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Applying In Silico Approaches for Designing a Chimeric InaV/N-DFPase Protein and Evaluating its Binding with Diisopropyl-Fluorophosphate

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Abstract:

The N-terminal domain of the ice-nucleation protein InaV (InaV-N) of Pseudomonas syringae was applied to display the DFPase on the cell surface. In silico techniques were used to generate a model in order to examine the possibility of DFPase exhibition on the cell surface. The secondary and tertiary structures of a chimeric protein were determined and then, the predicted model was subjected to several repeated cycles of stereochemical evaluation and energy minimization. The homology-modeled structure of the InaV/N-DFPase protein was docked to DFP. The optimized inaV/N-dfpase gene was translated to 519 amino acids. The minimum free energy of the best-predicted secondary structures was formed by RNA molecules (-215.45 kcal/mol). SOPMA analysis results showed that the main helix peak corresponded to the anchor fragment. Validation of the 3D model indicated that 86.1% of amino acid residues were incorporated into the favored regions. The moldock score was 360.22 for DFP. Results of this study indicated that according to in silico analysis, all of these findings were effective in targeting DFPase.

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Periodical:
International Letters of Natural Sciences (Volume 75)
Pages:
41-51
Citation:
H. Allahyari et al., "Applying In Silico Approaches for Designing a Chimeric InaV/N-DFPase Protein and Evaluating its Binding with Diisopropyl-Fluorophosphate", International Letters of Natural Sciences, Vol. 75, pp. 41-51, 2019
Online since:
May 2019
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[1] D. Cooney, R. Handschumacher, L-asparaginase and L-asparagine metabolism, Annu. Rev. Pharmacol. 10(1) (1970) 421-440.

DOI: https://doi.org/10.1146/annurev.pa.10.040170.002225

[2] M. Jokanovic, Biotransformation of organophosphorus compounds, Toxicology. 166(3) (2001) 139-160.

[3] J.M. Kuo, M.Y. Chae, F.M. Raushel, Perturbations to the active site of phosphotriesterase, Biochemistry. 36(8) (1997) 1982-1988.

DOI: https://doi.org/10.1021/bi962099l

[4] Z. Rezaeeyan et al., High carotenoid production by a halotolerant bacterium, Kocuria sp. strain QWT-12 and anticancer activity of its carotenoid, EXCLI J. 16 (2017) 840-851.

[5] M. Cycon, M. Wojcik, Z. Piotrowska-Seget, Biodegradation of the organophosphorus insecticide diazinon by Serratia sp. and Pseudomonas sp. and their use in bioremediation of contaminated soil, Chemosphere. 76(4) (2009) 494-501.

DOI: https://doi.org/10.1016/j.chemosphere.2009.03.023

[6] H. Yazdi et al., The Effects of some Physicochemical Stresses on Escherichia coli O157: H7 as Clinical Pathogenic Bacteria, Int. J. Agric. Biol. 18(6) (2016) 1237‒1241.

DOI: https://doi.org/10.17957/ijab/15.0237

[7] H. Tebyanian et al., Effect of Physical and Chemical Factors in Production of Alkaline Protease Enzyme by Bacillus Strains, ILNS. 71 (2018) 10-16.

[8] N.A. Burgess-Brown et al., Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study, Protein Expression and Purification. 59(1) (2008) 94-102.

DOI: https://doi.org/10.1016/j.pep.2008.01.008

[9] C.M. Theriot, A.M. Grunden, Hydrolysis of organophosphorus compounds by microbial enzymes, Appl. Microbiol Biotechnol. 89(1) (2011) 35-43.

DOI: https://doi.org/10.1007/s00253-010-2807-9

[10] T. Wille et al., Detoxification of G- and V-series nerve agents by the phosphotriesterase OpdA, Biocatalysis and Biotransformation. 30 (2012) 203-208.

DOI: https://doi.org/10.3109/10242422.2012.661724

[11] T.C. Cheng, S.P. Harvey, A.N. Stroup, Purification and Properties of a Highly Active Organophosphorus Acid Anhydrolase from Alteromonas undina, Appl. Environ. Microbiol. 59(9) (1993) 3138-3140.

[12] T.C. Cheng et al., G-type nerve agent decontamination by Alteromonas prolidase, Ann N Y Acad Sci. 864 (1998) 253-258.

[13] A.L. Simonian et al., Enzyme-based biosensor for the direct detection of fluorine-containing organophosphates, Anal Chim Acta. 442(1) (2001) 15-23.

[14] C.S. McDaniel, L.L. Harper, J.R. Wild, Cloning and sequencing of a plasmid-borne gene (opd) encoding a phosphotriesterase, J. Bacteriol. 170(5) (1988) 2306-2311.

DOI: https://doi.org/10.1128/jb.170.5.2306-2311.1988

[15] M. Shimazu et al., Cell surface display of organophosphorus hydrolase in Pseudomonas putida using an ice-nucleation protein anchor, Biotechnol. Prog. 19(5) (2003) 1612-1614.

DOI: https://doi.org/10.1021/bp0340640

[16] C. Huang et al., Spatiotemporal analyses of osteogenesis and angiogenesis via intravital imaging in cranial bone defect repair, J. Bone Mine.\r. Res. 30(7) (2015) 1217-1230.

DOI: https://doi.org/10.1002/jbmr.2460

[17] Z. Liu et al., Simultaneous degradation of organophosphates and 4-substituted phenols by Stenotrophomonas species LZ-1 with surface-displayed organophosphorus hydrolase, J. Agric Food Chem. 57(14) (2009) 6171-6177.

DOI: https://doi.org/10.1021/jf804008j

[18] C. Yang et al., Surface display of MPH on Pseudomonas putida JS444 using ice nucleation protein and its application in detoxification of organophosphates, Biotechnol. Bioeng. 99(1) (2008) 30-37.

DOI: https://doi.org/10.1002/bit.21535

[19] C. Li et al., Presentation of functional organophosphorus hydrolase fusions on the surface of Escherichia coli by the AIDA-I autotransporter pathway, Biotechnol. Bioeng. 99(2) (2008) 485-490.

DOI: https://doi.org/10.1002/bit.21548

[20] H. Shi, W. Wen Su, Display of green fluorescent protein on Escherichia coli cell surface, Enzyme Microb. Technol. 28(1) (2001) 25-34.

DOI: https://doi.org/10.1016/s0141-0229(00)00281-7

[21] Z. Yang et al., Novel bacterial surface display systems based on outer membrane anchoring elements from the marine bacterium Vibrio anguillarum, Appl. Environ. Microbiol. 74(14) (2008) 4359-4365.

DOI: https://doi.org/10.1128/aem.02499-07

[22] M. Saadi, A. Karkhah, H.R. Nouri, Development of a multi-epitope peptide vaccine inducing robust T cell responses against brucellosis using immunoinformatics based approaches, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 51 (2017) 227-234.

DOI: https://doi.org/10.1016/j.meegid.2017.04.009

[23] F. Shakeri et al., Introduction of fungal necrosis inducing phytotoxin for biocontrol of Sinapis arvensis as a common weed in Iran, J. Anim. Plant Sci. 27(5) (2017) 1702-1710.

[24] M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research. 31(13) (2003) 3406-3415.

DOI: https://doi.org/10.1093/nar/gkg595

[25] C. Yang et al., Cotranslocation of methyl parathion hydrolase to the periplasm and of organophosphorus hydrolase to the cell surface of Escherichia coli by the Tat pathway and ice nucleation protein display system, Appl. Environ. Microbiol. 76(2) (2010) 434-440.

DOI: https://doi.org/10.1128/aem.02162-09

[26] S.Y. Lee, J.H. Choi, Z. Xu, Microbial cell-surface display, Trends Biotechnol. 21(1) (2003) 45-52.

[27] A. Kondo et al., Applications of yeast cell-surface display in bio-refinery, Recent Pat Biotechnol. 4(3) (2010) 226-234.

[28] M. Desvaux et al., Protein cell surface display in Gram-positive bacteria: from single protein to macromolecular protein structure, FEMS Microbiol. Lett. 256(1) (2006) 1-15.

DOI: https://doi.org/10.1111/j.1574-6968.2006.00122.x

[29] Q. Zhang et al., [Construction of cell surface display system in lactic acid bacteria by using ice nucleation protein], Wei Sheng Wu Xue Bao. 53(4) (2013) 397-402.

[30] S. Khodi, A.M. Latifi, Comparison of the organophosphorus hydrolase surface display by using InaVN and Lpp-OmpA systems in Escherichia coli, J. Microbiol. Biotechnol. (2013).

DOI: https://doi.org/10.4014/jmb.1309.09066

[31] Q. Li et al., Molecular characterization of an ice nucleation protein variant (inaQ) from Pseudomonas syringae and the analysis of its transmembrane transport activity in Escherichia coli, Int. J. Biol. Sci. 8(8) (2012) 1097.

DOI: https://doi.org/10.7150/ijbs.4524

[32] N.M. Alto et al., Bioinformatic design of A-kinase anchoring protein-in silico: a potent and selective peptide antagonist of type II protein kinase A anchoring, PNAS. 100(8) (2003) 4445-4450.

DOI: https://doi.org/10.1073/pnas.0330734100

[33] H. Luo et al., In silico identification of potential inhibitors targeting Streptococcus mutans sortase A, Int. J. Oral. Sci. 9(1) (2017) 53.

[34] E.E. Murray et al., Analysis of unstable RNA transcripts of insecticidal crystal protein genes of Bacillus thuringiensis in transgenic plants and electroporated protoplasts, Plant Mol. Biol. 16(6) (1991) 1035-1050.

DOI: https://doi.org/10.1007/bf00016075

[35] P. Jarvis, F. Belzile, C. Dean, Inefficient and incorrect processing of the Ac transposase transcript in iae1 and wild-type Arabidopsis thaliana, Plant J. 11(5) (1997) 921-931.

DOI: https://doi.org/10.1046/j.1365-313x.1997.11050921.x

[36] J. Haseloff et al., Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly, Proc. Natl. Acad. Sci. U S A. 94(6) (1997) 2122-2127.

DOI: https://doi.org/10.1073/pnas.94.6.2122

[37] A. Karkhah, M. Saadi, H.R. Nouri, In silico analyses of heat shock protein 60 and calreticulin to designing a novel vaccine shifting immune response toward T helper 2 in atherosclerosis, Computational Biology and Chemistry. 67 (2017) 244-254.

DOI: https://doi.org/10.1016/j.compbiolchem.2017.01.011
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