Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis
| Autor: | Sonia Fieulaine, Isabelle Artaud, Carmela Giglione, Michel Desmadril, Frédéric Dardel, Thierry Meinnel, Adrien Boularot |
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| Přispěvatelé: | Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et biophysique moléculaire et cellulaire (IBBMC), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale ( IBS - UMR 5075 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Joseph Fourier - Grenoble 1 ( UJF ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques ( LCBPT - UMR 8601 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de biochimie et biophysique moléculaire et cellulaire ( IBBMC ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ) |
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
Models
Molecular MESH: Amidohydrolases MESH: Hydroxamic Acids [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology Amino Acid Motifs Arabidopsis MESH: Catalytic Domain Crystallography X-Ray Hydroxamic Acids Biochemistry MESH : Arabidopsis Proteins Peptide deformylase MESH: Amino Acid Motifs MESH : Arabidopsis Catalytic Domain MESH: Arabidopsis Enzyme Inhibitors Biology (General) 0303 health sciences MESH: Kinetics General Neuroscience 030302 biochemistry & molecular biology MESH : Catalytic Domain MESH : Protein Binding Enzyme structure MESH : Mutagenesis Site-Directed Enzymes MESH: Mutagenesis Site-Directed MESH : Amidohydrolases MESH: Enzyme Inhibitors Thermodynamics MESH : Kinetics MESH: Thermodynamics General Agricultural and Biological Sciences MESH: Models Molecular Protein Binding Research Article MESH : Amino Acid Motifs MESH : Models Molecular QH301-705.5 Mutation Missense MESH: Arabidopsis Proteins Biology Protein Chemistry General Biochemistry Genetics and Molecular Biology Enzyme catalysis Amidohydrolases 03 medical and health sciences Molecular recognition Hydrolase MESH : Hydrogen Bonding MESH: Protein Binding [SDV.BV]Life Sciences [q-bio]/Vegetal Biology Enzyme kinetics MESH: Hydrogen Bonding 030304 developmental biology MESH : Thermodynamics Enzyme Kinetics MESH : Enzyme Inhibitors MESH: Mutation Missense MESH : Hydroxamic Acids General Immunology and Microbiology Arabidopsis Proteins Substrate (chemistry) Active site Proteins Hydrogen Bonding MESH: Crystallography X-Ray Kinetics Small Molecules Enzyme Structure biology.protein Biophysics Mutagenesis Site-Directed Biocatalysis MESH : Crystallography X-Ray MESH : Mutation Missense |
| Zdroj: | PLoS Biology PLoS Biology, 2011, 9 (5), pp.e1001066. ⟨10.1371/journal.pbio.1001066⟩ PLoS Biology, Vol 9, Iss 5, p e1001066 (2011) PLoS Biology, Public Library of Science, 2011, 9 (5), pp.e1001066. ⟨10.1371/journal.pbio.1001066⟩ PLoS Biology, Public Library of Science, 2011, 9 (5), pp.e1001066. 〈10.1371/journal.pbio.1001066〉 |
| ISSN: | 1544-9173 1545-7885 |
| DOI: | 10.1371/journal.pbio.1001066⟩ |
| Popis: | For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally “zipped up” by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A “movie” that reconstructs this entire process can be further extrapolated to catalysis. Author Summary The notion of induced fit when a protein binds its ligand—like a glove adapting to the shape of a hand—is a central concept of structural biochemistry introduced over 50 years ago. A detailed molecular demonstration of this phenomenon has eluded biochemists, however, largely due to the difficulty of capturing the steps of this very transient process: the “conformational change.” In this study, we were able to see this process by using X-ray diffraction to determine more than 10 distinct structures adopted by a single enzyme when it binds a ligand. To do this, we took advantage of the “slow, tight-binding” of a potent inhibitor to its specific target enzyme to trap intermediates in the binding process, which allowed us to monitor the action of an enzyme in real-time at atomic resolution. We showed the kinetics of the conformational change from an initial open state, including the encounter complex, to the final closed state of the enzyme. From these data and other biochemical and biophysical analyses, we make a coherent causal reconstruction of the sequence of events leading to inhibition of the enzyme's activity. We also generated a movie that reconstructs the sequence of events during the encounter. Our data provide new insights into how enzymes achieve a catalytically competent conformation in which the reactive groups are brought into close proximity, resulting in catalysis. |
| Databáze: | OpenAIRE |
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