, ’RTFAMSSER’ and ’PAAPQPSAS’ were predicted as potential T and B cell epitopes, respectively. We hope our findings will help in better understating the pathogenesis and smoothen the way to the cure.

Serum Protein Fishing for Machine Learning-Boosted Diagnostic Classification of Small Nodules of Lung

“…The theoretical GRAVY value was measured by the online bioinformatics tool (). The GRAVY value was calculated by dividing the cumulative value of hydropathy for all the amino acid residues in the protein chain by the total number of residues in that protein sequence. , Of the 1174 proteins identified via protein fishing with SiO 2 , 1083 were hydrophilic, accounting for 92.2% of the total proteins, while only 91 were hydrophobic, accounting for 7.8% of the total proteins. The Gravy score in the heatmap suggests that most of the proteins adsorbed on the surface of the NPs are hydrophilic proteins.…”

Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity

“…Interaction between proteins plays a fundamental role in the biological processes of an organism. 141 Through PPI, protein cellular functions can be analyzed since execution of a function depends on the contact or regulatory interactions with another protein. 60 , 142 Furthermore, PPI can be useful to infer an unidentified or hypothetical protein function based on the evidence of their interaction with known proteome of a particular organism as it is rare for a protein to interact with different biomolecules.…”

A Green Approach of Zinc Oxide Nanoparticles from Dodonaea viscosa and Anti-Inflammatory Properties

“…The SOSUI tool is utilized to determine if a protein is transmembrane or soluble. Interpro protein sequencing and categorization were used to predict the super family and molecular function [15].…”