1
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Senoo N, Chinthapalli DK, Baile MG, Golla VK, Saha B, Oluwole AO, Ogunbona OB, Saba JA, Munteanu T, Valdez Y, Whited K, Sheridan MS, Chorev D, Alder NN, May ER, Robinson CV, Claypool SM. Functional diversity among cardiolipin binding sites on the mitochondrial ADP/ATP carrier. EMBO J 2024; 43:2979-3008. [PMID: 38839991 DOI: 10.1038/s44318-024-00132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
Lipid-protein interactions play a multitude of essential roles in membrane homeostasis. Mitochondrial membranes have a unique lipid-protein environment that ensures bioenergetic efficiency. Cardiolipin (CL), the signature mitochondrial lipid, plays multiple roles in promoting oxidative phosphorylation (OXPHOS). In the inner mitochondrial membrane, the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) exchanges ADP and ATP, enabling OXPHOS. AAC/ANT contains three tightly bound CLs, and these interactions are evolutionarily conserved. Here, we investigated the role of these buried CLs in AAC/ANT using a combination of biochemical approaches, native mass spectrometry, and molecular dynamics simulations. We introduced negatively charged mutations into each CL-binding site of yeast Aac2 and established experimentally that the mutations disrupted the CL interactions. While all mutations destabilized Aac2 tertiary structure, transport activity was impaired in a binding site-specific manner. Additionally, we determined that a disease-associated missense mutation in one CL-binding site in human ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.
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Affiliation(s)
- Nanami Senoo
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dinesh K Chinthapalli
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Matthew G Baile
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Vinaya K Golla
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Bodhisattwa Saha
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Abraham O Oluwole
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Oluwaseun B Ogunbona
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James A Saba
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Teona Munteanu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yllka Valdez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kevin Whited
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Macie S Sheridan
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dror Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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2
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Fuentes JM, Morcillo P. The Role of Cardiolipin in Mitochondrial Function and Neurodegenerative Diseases. Cells 2024; 13:609. [PMID: 38607048 PMCID: PMC11012098 DOI: 10.3390/cells13070609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
Cardiolipin (CL) is a mitochondria-exclusive phospholipid synthesized in the inner mitochondrial membrane. CL plays a key role in mitochondrial membranes, impacting a plethora of functions this organelle performs. Consequently, it is conceivable that abnormalities in the CL content, composition, and level of oxidation may negatively impact mitochondrial function and dynamics, with important implications in a variety of diseases. This review concentrates on papers published in recent years, combined with basic and underexplored research in CL. We capture new findings on its biological functions in the mitochondria, as well as its association with neurodegenerative diseases such as Alzheimer's disease or Parkinson's disease. Lastly, we explore the potential applications of CL as a biomarker and pharmacological target to mitigate mitochondrial dysfunction.
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Affiliation(s)
- José M. Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Patricia Morcillo
- Departmentof Neurology, Columbia University, New York, NY 10032, USA
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3
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Goyal S, Paspureddi A, Lu M, Chan H, Lyons SN, Wilson CN, Niere M, Ziegler M, Cambronne XA. Dynamics of SLC25A51 reveal preference for oxidized NAD + and substrate led transport. EMBO Rep 2023; 24:e56596. [PMID: 37575034 PMCID: PMC10561365 DOI: 10.15252/embr.202256596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023] Open
Abstract
SLC25A51 is a member of the mitochondrial carrier family (MCF) but lacks key residues that contribute to the mechanism of other nucleotide MCF transporters. Thus, how SLC25A51 transports NAD+ across the inner mitochondrial membrane remains unclear. To elucidate its mechanism, we use Molecular Dynamics simulations to reconstitute SLC25A51 homology models into lipid bilayers and to generate hypotheses to test. We observe spontaneous binding of cardiolipin phospholipids to three distinct sites on the exterior of SLC25A51's central pore and find that mutation of these sites impairs cardiolipin binding and transporter activity. We also observe that stable formation of the required matrix gate is controlled by a single salt bridge. We identify binding sites in SLC25A51 for NAD+ and show that its selectivity for NAD+ is guided by an electrostatic interaction between the charged nicotinamide ring in the ligand and a negatively charged patch in the pore. In turn, interaction of NAD+ with interior residue E132 guides the ligand to dynamically engage and weaken the salt bridge gate, representing a ligand-induced initiation of transport.
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Affiliation(s)
- Shivansh Goyal
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | | | - Mu‐Jie Lu
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Hsin‐Ru Chan
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Scott N Lyons
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Crystal N Wilson
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Marc Niere
- Department of BiomedicineUniversity of BergenBergenNorway
| | | | - Xiaolu A Cambronne
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
- Livestrong Cancer InstituteUniversity of Texas at AustinAustinTXUSA
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4
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Joshi A, Richard TH, Gohil VM. Mitochondrial phospholipid metabolism in health and disease. J Cell Sci 2023; 136:jcs260857. [PMID: 37655851 PMCID: PMC10482392 DOI: 10.1242/jcs.260857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Studies of rare human genetic disorders of mitochondrial phospholipid metabolism have highlighted the crucial role that membrane phospholipids play in mitochondrial bioenergetics and human health. The phospholipid composition of mitochondrial membranes is highly conserved from yeast to humans, with each class of phospholipid performing a specific function in the assembly and activity of various mitochondrial membrane proteins, including the oxidative phosphorylation complexes. Recent studies have uncovered novel roles of cardiolipin and phosphatidylethanolamine, two crucial mitochondrial phospholipids, in organismal physiology. Studies on inter-organellar and intramitochondrial phospholipid transport have significantly advanced our understanding of the mechanisms that maintain mitochondrial phospholipid homeostasis. Here, we discuss these recent advances in the function and transport of mitochondrial phospholipids while describing their biochemical and biophysical properties and biosynthetic pathways. Additionally, we highlight the roles of mitochondrial phospholipids in human health by describing the various genetic diseases caused by disruptions in their biosynthesis and discuss advances in therapeutic strategies for Barth syndrome, the best-studied disorder of mitochondrial phospholipid metabolism.
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Affiliation(s)
- Alaumy Joshi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Travis H. Richard
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vishal M. Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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5
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Ivontsin LA, Mashkovtseva EV, Nartsissov YR. Membrane Lipid Composition Influences the Hydration of Proton Half-Channels in F oF 1-ATP Synthase. Life (Basel) 2023; 13:1816. [PMID: 37763220 PMCID: PMC10532555 DOI: 10.3390/life13091816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
The membrane lipid composition plays an important role in the regulation of membrane protein activity. To probe its influence on proton half-channels' structure in FoF1-ATP synthase, we performed molecular dynamics simulations with the bacterial protein complex (PDB ID: 6VWK) embedded in three types of membranes: a model POPC, a lipid bilayer containing 25% (in vivo), and 75% (bacterial stress) of cardiolipin (CL). The structure proved to be stable regardless of the lipid composition. The presence of CL increased the hydration of half-channels. The merging of two water cavities at the inlet half-channel entrance and a long continuous chain of water molecules directly to cAsp61 from the periplasm were observed. Minor conformational changes in half-channels with the addition of CL caused extremely rare direct transitions between aGlu219-aAsp119, aGlu219-aHis245, and aGln252-cAsp61. Deeper penetration of water molecules (W1-W3) also increased the proton transport continuity. Stable spatial positions of significant amino acid (AA) residue aAsn214 were found under all simulation conditions indicate a prevailing influence of AA-AA or AA-W interactions on the side-chain dynamics. These results allowed us to put forward a model of the proton movement in ATP synthases under conditions close to in vivo and to evaluate the importance of membrane composition in simulations.
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Affiliation(s)
- Leonid A. Ivontsin
- Institute of Cytochemistry and Molecular Pharmacology, 24/14 6th Radialnaya Str., Moscow 115404, Russia; (E.V.M.); (Y.R.N.)
| | - Elena V. Mashkovtseva
- Institute of Cytochemistry and Molecular Pharmacology, 24/14 6th Radialnaya Str., Moscow 115404, Russia; (E.V.M.); (Y.R.N.)
| | - Yaroslav R. Nartsissov
- Institute of Cytochemistry and Molecular Pharmacology, 24/14 6th Radialnaya Str., Moscow 115404, Russia; (E.V.M.); (Y.R.N.)
- Biomedical Research Group, BiDiPharma GmbH, 5 Bültbek, 22962 Siek, Germany
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6
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Senoo N, Chinthapalli DK, Baile MG, Golla VK, Saha B, Ogunbona OB, Saba JA, Munteanu T, Valdez Y, Whited K, Chorev D, Alder NN, May ER, Robinson CV, Claypool SM. Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539595. [PMID: 37205478 PMCID: PMC10187269 DOI: 10.1101/2023.05.05.539595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mitochondrial phospholipid cardiolipin (CL) promotes bioenergetics via oxidative phosphorylation (OXPHOS). Three tightly bound CLs are evolutionarily conserved in the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) which resides in the inner mitochondrial membrane and exchanges ADP and ATP to enable OXPHOS. Here, we investigated the role of these buried CLs in the carrier using yeast Aac2 as a model. We introduced negatively charged mutations into each CL-binding site of Aac2 to disrupt the CL interactions via electrostatic repulsion. While all mutations disturbing the CL-protein interaction destabilized Aac2 monomeric structure, transport activity was impaired in a pocket-specific manner. Finally, we determined that a disease-associated missense mutation in one CL-binding site in ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.
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Affiliation(s)
- Nanami Senoo
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dinesh K. Chinthapalli
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Matthew G. Baile
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vinaya K. Golla
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bodhisattwa Saha
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Oluwaseun B. Ogunbona
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James A. Saba
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Teona Munteanu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yllka Valdez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kevin Whited
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dror Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Steven M. Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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7
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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8
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Pasquadibisceglie A, Quadrotta V, Polticelli F. In Silico Analysis of the Structural Dynamics and Substrate Recognition Determinants of the Human Mitochondrial Carnitine/Acylcarnitine SLC25A20 Transporter. Int J Mol Sci 2023; 24:ijms24043946. [PMID: 36835358 PMCID: PMC9961348 DOI: 10.3390/ijms24043946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The Carnitine-Acylcarnitine Carrier is a member of the mitochondrial Solute Carrier Family 25 (SLC25), known as SLC25A20, involved in the electroneutral exchange of acylcarnitine and carnitine across the inner mitochondrial membrane. It acts as a master regulator of fatty acids β-oxidation and is known to be involved in neonatal pathologies and cancer. The transport mechanism, also known as "alternating access", involves a conformational transition in which the binding site is accessible from one side of the membrane or the other. In this study, through a combination of state-of-the-art modelling techniques, molecular dynamics, and molecular docking, the structural dynamics of SLC25A20 and the early substrates recognition step have been analyzed. The results obtained demonstrated a significant asymmetry in the conformational changes leading to the transition from the c- to the m-state, confirming previous observations on other homologous transporters. Moreover, analysis of the MD simulations' trajectories of the apo-protein in the two conformational states allowed for a better understanding of the role of SLC25A20 Asp231His and Ala281Val pathogenic mutations, which are at the basis of Carnitine-Acylcarnitine Translocase Deficiency. Finally, molecular docking coupled to molecular dynamics simulations lend support to the multi-step substrates recognition and translocation mechanism already hypothesized for the ADP/ATP carrier.
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Affiliation(s)
| | | | - Fabio Polticelli
- Department of Sciences, University of Roma Tre, 00146 Rome, Italy
- National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy
- Correspondence:
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9
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Function-Related Asymmetry of the Interactions between Matrix Loops and Conserved Sequence Motifs in the Mitochondrial ADP/ATP Carrier. Int J Mol Sci 2022; 23:ijms231810877. [PMID: 36142790 PMCID: PMC9502086 DOI: 10.3390/ijms231810877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
The ADP/ATP carrier (AAC) plays a central role in oxidative metabolism by exchanging ATP and ADP across the inner mitochondrial membrane. Previous experiments have shown the involvement of the matrix loops of AAC in its function, yet potential mechanisms remain largely elusive. One obstacle is the limited information on the structural dynamics of the matrix loops. In the current work, unbiased all-atom molecular dynamics (MD) simulations were carried out on c-state wild-type AAC and mutants. Our results reveal that: (1) two ends of a matrix loop are tethered through interactions between the residue of triplet 38 (Q38, D143 and Q240) located at the C-end of the odd-numbered helix and residues of the [YF]xG motif located before the N-end of the short matrix helix in the same domain; (2) the initial progression direction of a matrix loop is determined by interactions between the negatively charged residue of the [DE]G motif located at the C-end of the short matrix helix and the capping arginine (R30, R139 and R236) in the previous domain; (3) the two chemically similar residues D and E in the highly conserved [DE]G motif are actually quite different; (4) the N-end of the M3 loop is clamped by the [DE]G motif and the capping arginine of domain 2 from the two sides, which strengthens interactions between domain 2 and domain 3; and (5) a highly asymmetric stable core exists within domains 2 and 3 at the m-gate level. Moreover, our results help explain almost all extremely conserved residues within the matrix loops of the ADP/ATP carriers from a structural point of view. Taken together, the current work highlights asymmetry in the three matrix loops and implies a close relationship between asymmetry and ADP/ATP transport.
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10
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Giangregorio N, Pierri CL, Tonazzi A, Incampo G, Tragni V, De Grassi A, Indiveri C. Proline/Glycine residues of the PG-levels guide conformational changes along the transport cycle in the mitochondrial carnitine/acylcarnitine carrier (SLC25A20). Int J Biol Macromol 2022; 221:1453-1465. [PMID: 36122779 DOI: 10.1016/j.ijbiomac.2022.09.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
Mitochondrial carnitine/acylcarnitine carrier (CAC) is a member of the mitochondrial carrier (MC) family and imports acylcarnitine into the mitochondrial matrix in exchange for carnitine, playing a pivotal role in carnitine shuttle, crucial for fatty acid oxidation. The crystallized structure of CAC has not been solved yet, however, the availability of several in vitro/in silico studies, also based on the crystallized structures of the ADP/ATP carrier in the cytosolic-conformation and in the matrix-conformation, has made possible to confirm the hypothesis of the single-binding centered-gated pore mechanism for all the members of the MC family. In addition, our recent bioinformatics analyses allowed quantifying in silico the importance of protein residues of MC substrate binding region, of those involved in the formation of the matrix and cytosolic gates, and of those belonging to the Pro/Gly (PG) levels, proposed to be crucial for the tilting/kinking/bending of the six MC transmembrane helices, funneling the substrate translocation pathway. Here we present a combined in silico/in vitro analysis employed for investigating the role played by a group of 6 proline residues and 6 glycine residues, highly conserved in CAC, belonging to MC PG-levels. Residues of the PG-levels surround the similarly located MC common substrate binding region, and were proposed to lead conformational changes and substrate translocation, following substrate binding. For our analysis, we employed 3D molecular modeling approaches, alanine scanning site-directed mutagenesis and in vitro transport assays. Our analysis reveals that P130 (H3), G268 (H6) and G220 (H5), mutated in alanine, affect severely CAC transport activity (mutant catalytic efficiency lower than 5 % compared to the wild type CAC), most likely due to their major role in triggering CAC conformational changes, following carnitine binding. Notably, P30A (H1) and G121A (H3) CAC mutants, increase the carnitine uptake up to 217 % and 112 %, respectively, compared to the wild type CAC.
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Affiliation(s)
- Nicola Giangregorio
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy.
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy.
| | - Annamaria Tonazzi
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy
| | - Giovanna Incampo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Vincenzo Tragni
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Cesare Indiveri
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy; Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via Bucci 4C, 87036 Arcavacata di Rende, Italy
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