Functional annotation and sequence-structure characterization of a hypothetical protein putatively involved in carotenoid biosynthesis in microalgae

Narang, Parminder Kaur; Dey, Jyotirmayee; Mahapatra, Soumya Ranjan; Ghosh, Mrinmoy; Misra, Namrata; Suar, Mrutyunjay; Kumar, Vijay; Raina, Vishakha

doi:10.1016/j.sajb.2021.04.014

Cited by 35 publications

(15 citation statements)

References 34 publications

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“…In fact, synthetic vaccines are more reliable than conventional [ 56 ]. This approach has been used against various pathogens such as Klebsiella pneumonia , Acinetobacter baumannii , SARS-CoV-2, microalgae, and Staphylococcus aureus [ [57] , [58] , [59] , [60] ]. In this scientific approach, based on the scientific evidence from the literature, we selected four candidate proteins that are reportedly involved in S. gordonii Infection.…”

Section: Discussionmentioning

confidence: 99%

Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

Nasir,

Iftikhar,

Zubair

et al. 2023

Heliyon

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Section: Discussionmentioning

confidence: 99%

Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

Nasir,

Iftikhar,

Zubair

et al. 2023

Heliyon

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“…PSIPRED V3.3 was used to predict and analyze the vaccine’s secondary structure, which indicated the presence of 32.17% alpha-helix, 11.41% beta-strand, and 55.90% coil. Following that, a homology modelling approach was utilized to construct the tertiary structure of the final designed vaccine [ 40 ]. Ramachandran plot results showed that the overall model is reasonable because more than 99% of residues were located in the allowed region.…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterization and Designing of a Novel Multiepitope Vaccine Construct Against Pseudomonas aeruginosa

Dey

Mahapatra

Patnaik

et al. 2022

Int J Pept Res Ther

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Pseudomonas aeruginosa , an ESKAPE pathogen causes many fatal clinical diseases in humans across the globe. Despite an increase in clinical instances of Pseudomonas infection, there is currently no effective vaccine or treatment available. The major membrane protein candidate of the P. aeruginosa bacterial cell is known to be a critical component for cellular bacterial susceptibility to antimicrobial peptides and survival inside the host organisms. Therefore, the current computational study aims to examine P. aeruginosa’s major membrane protein, OprF, and OprI, in order to design linear B-cell, cytotoxic T-cell, and helper T-cell peptide-based vaccine constructs. Utilizing various immune-informatics tools and databases, a total of two B-cells and twelve T-cells peptides were predicted. The final vaccine design was simulated to generate a high-quality three-dimensional structure, which included epitopes, adjuvant, and linkers. The vaccine was shown to be nonallergenic, antigenic, soluble, and had the best biophysical properties. The vaccine and Toll-like receptor 4 have a strong and stable interaction, according to protein-protein docking and molecular dynamics simulations. Additionally, in silico cloning was employed to see how the developed vaccine expressed in the pET28a (+) vector. Ultimately, an immune simulation was performed to see the vaccine efficacy. In conclusion, the newly developed vaccine appears to be a promising option for a vaccine against P. aeruginosa infection. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10356-z.

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“…This retrieved amino acid sequence is used to generate a novel vaccine construct. The NCBI and UniProt databases provide a huge amount of biological protein information (Narang et al 2021 ; Panda et al 2022 ). The amino acid sequence of the target protein can be extracted in FASTA format (Shawan et al 2014 , 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine

Shawan,

Sharma,

Halder

et al. 2023

Int J Pept Res Ther

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A vaccine is defined as a biologic preparation that trains the immune system, boosts immunity, and protects against a deadly microbial infection. They have been used for centuries to combat a variety of contagious illnesses by means of subsiding the disease burden as well as eradicating the disease. Since infectious disease pandemics are a recurring global threat, vaccination has emerged as one of the most promising tools to save millions of lives and reduce infection rates. The World Health Organization reports that immunization protects three million individuals annually. Currently, multi-epitope-based peptide vaccines are a unique concept in vaccine formulation. Epitope-based peptide vaccines utilize small fragments of proteins or peptides (parts of the pathogen), called epitopes, that trigger an adequate immune response against a particular pathogen. However, conventional vaccine designing and development techniques are too cumbersome, expensive, and time-consuming. With the recent advancement in bioinformatics, immunoinformatics, and vaccinomics discipline, vaccine science has entered a new era accompanying a modern, impressive, and more realistic paradigm in designing and developing next-generation strong immunogens. In silico designing and developing a safe and novel vaccine construct involves knowledge of reverse vaccinology, various vaccine databases, and high throughput techniques. The computational tools and techniques directly associated with vaccine research are extremely effective, economical, precise, robust, and safe for human use. Many vaccine candidates have entered clinical trials instantly and are available prior to schedule. In light of this, the present article provides researchers with up-to-date information on various approaches, protocols, and databases regarding the computational designing and development of potent multi-epitope-based peptide vaccines that can assist researchers in tailoring vaccines more rapidly and cost-effectively.

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Functional annotation and sequence-structure characterization of a hypothetical protein putatively involved in carotenoid biosynthesis in microalgae

Cited by 35 publications

References 34 publications

Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

Molecular Characterization and Designing of a Novel Multiepitope Vaccine Construct Against Pseudomonas aeruginosa

Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine

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