Proposing the Promiscuous Protein Structures in JNK1 and JNK3 for Virtual Screening in Pursuit of Potential Leads

Sailapathi, Ananthasri; Murugan, Gopinath; Somarathinam, Kanagasabai; Gunalan, Seshan; Jagadeesan, Rahul; Yoosuf, Niyaz; Sekar, K.; Kothandan, Gugan

doi:10.1021/acsomega.9b03458

Cited by 3 publications

(1 citation statement)

References 22 publications

(31 reference statements)

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“…In this sense, protein homology modelling using online servers and computer software can provide valuable models that help establish hypotheses about protein Tahera Hashimi, Deborah Joyce, Sufia Mohd Nasir, Mas Jaffri Masarudin, Annas Salleh and Sarah Othman function and drive additional experimental effort in the shortest time attainable while being cost-effective (Haddad et al, 2020). Such downstream applications include designing site-directed mutations through primer design and predictions of receptorligand binding for drug targeting (Sailapathi et al, 2020). Freely available sites for molecular docking are LightDock (Jiménez-García et al, 2018), MedusaDock 2.0 (Wang & Dokholyan, 2019), and LeDock (N. Liu & Xu, 2019).…”

Section: D Homology Structure Modellingmentioning

confidence: 99%

Characterisation of the Putative Antigenic Genes of the Outer Membrane Proteins of Pasteurella multocida B:2 Strain PMTB2.1 through in silico Analysis

Hashimi¹,

Joyce²,

Nasir³

et al. 2023

JTAS

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Outer membrane proteins (OMPs), usually found in Gram-negative bacteria, have long been shown to elicit immune responses in infected hosts. This tendency of OMPs to generate immune reactions makes them ideal candidates for vaccine development against pathogenic bacteria. Pasteurella multocida is a Gram-negative pathogen responsible for the economically significant veterinary disease, hemorrhagic septicemia (HS). HS is an endemic and highly fatal disease affecting buffaloes and cattle. In Malaysia, outbreaks of this disease cost about half a million USD each year. Thus, despite current treatment and prevention measures, HS is a prevalent issue that needs to be overcome. Pasteurella multocida subsp. multocida PMTB2.1, a Malaysian strain of the pathogen, has recently had its entire genome sequenced after being isolated from HS outbreaks in the region. Antigenic OMPs from this strain have since been identified and published for further characterisation. LptD, Wza, and TbpA are integral membrane proteins, while Pal is a peripheral membrane protein that has not been characterised in-depth. This study, therefore, aims to analyse these OMPs through in silico methods. First, protein homology modelling was performed using SWISS-MODEL, whereafter, the structures generated were validated using the SWISS-MODEL structure assessment page, PROCHECK, ERRAT, and PROSA programs. The Pal, Wza, and TbpA structures were good models, while the LptD structure was found to be a near-good model based on the validation performed. Analyses using BCPREDS, NetMHCpan4.1, and NetBoLAIIpan1.0 revealed that these four OMPs could potentially elicit humoral and cellular immune responses.

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Section: D Homology Structure Modellingmentioning

confidence: 99%

Characterisation of the Putative Antigenic Genes of the Outer Membrane Proteins of Pasteurella multocida B:2 Strain PMTB2.1 through in silico Analysis

Hashimi¹,

Joyce²,

Nasir³

et al. 2023

JTAS

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Surface chemistry of bovine serum albumin with hematite nanoparticles and its effect on arsenate adsorption

2021

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Environmental contextHematite nanoparticles are efficient adsorbents for proteins and pollutants in environmental and biological systems. Hematite and the protein bovine serum albumin (BSA) were used as models to investigate the surface chemistry and competitive role of BSA in arsenate adsorption. Results show that surface BSA inhibits arsenate adsorption, potentially altering its mobility and bioavailability. AbstractThe surface chemistry of metal oxide nanomaterials controls their health impacts and fate in environmental and biological systems. These systems contain proteins capable of binding to nanoparticles, which forms a protein corona that modifies the surface properties of the nanoparticles and reactivity towards pollutants. Using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, we investigate the adsorption of bovine serum albumin (BSA) and quantify the competitive effect of BSA on the adsorption kinetics of arsenate, AsV, to hematite nanoparticles. Experiments were conducted in the flow mode at pH 7. BSA was first adsorbed on hematite, then AsV was allowed to flow over the BSA/hematite thin film. Adsorption kinetic and thermodynamic parameters were calculated using a modified Langmuir adsorption model for both BSA and AsV. The adsorption thermodynamic model showed that BSA binds through two active sites with a binding energy of –41 kJ mol−1, which corresponds to the spontaneous formation of chemisorbed and physisorbed species. When AsV flowed over the BSA/hematite film, only 11 % of surface BSA was desorbed by AsV. This result highlights the inhibitory effect of BSA for AsV adsorption. Structural analysis of BSA revealed changes to the local conformational geometry upon adsorption to and desorption from hematite nanoparticles. Molecular docking simulations showed that the binding free energy of a modelled hematite nanoparticle towards the BSA surface is –6.8 kcal mol−1 (−28.5 kJ mol−1) owing to the formation of various bonds, which agrees with the adsorption kinetics modelling. Overall, surface BSA inhibits arsenate adsorption and therefore increases its mobility and bioavailability.

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Analysis Interaction of Immunoglobulin G and Immunoglobulin A Against PstS1 as a Basis Specimen Selection for M. tuberculosis Rapid Test Diagnostic Agent

Rahmadani,

Raras,

Arthamin

2023

J. Biomed. Transl. Res.

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Background: The recombinant Ag38 protein developed from a local strain of Mycobacterium tuberculosis has great potential to be used as a sero-diagnosis agent using the antigen rapid test because it has several epitopes that bind to antibodies. However, it is not yet known which antibody Ag38-recombinant binds maximally between IgA and IgG.Objective: The aim of this study is to compare the interaction between IgG and IgA on Ag-38 rec in silico as a basis for the selection of sero-diagnosis agents in the TB rapid test.Methods: The results show that the protein PstS1 has a higher binding sensitivity to IgG based on one of the docking models which shows a docking score of -229.70, a confident score of 0.8312 and RMSD 1.060 A. The ramachandran plot also shows that testing on this model has a protein structure that is good, with disallowed regions [X,X] values of 0.5% (less than 0.8%). The results of this analysis show that the most favored regions are 90.5% with a G-factor of -0.27. The quality of the structure of the 3D mooring model can be said to be good because it fulfills the ideal structure requirements.Conclusion: Ag38-rec antigen M. tuberculosis H37Rv binds to IgG more strongly than IgA.

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Proposing the Promiscuous Protein Structures in JNK1 and JNK3 for Virtual Screening in Pursuit of Potential Leads

Cited by 3 publications

References 22 publications

Characterisation of the Putative Antigenic Genes of the Outer Membrane Proteins of Pasteurella multocida B:2 Strain PMTB2.1 through in silico Analysis

Characterisation of the Putative Antigenic Genes of the Outer Membrane Proteins of Pasteurella multocida B:2 Strain PMTB2.1 through in silico Analysis

Surface chemistry of bovine serum albumin with hematite nanoparticles and its effect on arsenate adsorption

Analysis Interaction of Immunoglobulin G and Immunoglobulin A Against PstS1 as a Basis Specimen Selection for M. tuberculosis Rapid Test Diagnostic Agent

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