1
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Hu G, Ou X, Li J. Mechanistic Insight on General Protein-Binding Ability of ATP and the Impacts of Arginine Residues. J Phys Chem B 2022; 126:4647-4658. [PMID: 35713479 DOI: 10.1021/acs.jpcb.2c01478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent experiments suggested that adenosine triphosphate (ATP) can regulate liquid-liquid phase separation (LLPS) of various proteins and inhibit protein aggregations at its physiological concentration, which is highly correlated with the nonspecific interactions of ATP to a wide variety of proteins. However, the mechanism underlying the general binding capability of ATP largely remains unclear. In this work, we used molecular dynamics simulation to study the binding of ATPs to three proteins with distinct net charges: TDP-43 NTD (-7 e), TAF15-RRM (0 e), HWEL (+8 e). Negatively charged ATP exhibits a strong trend to accumulate around all of these proteins. While only a fraction of the accumulated ATPs directly binds to the limited regions of the protein surface, additional ATPs indirectly bind to proteins by aggregating into ATP clusters. Hence, the proportion of the directly bound ATPs in the clusters as well as their binding regions can be adjusted in response to different proteins, which makes ATP well adapted to a variety of proteins. Moreover, our results suggest that ATP tightly binds to Arg with high affinity, and Arg dominates the direct binding of ATP. Meanwhile, Arg also affects the self-association of accumulated ATPs. The size of the ATP cluster is effectively regulated by the distribution of Arg. Considering the ubiquity of Arg in proteins, our findings are helpful to understand the general binding capability of ATP.
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Affiliation(s)
- Guorong Hu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, School of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, School of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, School of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
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2
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Bround MJ, Bers DM, Molkentin JD. A 20/20 view of ANT function in mitochondrial biology and necrotic cell death. J Mol Cell Cardiol 2020; 144:A3-A13. [PMID: 32454061 DOI: 10.1016/j.yjmcc.2020.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/16/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022]
Abstract
The adenosine nucleotide translocase (ANT) family of proteins are inner mitochondrial membrane proteins involved in energy homeostasis and cell death. The primary function of ANT proteins is to exchange cytosolic ADP with matrix ATP, facilitating the export of newly synthesized ATP to the cell while providing new ADP substrate to the mitochondria. As such, the ANT proteins are central to maintaining energy homeostasis in all eukaryotic cells. Evidence also suggests that the ANTs constitute a pore-forming component of the mitochondrial permeability transition pore (MPTP), a structure that forms in the inner mitochondrial membrane that is thought to underlie regulated necrotic cell death. Additionally, emerging studies suggest that ANT proteins are also critical for mitochondrial uncoupling and for promoting mitophagy. Thus, the ANTs are multifunctional proteins that are poised to participate in several aspects of mitochondrial biology and the greater regulation of cell death, which will be discussed here.
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Affiliation(s)
- Michael J Bround
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Donald M Bers
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Jeffery D Molkentin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA; Howard Hughes Medical Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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3
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Hoshino A, Wang WJ, Wada S, McDermott-Roe C, Evans CS, Gosis B, Morley MP, Rathi KS, Li J, Li K, Yang S, McManus MJ, Bowman C, Potluri P, Levin M, Damrauer S, Wallace DC, Holzbaur ELF, Arany Z. The ADP/ATP translocase drives mitophagy independent of nucleotide exchange. Nature 2019; 575:375-379. [PMID: 31618756 PMCID: PMC6858570 DOI: 10.1038/s41586-019-1667-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/09/2019] [Indexed: 12/29/2022]
Abstract
Mitochondrial homeostasis depends on mitophagy, the programmed degradation of mitochondria. Only a few proteins are known to participate in mitophagy. Here we develop a multidimensional CRISPR-Cas9 genetic screen, using multiple mitophagy reporter systems and pro-mitophagy triggers, and identify numerous components of parkin-dependent mitophagy1. Unexpectedly, we find that the adenine nucleotide translocator (ANT) complex is required for mitophagy in several cell types. Whereas pharmacological inhibition of ANT-mediated ADP/ATP exchange promotes mitophagy, genetic ablation of ANT paradoxically suppresses mitophagy. Notably, ANT promotes mitophagy independently of its nucleotide translocase catalytic activity. Instead, the ANT complex is required for inhibition of the presequence translocase TIM23, which leads to stabilization of PINK1, in response to bioenergetic collapse. ANT modulates TIM23 indirectly via interaction with TIM44, which regulates peptide import through TIM232. Mice that lack ANT1 show blunted mitophagy and consequent profound accumulation of aberrant mitochondria. Disease-causing human mutations in ANT1 abrogate binding to TIM44 and TIM23 and inhibit mitophagy. Together, our findings show that ANT is an essential and fundamental mediator of mitophagy in health and disease.
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Affiliation(s)
- Atsushi Hoshino
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Wei-Jia Wang
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shogo Wada
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chris McDermott-Roe
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chantell S Evans
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bridget Gosis
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P Morley
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Komal S Rathi
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jian Li
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina Li
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Yang
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meagan J McManus
- Department of Anesthesiology & Critical Care Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, and the Division of Human Genetics and Metabolism, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Caitlyn Bowman
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, and the Division of Human Genetics and Metabolism, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Levin
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott Damrauer
- Department of Surgery, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, and the Division of Human Genetics and Metabolism, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Arany
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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5
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Sounier R, Bellot G, Chou JJ. Mapping Conformational Heterogeneity of Mitochondrial Nucleotide Transporter in Uninhibited States. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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6
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Sounier R, Bellot G, Chou JJ. Mapping conformational heterogeneity of mitochondrial nucleotide transporter in uninhibited states. Angew Chem Int Ed Engl 2015; 54:2436-41. [PMID: 25605594 DOI: 10.1002/anie.201408417] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/09/2014] [Indexed: 12/18/2022]
Abstract
One of the less well understood aspects of membrane transporters is the dynamic coupling between conformational change and substrate transport. NMR approaches are used herein to investigate conformational heterogeneity of the GTP/GDP carrier (GGC) from yeast mitochondria. NMR residual dipolar coupling (RDC) analysis of GGC in a DNA-origami nanotube liquid crystal shows that several structured segments have different generalized degrees of order (GDO), thus indicating the presence of conformational heterogeneity. Complete GDO mapping reveals asymmetry between domains of the transporter and even within certain transmembrane helices. Nucleotide binding partially reduces local structural heterogeneity, and the substrate binds to multiple sites along the transport cavity. These observations suggest that mitochondrial carriers in the uninhibited states are intrinsically plastic and structural plasticity is asymmetrically distributed among the three homologous domains.
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Affiliation(s)
- Remy Sounier
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA); Present address: Institut de Génomique Fonctionnelle, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 5203, Institut National de la Santé et de la Recherche Médicale (INSERM) U1191, Université de Montpellier, F-34000 Montpellier (France)
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7
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Mielke C, Lefort N, McLean C, Cordova JM, Langlais PR, Bordner AJ, Te JA, Ozkan SB, Willis WT, Mandarino LJ. Adenine nucleotide translocase is acetylated in vivo in human muscle: Modeling predicts a decreased ADP affinity and altered control of oxidative phosphorylation. Biochemistry 2014; 53:3817-29. [PMID: 24884163 PMCID: PMC4067143 DOI: 10.1021/bi401651e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Proteomics techniques have revealed that lysine acetylation is abundant in mitochondrial proteins. This study was undertaken (1) to determine the relationship between mitochondrial protein acetylation and insulin sensitivity in human skeletal muscle, identifying key acetylated proteins, and (2) to use molecular modeling techniques to understand the functional consequences of acetylation of adenine nucleotide translocase 1 (ANT1), which we found to be abundantly acetylated. Eight lean and eight obese nondiabetic subjects had euglycemic clamps and muscle biopsies for isolation of mitochondrial proteins and proteomics analysis. A number of acetylated mitochondrial proteins were identified in muscle biopsies. Overall, acetylation of mitochondrial proteins was correlated with insulin action (r = 0.60; P < 0.05). Of the acetylated proteins, ANT1, which catalyzes ADP-ATP exchange across the inner mitochondrial membrane, was acetylated at lysines 10, 23, and 92. The extent of acetylation of lysine 23 decreased following exercise, depending on insulin sensitivity. Molecular dynamics modeling and ensemble docking simulations predicted the ADP binding site of ANT1 to be a pocket of positively charged residues, including lysine 23. Calculated ADP-ANT1 binding affinities were physiologically relevant and predicted substantial reductions in affinity upon acetylation of lysine 23. Insertion of these derived binding affinities as parameters into a complete mathematical description of ANT1 kinetics predicted marked reductions in adenine nucleotide flux resulting from acetylation of lysine 23. Therefore, acetylation of ANT1 could have dramatic physiological effects on ADP-ATP exchange. Dysregulation of acetylation of mitochondrial proteins such as ANT1 therefore could be related to changes in mitochondrial function that are associated with insulin resistance.
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Affiliation(s)
- Clinton Mielke
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Natalie Lefort
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Carrie
G. McLean
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Jeanine M. Cordova
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Paul R. Langlais
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
| | - Andrew J. Bordner
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
| | - Jerez A. Te
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
| | - S. Banu Ozkan
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Wayne T. Willis
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Lawrence J. Mandarino
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
- Department of Medicine, Mayo
Clinic in Arizona, Scottsdale, Arizona 85259, United States
- Mayo Clinic in Arizona, 13400 E.
Shea Blvd., Scottsdale, AZ 85259. E-mail: . Phone: (480) 965-8365. Fax: (480) 965-6899
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