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      The involvement of CYP1A2 in biodegradation of dioxins in pigs

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          Abstract

          2,3,7,8-tetrachlorodibenzo- p-dioxin (TCDD) is one of the most harmful chemicals showing resistance to biodegradation. The majority of TCDD effects is mediated by the aryl hydrocarbon receptor (AhR) pathway. TCDD binding to AhR results in the activation of cytochrome P450 enzymes (CYP1A1, CYP1A2, CYP1B1) involved in dioxin biodegradation. The goal of the study was to explore the potential role of CYP1A2 in the metabolism of TCDD. We investigated a molecular structure of CYP1A2 and the binding selectivity and affinity between the pig CYP1A2 and: 1/ DiCDD or TCDD (dioxins differing in toxicity and biodegradability) or 2/ their selected metabolites. pCYP1A2 demonstrated higher affinity towards DiCDD and TCDD than other pCYP1 enzymes. All dioxin-pCYP1A2 complexes were found to be stabilized by hydrophobic interactions. The calculated distances between the heme oxygen and the dioxin carbon nearest to the oxygen, reflecting the hydroxylating potential of CYP1A2, were higher than in other pCYP1 enzymes. The distances between the heme iron and the nearest dioxin carbon exceeded 5 Å, a distance sufficient to allow the metabolites to leave the active site. However, the molecular dynamics simulations revealed that two access channels of CYP1A2 were closed upon binding the majority of the examined dioxins. Moreover, the binding of dioxin metabolites did not promote opening of channel S–an exit for hydroxylated products. It appears that the undesired changes in the behavior of access channels prevail over the hydroxylating potential of CYP1A2 towards TCDD and the favorable distances, ultimately trapping the metabolites at the enzyme’s active site.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

            AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.
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              AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.

              We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique. (c) 2009 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: Funding acquisitionRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Formal analysisRole: Writing – original draftRole: Writing – review & editing
                Role: Funding acquisitionRole: Project administrationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                26 May 2022
                2022
                : 17
                : 5
                : e0267162
                Affiliations
                [1 ] Laboratory of Molecular Diagnostics, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
                [2 ] Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
                [3 ] Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
                Brooklyn College of the City University of New York, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0003-2287-3243
                https://orcid.org/0000-0002-0380-0156
                https://orcid.org/0000-0002-1807-6148
                https://orcid.org/0000-0002-6896-5023
                Article
                PONE-D-21-34399
                10.1371/journal.pone.0267162
                9135293
                35617319
                e14b1de0-c64a-4ee1-b60c-97140da1c9b2
                © 2022 Swigonska et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 November 2021
                : 29 March 2022
                Page count
                Figures: 8, Tables: 4, Pages: 22
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100004281, Narodowe Centrum Nauki;
                Award ID: 2016/21/N/NZ9/02320
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004442, Narodowym Centrum Nauki;
                Award ID: 2012/05/B/NZ9/03333
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004569, Ministerstwo Nauki i Szkolnictwa Wyższego;
                Award ID: 528.0206.0806
                Funded by: funder-id http://dx.doi.org/10.13039/501100011089, Infrastruktura PL-Grid;
                Award Recipient :
                This study was supported by National Science Centre, Poland (2016/21/N/NZ9/02320, 2012/05/B/NZ9/03333) and The Ministry of Science and Higher Education in Poland (UWM No. 528.0206.0806). This research was supported in part by PLGrid Infrastructure. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Metabolism
                Metabolites
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzyme Chemistry
                Enzyme Metabolism
                Biology and Life Sciences
                Biochemistry
                Proteins
                Post-Translational Modification
                Heme
                Physical Sciences
                Chemistry
                Chemical Elements
                Oxygen
                Physical Sciences
                Physics
                Thermodynamics
                Free Energy
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Biology and Life Sciences
                Bioengineering
                Biotechnology
                Applied Microbiology
                Biodegradation
                Engineering and Technology
                Bioengineering
                Biotechnology
                Applied Microbiology
                Biodegradation
                Biology and Life Sciences
                Microbiology
                Applied Microbiology
                Biodegradation
                Biology and Life Sciences
                Bioengineering
                Biotechnology
                Environmental Biotechnology
                Biodegradation
                Engineering and Technology
                Bioengineering
                Biotechnology
                Environmental Biotechnology
                Biodegradation
                Physical Sciences
                Chemistry
                Computational Chemistry
                Molecular Dynamics
                Custom metadata
                All relevant data are within the paper, its Supporting Information files, and in GenBank under the following accession number: AIY35109.1.

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