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Gagelin A, Largeau C, Masscheleyn S, Piel MS, Calderón-Mora D, Bouillaud F, Hénin J, Miroux B. Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling. Nat Commun 2023; 14:2594. [PMID: 37147287 PMCID: PMC10162991 DOI: 10.1038/s41467-023-38219-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/21/2023] [Indexed: 05/07/2023] Open
Abstract
Brown adipose tissue expresses uncoupling protein 1 (UCP1), which dissipates energy as heat, making it a target for treating metabolic disorders. Here, we investigate how purine nucleotides inhibit respiration uncoupling by UCP1. Our molecular simulations predict that GDP and GTP bind UCP1 in the common substrate binding site in an upright orientation, where the base moiety interacts with conserved residues R92 and E191. We identify a triplet of uncharged residues, F88/I187/W281, forming hydrophobic contacts with nucleotides. In yeast spheroplast respiration assays, both I187A and W281A mutants increase the fatty acid-induced uncoupling activity of UCP1 and partially suppress the inhibition of UCP1 activity by nucleotides. The F88A/I187A/W281A triple mutant is overactivated by fatty acids even at high concentrations of purine nucleotides. In simulations, E191 and W281 interact with purine but not pyrimidine bases. These results provide a molecular understanding of the selective inhibition of UCP1 by purine nucleotides.
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Affiliation(s)
- Antoine Gagelin
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
| | - Corentin Largeau
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Sandrine Masscheleyn
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Mathilde S Piel
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Daniel Calderón-Mora
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France
| | - Frédéric Bouillaud
- Université Paris Cité, Institut Cochin, Inserm U1016, CNRS UMR8104, Paris, 75014, France
| | - Jérôme Hénin
- Université Paris Cité, Laboratoire de Biochimie Théorique CNRS UPR9080, Paris, 75005, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France.
| | - Bruno Miroux
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, 75005, France.
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, Paris, 75005, France.
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Škulj S, Brkljača Z, Kreiter J, Pohl EE, Vazdar M. Molecular Dynamics Simulations of Mitochondrial Uncoupling Protein 2. Int J Mol Sci 2021; 22:ijms22031214. [PMID: 33530558 PMCID: PMC7866055 DOI: 10.3390/ijms22031214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamics (MD) simulations of uncoupling proteins (UCP), a class of transmembrane proteins relevant for proton transport across inner mitochondrial membranes, represent a complicated task due to the lack of available structural data. In this work, we use a combination of homology modelling and subsequent microsecond molecular dynamics simulations of UCP2 in the DOPC phospholipid bilayer, starting from the structure of the mitochondrial ATP/ADP carrier (ANT) as a template. We show that this protocol leads to a structure that is impermeable to water, in contrast to MD simulations of UCP2 structures based on the experimental NMR structure. We also show that ATP binding in the UCP2 cavity is tight in the homology modelled structure of UCP2 in agreement with experimental observations. Finally, we corroborate our results with conductance measurements in model membranes, which further suggest that the UCP2 structure modeled from ANT protein possesses additional key functional elements, such as a fatty acid-binding site at the R60 region of the protein, directly related to the proton transport mechanism across inner mitochondrial membranes.
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Affiliation(s)
- Sanja Škulj
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (S.Š.); (Z.B.)
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (S.Š.); (Z.B.)
| | - Jürgen Kreiter
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Elena E. Pohl
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210 Vienna, Austria;
- Correspondence: (E.E.P.); (M.V.)
| | - Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (S.Š.); (Z.B.)
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Correspondence: (E.E.P.); (M.V.)
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3
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Piel MS, Masscheleyn S, Bouillaud F, Moncoq K, Miroux B. Structural models of mitochondrial uncoupling proteins obtained in DPC micelles are not functionally relevant. FEBS J 2020; 288:3024-3033. [DOI: 10.1111/febs.15629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/15/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Mathilde S. Piel
- Laboratoire de Biologie Physico‐Chimique des Protéines Membranaires, LBPC‐PM CNRS UMR7099 Université de Paris France
- Institut de Biologie Physico‐Chimique Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique Paris France
| | - Sandrine Masscheleyn
- Laboratoire de Biologie Physico‐Chimique des Protéines Membranaires, LBPC‐PM CNRS UMR7099 Université de Paris France
- Institut de Biologie Physico‐Chimique Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique Paris France
| | | | - Karine Moncoq
- Laboratoire de Biologie Physico‐Chimique des Protéines Membranaires, LBPC‐PM CNRS UMR7099 Université de Paris France
- Institut de Biologie Physico‐Chimique Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique Paris France
| | - Bruno Miroux
- Laboratoire de Biologie Physico‐Chimique des Protéines Membranaires, LBPC‐PM CNRS UMR7099 Université de Paris France
- Institut de Biologie Physico‐Chimique Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique Paris France
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4
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Škulj S, Brkljača Z, Vazdar M. Molecular Dynamics Simulations of the Elusive Matrix‐Open State of Mitochondrial ADP/ATP Carrier. Isr J Chem 2020. [DOI: 10.1002/ijch.202000011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sanja Škulj
- Division of Organic Chemistry and BiochemistryRuđer Bošković Institute Bijenička 54 HR-10000 Zagreb Croatia
| | - Zlatko Brkljača
- Division of Organic Chemistry and BiochemistryRuđer Bošković Institute Bijenička 54 HR-10000 Zagreb Croatia
| | - Mario Vazdar
- Division of Organic Chemistry and BiochemistryRuđer Bošković Institute Bijenička 54 HR-10000 Zagreb Croatia
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5
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Yang Q, Brüschweiler S, Zhao L, Chou JJ. Reply to 'Concerns with yeast mitochondrial ADP/ATP carrier's integrity in DPC' and 'Dynamics and interactions of AAC3 in DPC are not functionally relevant'. Nat Struct Mol Biol 2019; 25:749-750. [PMID: 30177759 DOI: 10.1038/s41594-018-0126-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Qin Yang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Aptitude Medical Systems, Inc., Santa Barbara, CA, USA
| | - Sven Brüschweiler
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Linlin Zhao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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6
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Kieber M, Ono T, Oliver RC, Nyenhuis SB, Tieleman DP, Columbus L. The Fluidity of Phosphocholine and Maltoside Micelles and the Effect of CHAPS. Biophys J 2019; 116:1682-1691. [PMID: 31023535 DOI: 10.1016/j.bpj.2019.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 11/17/2022] Open
Abstract
The dynamics of phosphocholine and maltoside micelles, detergents frequently used for membrane protein structure determination, were investigated using electron paramagnetic resonance of spin probes doped into the micelles. Specifically, phosphocholines are frequently used detergents in NMR studies, and maltosides are frequently used in x-ray crystallography structure determination. Beyond the structural and electrostatic differences, this study aimed to determine whether there are differences in the local chain dynamics (i.e., fluidity). The nitroxide probe rotational dynamics in longer chain detergents is more restricted than in shorter chain detergents, and maltoside micelles are more restricted than phosphocholine micelles. Furthermore, the micelle microviscosity can be modulated with mixtures, as demonstrated with mixtures of 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate with n-dodecylphosphocholine, n-tetradecylphosphocholine, n-decyl-β-D-maltoside, or n-dodecyl-β-D-maltoside. These results indicate that observed differences in membrane protein stability in these detergents could be due to fluidity in addition to the already determined structural differences.
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Affiliation(s)
- Marissa Kieber
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Tomihiro Ono
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Ryan C Oliver
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Sarah B Nyenhuis
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia.
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