B-cell and T-cell epitope identification with stability analysis of AI-2 import ATP-binding cassette LsrA from S. typhi In silico approach

Vijayababu, Princy; Samykannu, Gopinath; Antonyraj, Christian Bharathi; Narayanan, Shridhar; Ahamed, Syed Ibrahim Basheer; Perumal, Perumal; Shanmughavel, P.

doi:10.1016/j.micpath.2018.08.012

Cited by 3 publications

(1 citation statement)

References 48 publications

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“…Approximately 60% of membrane proteins were used as a drug targets in the pharmaceutical industries for several disease. Although, the importance of membrane proteins in cell function, extraordinary deficit of membrane protein structures is largely due to the insolubility of membrane proteins in aqueous solution [1,[5], [6], [7]]. Membrane proteins were consisting of more hydrophobic patches on their surfaces that enable the proteins to occupy the hydrophobic interior of a lipid bilayer in a membrane [8,9].…”

Section: Introductionmentioning

confidence: 99%

Structural investigation of APRs to improve the solubility of outer membrane protease (PgtE) from Salmonella enterica serotype typhi- A multi-constraint approach

Samykannu

Vijayababu

Antonyraj

et al. 2020

Biochemistry and Biophysics Reports

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Outer membrane proteins were playing a crucial role on the several functions controlled by cell membranes even though they are not naturally expressed at higher levels. In order to obtain biologically active protein, the denaturation of these inclusion bodies must be optimized using chaotropic agents. Hence, this study focuses on improving the yield of Outer Membrane Protease (PgtE) from Salmonella enterica serotype Typhi (S. Typhi) using chaotropes and additives. Denaturation methods were tried with various pH, detergents, and reducing agents were used to optimize the solubility of PgtE with biologically active form. Due to the aggregation, we failed to achieve the maximum yield of PgtE. Consequently, we predicted 9 Aggregation Prone Regions (APRs) in PgtE, which are mutated by known structural Gatekeepers. We calculated the Aggregation Index (AI) of PgtE with 10 mM of aspartic acid as an additive in optimized buffer. In addition, the mutations at specific positions within the protein structure can act as APRs suppressors without affecting protein stability with CABS flex dynamics. The multiple sequence analysis demonstrate that aspartic acid is appropriate denaturing additive for other Gram-negative pathogens of Omptin family.

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Section: Introductionmentioning

confidence: 99%

Structural investigation of APRs to improve the solubility of outer membrane protease (PgtE) from Salmonella enterica serotype typhi- A multi-constraint approach

Samykannu

Vijayababu

Antonyraj

et al. 2020

Biochemistry and Biophysics Reports

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Computer aided novel antigenic epitopes selection from the outer membrane protein sequences of Aeromonas hydrophila and its analyses

Bhattacharya

Sharma

et al. 2020

Infection, Genetics and Evolution

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Using immunoinformatic and reverse vaccinology approach epitope-based Vaccine design for three Vibrio sp

Baradia

Mukherjee

2023

Preprint

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Aquaculture is a rapidly growing industry both in India and globally. After Carps, Tilapia is the most cultured fish in the industry. Due to stress and overexploitation of the aquatic ecosystem, there has been rise and propagation of variety of diseases which is a major bottleneck for the industry. Bacterial diseases particularly Vibriosis caused by V. vulnificus, V. harveyi and V. alginolyticus is of great concern as it causes severe illness in humans along with the aquatic organisms. Using reverse vaccinology technique, arranging the epitopes present in OMPs of V. vulnificus, V. harveyi and V. alginolyticus with respect to MHC-I, MHC-II, T-cell and B-cell with the help of advanced bio-computational techniques, it is predicted that YTSTDNFAV, QSIQGNTMN and SQLCIAISL might be potential vaccine candidates elucidating both humoral and cell-mediated immune response. A multi-epitope vaccine is also designed to target the three microbes together by linking the peptide sequences using amino acid linker GPGPG. The cholera toxin B subunit was added in the adjuvant in the N-terminal side using EAAAK linker. Analysis of the multi-epitope vaccine candidate showed that it has all the properties of a potential robust vaccine including antigenic, immunogenic, soluble and thermostable.

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B-cell and T-cell epitope identification with stability analysis of AI-2 import ATP-binding cassette LsrA from S. typhi In silico approach

Cited by 3 publications

References 48 publications

Structural investigation of APRs to improve the solubility of outer membrane protease (PgtE) from Salmonella enterica serotype typhi- A multi-constraint approach

Structural investigation of APRs to improve the solubility of outer membrane protease (PgtE) from Salmonella enterica serotype typhi- A multi-constraint approach

Computer aided novel antigenic epitopes selection from the outer membrane protein sequences of Aeromonas hydrophila and its analyses

Using immunoinformatic and reverse vaccinology approach epitope-based Vaccine design for three Vibrio sp

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