Deciphering the Binding of Salicylic Acid to Arabidopsis thaliana Chloroplastic GAPDH-A1
| Autor: | Christophe Espinasse, Isabelle Kleiner, Tahar Bouceba, Luis Leitao, Miguel Hernandez-Martinez, Igor Pokotylo, Denis Hellal, V. S. Kravets, Eric Ruelland |
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| Přispěvatelé: | Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Marie Curie/Universite Paris-Est Creteil post doc fellowship (Prestige programme), PHC DNIPRO grant, M2 grants from iEES-Paris. OSU Efluve, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine In silico salicylic acid Dehydrogenase 01 natural sciences Article Catalysis Cofactor Inorganic Chemistry lcsh:Chemistry 03 medical and health sciences chemistry.chemical_compound Glyceraldehyde biacore Arabidopsis thaliana [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Physical and Theoretical Chemistry Molecular Biology lcsh:QH301-705.5 Spectroscopy Glyceraldehyde 3-phosphate dehydrogenase chemistry.chemical_classification biology Organic Chemistry General Medicine molecular docking [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics biology.organism_classification Ligand (biochemistry) molecular dynamics Computer Science Applications 030104 developmental biology Enzyme Biochemistry chemistry glyceraldehyde 3-phosphate dehydrogenase lcsh:Biology (General) lcsh:QD1-999 biology.protein protein ligand interaction surface plasmon resonance 010606 plant biology & botany |
| Zdroj: | International Journal of Molecular Sciences, Vol 21, Iss 4678, p 4678 (2020) International Journal of Molecular Sciences International Journal of Molecular Sciences, MDPI, 2020, 21 (13), pp.4678. ⟨10.3390/ijms21134678⟩ Volume 21 Issue 13 International Journal of Molecular Sciences, 2020, 21 (13), pp.4678. ⟨10.3390/ijms21134678⟩ |
| ISSN: | 1661-6596 1422-0067 |
| Popis: | Salicylic acid (SA) has an essential role in the responses of plants to pathogens. SA initiates defence signalling via binding to proteins. NPR1 is a transcriptional co-activator and a key target of SA binding. Many other proteins have recently been shown to bind SA. Amongst these proteins are important enzymes of primary metabolism. This fact could stand behind SA&rsquo s ability to control energy fluxes in stressed plants. Nevertheless, only sparse information exists on the role and mechanisms of such binding. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was previously demonstrated to bind SA both in human and plants. Here, we detail that the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM, as shown in surface plasmon resonance experiments. Besides, we show that SA inhibits its GAPDH activity in vitro. To gain some insight into the underlying molecular interactions and binding mechanism, we combined in silico molecular docking experiments and molecular dynamics simulations on the free protein and protein&ndash ligand complex. The molecular docking analysis yielded to the identification of two putative binding pockets for SA. A simulation in water of the complex between SA and the protein allowed us to determine that only one pocket&mdash a surface cavity around Asn35&mdash would efficiently bind SA in the presence of solvent. In silico mutagenesis and simulations of the ligand/protein complexes pointed to the importance of Asn35 and Arg81 in the binding of SA to GAPA1. The importance of this is further supported through experimental biochemical assays. Indeed, mutating GAPA1 Asn35 into Gly or Arg81 into Leu strongly diminished the ability of the enzyme to bind SA. The very same cavity is responsible for the NADP+ binding to GAPA1. More precisely, modelling suggests that SA binds to the very site where the pyrimidine group of the cofactor fits. NADH inhibited in a dose-response manner the binding of SA to GAPA1, validating our data. |
| Databáze: | OpenAIRE |
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