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Rout M, Dey S, Mishra S, Panda S, Singh MK, Sinha R, Dehury B, Pati S. Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus. J Biomol Struct Dyn 2024; 42:3935-3948. [PMID: 37221882 DOI: 10.1080/07391102.2023.2216290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/16/2023] [Indexed: 05/25/2023]
Abstract
Monkeypox virus (MPXV) outbreak is a serious public health concern that requires international attention. P37 of MPXV plays a pivotal role in DNA replication and acts as one of the promising targets for antiviral drug design. In this study, we intent to screen potential analogs of existing FDA approved drugs of MPXV against P37 using state-of-the-art machine learning and computational biophysical techniques. AlphaFold2 guided all-atoms molecular dynamics simulations optimized P37 structure is used for molecular docking and binding free energy calculations. Similar to members of Phospholipase-D family , the predicted P37 structure also adopts a β-α-β-α-β sandwich fold, harbouring strongly conserved HxKxxxxD motif. The binding pocket comprises of Tyr48, Lys86, His115, Lys117, Ser130, Asn132, Trp280, Asn240, His325, Lys327 and Tyr346 forming strong hydrogen bonds and dense hydrophobic contacts with the screened analogs and is surrounded by positively charged patches. Loops connecting the two domains and C-terminal region exhibit high degree of flexibility. In some structural ensembles, the partial disorderness in the C-terminal region is presumed to be due to its low confidence score, acquired during structure prediction. Transition from loop to β-strands (244-254 aa) in P37-Cidofovir and its analog complexes advocates the need for further investigations. MD simulations support the accuracy of the molecular docking results, indicating the potential of analogs as potent binders of P37. Taken together, our results provide preferable understanding of molecular recognition and dynamics of ligand-bound states of P37, offering opportunities for development of new antivirals against MPXV. However, the need of in vitro and in vivo assays for confirmation of these results still persists.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Suchanda Dey
- Biomics and Biodiversity Lab, Siksha 'O' Anusandhan (deemed to be) University, Bhubaneswar, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Rohan Sinha
- Computer Science, National Institute of Technology Patna, Patna, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
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Panda S, Rout M, Mishra S, Turuk J, Pati S, Dehury B. Molecular docking and MD simulations reveal protease inhibitors block the catalytic residues in Prp8 intein of Aspergillus fumigatus: a potential target for antimycotics. J Biomol Struct Dyn 2023:1-16. [PMID: 38149850 DOI: 10.1080/07391102.2023.2298735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023]
Abstract
Resistance to azoles and amphotericin B especially in Aspergillus fumigatus is a growing concern towards the treatment of invasive fungal infection. At this critical juncture, intein splicing would be a productive, and innovative target to establish therapies against resistant strains. Intein splicing is the central event for the activation of host protein, essential for the growth and survival of various microorganisms including A. fumigatus. The splicing process is a four-step protease-like nucleophilic cascade. Thus, we hypothesise that protease inhibitors would successfully halt intein splicing and potentially restrict the growth of the aforementioned pathogen. Using Rosetta Fold and molecular dynamics simulations, we modelled Prp8 intein structure; resembling classic intein fold with horse shoe shaped splicing domain. To fully comprehend the active site of Afu Prp8 intein, C1, T62, H65, H818, N819 from intein sequences and S820, the first C-extein residue are selected. Molecular docking shows that two FDA-approved drugs, i.e. Lufotrelvir and Remdesivir triphosphate efficiently interact with Prp8 intein from the assortment of 212 protease inhibitors. MD simulation portrayed that Prp8 undergoes conformational change upon ligand binding, and inferred the molecular recognition and stability of the docked complexes. Per-residue decomposition analysis confirms the importance of F: block R802, V803, and Q807 binding pocket in intein splicing domain towards recognition of inhibitors, along with active site residues through strong hydrogen bonds and hydrophobic contacts. However, in vitro and in vivo assays are required to confirm the inhibitory action on Prp8 intein splicing; which may pave the way for the development of new antifungals for A. fumigatus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Jyotirmayee Turuk
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sanghamitra Pati
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
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Rout M, Mishra S, Dey S, Singh MK, Dehury B, Pati S. Exploiting the potential of natural polyphenols as antivirals against monkeypox envelope protein F13 using machine learning and all-atoms MD simulations. Comput Biol Med 2023; 162:107116. [PMID: 37302336 PMCID: PMC10239311 DOI: 10.1016/j.compbiomed.2023.107116] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/12/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
The re-emergence of monkeypox (MPX), in the era of COVID-19 pandemic is a new global menace. Regardless of its leniency, there are chances of MPX expediting severe health deterioration. The role of envelope protein, F13 as a critical component for production of extracellular viral particles makes it a crucial drug target. Polyphenols, exhibiting antiviral properties have been acclaimed as an effective alternative to the traditional treatment methods for management of viral diseases. To facilitate the development of potent MPX specific therapeutics, herein, we have employed state-of-the-art machine learning techniques to predict a highly accurate 3-dimensional structure of F13 as well as identify binding hotspots on the protein surface. Additionally, we have effectuated high-throughput virtual screening methodology on 57 potent natural polyphenols having antiviral activities followed by all-atoms molecular dynamics (MD) simulations, to substantiate the mode of interaction of F13 protein and polyphenol complexes. The structure-based virtual screening based on Glide SP, XP and MM/GBSA scores enables the selection of six potent polyphenols having higher binding affinity towards F13. Non-bonded contact analysis, of pre- and post- MD complexes propound the critical role of Glu143, Asp134, Asn345, Ser321 and Tyr320 residues in polyphenol recognition, which is well supported by per-residue decomposition analysis. Close-observation of the structural ensembles from MD suggests that the binding groove of F13 is mostly hydrophobic in nature. Taken together, this structure-based analysis from our study provides a lead on Myricetin, and Demethoxycurcumin, which may act as potent inhibitors of F13. In conclusion, our study provides new insights into the molecular recognition and dynamics of F13-polyphenol bound states, offering new promises for development of antivirals to combat monkeypox. However, further in vitro and in vivo experiments are necessary to validate these results.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Suchanda Dey
- Biomics and Biodiversity Lab, Siksha 'O' Anusandhan (deemed to be) University, Kalinga Nagar, Ghatikia, Bhubaneswar, 751003, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, 122052, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
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Khorramnejad A, Bel Y, Talaei-Hassanloui R, Escriche B. Activation of Bacillus thuringiensis Cry1I to a 50 kDa stable core impairs its full toxicity to Ostrinia nubilalis. Appl Microbiol Biotechnol 2022; 106:1745-1758. [PMID: 35138453 PMCID: PMC8882101 DOI: 10.1007/s00253-022-11808-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/28/2021] [Accepted: 01/26/2022] [Indexed: 11/30/2022]
Abstract
Bacillus thuringiensis Cry1I insecticidal proteins are structurally similar to other three-domain Cry proteins, although their size, activity spectrum, and expression at the stationary phase are unique among other members of the Cry1 family. The mode of action of Cry1 proteins is not completely understood but the existence of an activation step prior to specific binding is widely accepted. In this study, we attempted to characterize and determine the importance of the activation process in the mode of action of Cry1I, as Cry1Ia protoxin or its partially processed form showed significantly higher toxicity to Ostrinia nubilalis than the fully processed protein either activated with trypsin or with O. nubilalis midgut juice. Oligomerization studies showed that Cry1Ia protoxin, in solution, formed dimers spontaneously, and the incubation of Cry1Ia protoxin with O. nubilalis brush border membrane vesicles (BBMV) promoted the formation of dimers of the partially processed form. While no oligomerization of fully activated proteins after incubation with BBMV was detected. The results of the in vitro competition assays showed that both the Cry1Ia protoxin and the approx. 50 kDa activated proteins bind specifically to the O. nubilalis BBMV and compete for the same binding sites. Accordingly, the in vivo binding competition assays show a decrease in toxicity following the addition of an excess of 50 kDa activated protein. Consequently, as full activation of Cry1I protein diminishes its toxicity against lepidopterans, preventing or decelerating proteolysis might increase the efficacy of this protein in Bt-based products. KEY POINTS: • Processing Cry1I to a 50 kDa stable core impairs its full toxicity to O. nubilalis • Partially processed Cry1Ia protoxin retains the toxicity of protoxin vs O. nubilalis • Protoxin and its final processed forms compete for the same functional binding sites.
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Affiliation(s)
- Ayda Khorramnejad
- Laboratory of Biotechnological Control of Pests, Departamento de Genética, Instituto BioTecMed, Universitat de València, Burjassot, València, Spain.,Laboratory of Biological Control of Pest, Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Yolanda Bel
- Laboratory of Biotechnological Control of Pests, Departamento de Genética, Instituto BioTecMed, Universitat de València, Burjassot, València, Spain.
| | - Reza Talaei-Hassanloui
- Laboratory of Biological Control of Pest, Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Baltasar Escriche
- Laboratory of Biotechnological Control of Pests, Departamento de Genética, Instituto BioTecMed, Universitat de València, Burjassot, València, Spain.
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Rout AK, Paramanik S, Dehury B, Acharya V, Swain HS, Pradhan SK, Behera B, Pati SK, Behera BK, Das BK. Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches. J Biomol Struct Dyn 2019; 38:3687-3699. [DOI: 10.1080/07391102.2019.1666742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sunanda Paramanik
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Budheswar Dehury
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Varsha Acharya
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Himanshu Sekhar Swain
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore, India
| | - Soumen Kumar Pati
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
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Wei S, Chelliah R, Park BJ, Kim SH, Forghani F, Cho MS, Park DS, Jin YG, Oh DH. Differentiation of Bacillus thuringiensis From Bacillus cereus Group Using a Unique Marker Based on Real-Time PCR. Front Microbiol 2019; 10:883. [PMID: 31114555 PMCID: PMC6503103 DOI: 10.3389/fmicb.2019.00883] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
The efficiency of a novel biomarker (the transcriptional regulator, XRE) was tested and evaluated in differentiating Bacillus thuringiensis from Bacillus cereus group species in environmental and spiked samples based on PCR and real-time PCR. Totally 120 strains, representing two bacterial groups, B. cereus group and non-Bacillus sp., were used to evaluate the performance of XRE and crystal protein (cry2, an existing biomarker). Further, three diverse samples (kimbap, lettuce, and spinach) were inoculated with B. thuringiensis and prominent biomarkers XRE and cry2 were used as targets. Direct analysis of the detection results for the pure cultures of B. cereus group wild-types, references and type strains revealed an accuracy rate of 97.5% targeting XRE, and 83.3% targeting cry2. The real-time PCR was constructed with a R 2-value of 0.993. For the artificially contaminated samples, a concentration of 103 CFU/g of B. thuringiensis in spiked food samples could be detected using real-time PCR targeting XRE. A good performance was obtained with XRE in discriminating B. thuringiensis from B. cereus groups, as well as detecting B. thuringiensis in spiked food samples with PCR or real-time PCR. Therefore, this real-time PCR targeting XRE can be used as a dependable and promising tool to identify B. thuringiensis in foods.
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Affiliation(s)
- Shuai Wei
- Department of Medical Biomaterials Engineering, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Byung-Jae Park
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Se-Hun Kim
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Fereidoun Forghani
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, United States
| | - Min Seok Cho
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Dong-Suk Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Yong-Guo Jin
- National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
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Chelliah R, Wei S, Park BJ, Rubab M, Banan-Mwine Dalirii E, Barathikannan K, Jin YG, Oh DH. Whole genome sequence of Bacillus thuringiensis ATCC 10792 and improved discrimination of Bacillus thuringiensis from Bacillus cereus group based on novel biomarkers. Microb Pathog 2019; 129:284-297. [DOI: 10.1016/j.micpath.2019.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 11/17/2022]
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Rathinam M, Kesiraju K, Singh S, Thimmegowda V, Rai V, Pattanayak D, Sreevathsa R. Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF. Toxins (Basel) 2019; 11:toxins11030143. [PMID: 30832332 PMCID: PMC6468889 DOI: 10.3390/toxins11030143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 11/16/2022] Open
Abstract
Bacillus thuringiensis insecticidal proteins (Bt ICPs) are reliable and valuable options for pest management in crops. Protein engineering of Bt ICPs is a competitive alternative for resistance management in insects. The primary focus of the study was to reiterate the translational utility of a protein-engineered chimeric Cry toxin, Cry1AcF, for its broad spectrum insecticidal efficacy using molecular modeling and docking studies. In-depth bioinformatic analysis was undertaken for structure prediction of the Cry toxin as the ligand and aminopeptidase1 receptors (APN1) from Helicoverpa armigera (HaAPN1) and Spodoptera litura (SlAPN1) as receptors, followed by interaction studies using protein-protein docking tools. The study revealed feasible interactions between the toxin and the two receptors through H-bonding and hydrophobic interactions. Further, molecular dynamics simulations substantiated the stability of the interactions, proving the broad spectrum efficacy of Cry1AcF in controlling H. armigera and S. litura. These findings justify the utility of protein-engineered toxins in pest management.
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Affiliation(s)
- Maniraj Rathinam
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Karthik Kesiraju
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Shweta Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Vinutha Thimmegowda
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Vandna Rai
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Debasis Pattanayak
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Rohini Sreevathsa
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
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Plácido A, Coelho A, Abreu Nascimento L, Gomes Vasconcelos A, Fátima Barroso M, Ramos-Jesus J, Costa V, das Chagas Alves Lima F, Delerue-Matos C, Martins Ramos R, Marani MM, Roberto de Souza de Almeida Leite J. Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three-dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms. Proteins 2017; 85:1248-1257. [PMID: 28316108 DOI: 10.1002/prot.25285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/24/2017] [Accepted: 03/08/2017] [Indexed: 11/10/2022]
Abstract
Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody-peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248-1257. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexandra Plácido
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - Andreia Coelho
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - Lucas Abreu Nascimento
- Grupo de Química Quântica Computacional e Planejamento de Fármaco, GQQCPF, Departamento de Química, Universidade Estadual do Piauí, UESPI, Teresina, Brasil.,Laboratório de Pesquisa em Sistemas de Informação, LaPeSI, Departamento de Informação, Ambiente, Saúde e Produção Alimentícia, Instituto Federal do Piauí, Teresina, Brasil
| | - Andreanne Gomes Vasconcelos
- Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Biotec, Campus Ministro Reis Velloso, Universidade Federal do Piauí, Parnaíba, Brasil
| | - Maria Fátima Barroso
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - Joilson Ramos-Jesus
- Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Biotec, Campus Ministro Reis Velloso, Universidade Federal do Piauí, Parnaíba, Brasil
| | - Vladimir Costa
- Laboratório de Pesquisas em Leishmanioses, Instituto de Doenças Tropicais Natan Portela, IDTNP, Teresina, Piauí, Brasil
| | - Francisco das Chagas Alves Lima
- Grupo de Química Quântica Computacional e Planejamento de Fármaco, GQQCPF, Departamento de Química, Universidade Estadual do Piauí, UESPI, Teresina, Brasil
| | - Cristina Delerue-Matos
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - Ricardo Martins Ramos
- Grupo de Química Quântica Computacional e Planejamento de Fármaco, GQQCPF, Departamento de Química, Universidade Estadual do Piauí, UESPI, Teresina, Brasil.,Laboratório de Pesquisa em Sistemas de Informação, LaPeSI, Departamento de Informação, Ambiente, Saúde e Produção Alimentícia, Instituto Federal do Piauí, Teresina, Brasil
| | - Mariela M Marani
- IPEEC-CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
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Costa J, Marani MM, Grazina L, Villa C, Meira L, Oliveira MBPP, Leite JRSA, Mafra I. Peptide selection and antibody generation for the prospective immunorecognition of Cry1Ab16 protein of transgenic maize. Food Chem 2017; 231:340-347. [PMID: 28450016 DOI: 10.1016/j.foodchem.2017.03.154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 03/13/2017] [Accepted: 03/29/2017] [Indexed: 10/19/2022]
Abstract
The introduction of genes isolated from different Bacillus thuringiensis strains to express Cry-type toxins in transgenic crops is a common strategy to confer insect resistance traits. This work intended to extensively in silico analyse Cry1A(b)16 protein for the identification of peptide markers for the biorecognition of transgenic crops. By combining two different strategies based on several bioinformatic tools for linear epitope prediction, a set of seven peptides was successfully selected as potential Cry1A(b)16 immunogens. For the prediction of conformational epitopes, Cry1A(b)16 models were built on the basis of three independent templates of homologue proteins of Cry1A(a) and Cry1A(c) using an integrated approach. PcH_736-746 and PcH_876-886 peptides were selected as the best candidates, being synthesised and used for the production of polyclonal antibodies. To the best of our knowledge, this is the first attempt of selecting and defining linear peptides as immunogenic markers of Cry1A(b)-type toxins in transgenic maize.
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Affiliation(s)
- Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; IPEEC-CONICET, Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina.
| | - Mariela M Marani
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; IPEEC-CONICET, Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina.
| | - Liliana Grazina
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Liliana Meira
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | | | - José R S A Leite
- Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Biotec, Campus de Parnaíba, Universidade Federal do Piauí, Parnaíba, Brazil; Area de Morfologia, Faculdade de Medicina, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; IPEEC-CONICET, Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
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Buzatto D, de Castro França S, Zingaretti SM. CryGetter: a tool to automate retrieval and analysis of Cry protein data. BMC Bioinformatics 2016; 17:325. [PMID: 27578522 PMCID: PMC5004295 DOI: 10.1186/s12859-016-1207-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/24/2016] [Indexed: 11/30/2022] Open
Abstract
Background For many years, the use of chemical agents to control crop pests has been degrading the environment, bringing problems to humans and all living things. An alternative to deal with the pests is the use of biopesticides, biological agents capable of controlling these harmful organisms. One kind of biopesticide is Bacillus thuringiensis, a Gram-positive bacterium that synthesizes a protein that, when ingested by the pests, kills them and does not harm other species. Results Since the economical importance of Bacillus thuringiensis and its proteins significance, this work presents a software tool, called CryGetter, that is capable of retrieving data related to these proteins, store it and present it in a user friendly manner. The tool also aims to align the protein sequences and generate reports containing some statistical data concerning the alignments that were made. Conclusions CryGetter was created to help researchers of Bacillus thuringiensis and its proteins to speed up their data retrieval and analysis, allowing them to generate more accurate results. In this sense, the tool circumvents the error prone task of manually getting all the necessary data and processing them in various software systems to get the same result as CryGetter gets in a unique semiautomatic environment.
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Affiliation(s)
- David Buzatto
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo - IFSP, Câmpus São João da Boa Vista, Acesso Dr. João Batista Merlin, s/n, Jardim Itália, São João da Boa Vista, 13872-551, SP, Brazil.
| | - Suzelei de Castro França
- Universidade de Ribeirão Preto - UNAERP, Av. Costábile Romano, 2201, Ribeirânia, Ribeirão Preto, 14096-000, SP, Brazil
| | - Sônia Marli Zingaretti
- Universidade de Ribeirão Preto - UNAERP, Av. Costábile Romano, 2201, Ribeirânia, Ribeirão Preto, 14096-000, SP, Brazil
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