Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies.

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  • Additional Information
    • Source:
      Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X (Electronic) Linking ISSN: 2218273X NLM ISO Abbreviation: Biomolecules Subsets: MEDLINE
    • Publication Information:
      Original Publication: Basel, Switzerland : MDPI, 2011-
    • Subject Terms:
      Lipoxygenases*/chemistry ; Lipoxygenases*/genetics ; Diatoms*/genetics; Oxylipins ; Phylogeny ; Molecular Docking Simulation ; Ecosystem ; Computational Biology
    • Abstract:
      Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms' lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity.
    • References:
      Biochim Biophys Acta. 2004 Nov 8;1686(1-2):100-7. (PMID: 15522826)
      Int J Mol Sci. 2023 Aug 19;24(16):. (PMID: 37629162)
      Protein Sci. 2015 Mar;24(3):298-309. (PMID: 25524168)
      Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W362-5. (PMID: 16845026)
      Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W5-9. (PMID: 18440982)
      Molecules. 2023 Sep 22;28(19):. (PMID: 37836615)
      Chembiochem. 2006 Mar;7(3):450-6. (PMID: 16470764)
      Mol Syst Biol. 2011 Oct 11;7:539. (PMID: 21988835)
      Mar Biotechnol (NY). 2022 Jun;24(3):468-479. (PMID: 35397048)
      Front Bioeng Biotechnol. 2020 Dec 11;8:602721. (PMID: 33363132)
      Nat Methods. 2022 Jun;19(6):679-682. (PMID: 35637307)
      Bioinformatics. 2014 May 1;30(9):1236-40. (PMID: 24451626)
      Nat Genet. 1994 Feb;6(2):119-29. (PMID: 8162065)
      J Comput Chem. 2009 Dec;30(16):2785-91. (PMID: 19399780)
      Mar Drugs. 2023 Feb 22;21(3):. (PMID: 36976185)
      Mar Drugs. 2020 Jun 30;18(7):. (PMID: 32629777)
      Structure. 2012 Sep 5;20(9):1490-7. (PMID: 22795085)
      Mar Drugs. 2020 Jul 27;18(8):. (PMID: 32727111)
      Chembiochem. 2007 Oct 15;8(15):1810-8. (PMID: 17886321)
      Chem Biol. 2001 Aug;8(8):779-90. (PMID: 11514227)
      Nucleic Acids Res. 2003 Jul 1;31(13):3784-8. (PMID: 12824418)
      Prostaglandins Leukot Essent Fatty Acids. 2018 Oct;137:26-38. (PMID: 30293594)
      Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15579-84. (PMID: 15496467)
      Methods Mol Biol. 2008;426:145-59. (PMID: 18542861)
      Mol Biol Evol. 2011 Oct;28(10):2731-9. (PMID: 21546353)
      New Phytol. 2022 Jan;233(2):809-822. (PMID: 34533849)
      Mar Environ Res. 2014 Feb;93:31-7. (PMID: 23992954)
      BMC Genomics. 2020 Oct 6;21(1):693. (PMID: 33023465)
      Nucleic Acids Res. 2007 Jul;35(Web Server issue):W407-10. (PMID: 17517781)
      ISME J. 2020 Jan;14(1):164-177. (PMID: 31611654)
      Biochim Biophys Acta. 1993 Feb 24;1166(2-3):171-6. (PMID: 8443233)
      Methods Enzymol. 2018;605:69-100. (PMID: 29909839)
      Biochem Biophys Res Commun. 2019 Feb 5;509(2):506-513. (PMID: 30595384)
      J Biol Chem. 2014 Nov 14;289(46):31905-31913. (PMID: 25231982)
      Proteins. 2008 Apr;71(1):261-77. (PMID: 17932912)
      Nucleic Acids Res. 2018 Jul 2;46(W1):W296-W303. (PMID: 29788355)
      New Phytol. 2009;183(4):1064-1071. (PMID: 19538551)
      Vopr Pitan. 2020;89(6):6-13. (PMID: 33476493)
      PLoS One. 2014 Jul 03;9(7):e101220. (PMID: 24992192)
      Mar Drugs. 2020 Jan 19;18(1):. (PMID: 31963814)
      Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8. (PMID: 19458158)
      Mar Drugs. 2014 Jan 17;12(1):368-84. (PMID: 24445306)
    • Contributed Indexing:
      Keywords: diatoms; docking analysis; lipoxygenase; protein modelling; sequence clustering
    • Accession Number:
      EC 1.13.11.- (Lipoxygenases)
      0 (Oxylipins)
    • Publication Date:
      Date Created: 20240328 Date Completed: 20240329 Latest Revision: 20240330
    • Publication Date:
      20240330
    • Accession Number:
      PMC10968607
    • Accession Number:
      10.3390/biom14030276
    • Accession Number:
      38540697