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Kreiter J, Škulj S, Brkljača Z, Bardakji S, Vazdar M, Pohl EE. FA Sliding as the Mechanism for the ANT1-Mediated Fatty Acid Anion Transport in Lipid Bilayers. Int J Mol Sci 2023; 24:13701. [PMID: 37762012 PMCID: PMC10531397 DOI: 10.3390/ijms241813701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Mitochondrial adenine nucleotide translocase (ANT) exchanges ADP for ATP to maintain energy production in the cell. Its protonophoric function in the presence of long-chain fatty acids (FA) is also recognized. Our previous results imply that proton/FA transport can be best described with the FA cycling model, in which protonated FA transports the proton to the mitochondrial matrix. The mechanism by which ANT1 transports FA anions back to the intermembrane space remains unclear. Using a combined approach involving measurements of the current through the planar lipid bilayers reconstituted with ANT1, site-directed mutagenesis and molecular dynamics simulations, we show that the FA anion is first attracted by positively charged arginines or lysines on the matrix side of ANT1 before moving along the positively charged protein-lipid interface and binding to R79, where it is protonated. We show that R79 is also critical for the competitive binding of ANT1 substrates (ADP and ATP) and inhibitors (carboxyatractyloside and bongkrekic acid). The binding sites are well conserved in mitochondrial SLC25 members, suggesting a general mechanism for transporting FA anions across the inner mitochondrial membrane.
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Affiliation(s)
- Jürgen Kreiter
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Sanja Škulj
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, 10000 Zagreb, Croatia;
| | - Sarah Bardakji
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Mario Vazdar
- Department of Mathematics, Informatics, and Cybernetics, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Elena E. Pohl
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
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2
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Chowdhury UD, Bhargava BL. Understanding the conformational changes in the influenza B M2 ion channel at various protonation states. Biophys Chem 2022; 289:106859. [PMID: 35905599 DOI: 10.1016/j.bpc.2022.106859] [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: 05/25/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
The characterization of influenza (A/B M2) ion channels is very important as they are potential binding sites for the drugs. We report the all-atom molecular dynamics study of the influenza B M2 ion channel in the presence of explicit solvent and lipid bilayers using the high resolution solid-state NMR structures. The importance of the various protonation states of histidine in the activation of the ion channel is discussed. The conformational changes at the closed and the open structures clearly show that the increase in tilt angle is necessary for the activation of the ion channel. Additionally, the free energy surfaces of the eight systems show the importance of the protonation state of the histidine residues in the activation of the influenza B M2 ion channel. The protonation of the histidine residues increases the tilt angle and the intra-helix distance which is evident from the superimposition of the structures corresponding to the maxima and the minima in the free energy landscape. The findings imply differences in the singly protonated and double protonated conformational states of BM2 ion channel and provide insights to help further studies of these ion channels as the drug targets for the influenza virus.
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Affiliation(s)
- Unmesh D Chowdhury
- School of Chemical Sciences, National Institute of Science Education & Research - Bhubaneswar, an OCC of Homi Bhabha National Institute, P.O.Jatni, Khurda, Odisha 752050, India
| | - B L Bhargava
- School of Chemical Sciences, National Institute of Science Education & Research - Bhubaneswar, an OCC of Homi Bhabha National Institute, P.O.Jatni, Khurda, Odisha 752050, India.
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3
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Naz Z, Moin ST. Investigation of the structural and dynamical properties of human uncoupling protein 2 through molecular dynamics simulations. J Mol Graph Model 2022; 114:108203. [DOI: 10.1016/j.jmgm.2022.108203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
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4
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Schiffer TA, Löf L, Gallini R, Kamali-Moghaddam M, Carlström M, Palm F. Mitochondrial Respiration-Dependent ANT2-UCP2 Interaction. Front Physiol 2022; 13:866590. [PMID: 35694398 PMCID: PMC9177158 DOI: 10.3389/fphys.2022.866590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Adenine nucleotide translocases (ANTs) and uncoupling proteins (UCPs) are known to facilitate proton leak across the inner mitochondrial membrane. However, it remains to be unravelled whether UCP2/3 contribute to significant amount of proton leak in vivo. Reports are indicative of UCP2 dependent proton-coupled efflux of C4 metabolites from the mitochondrial matrix. Previous studies have suggested that UCP2/3 knockdown (KD) contributes to increased ANT-dependent proton leak. Here we investigated the hypothesis that interaction exists between the UCP2 and ANT2 proteins, and that such interaction is regulated by the cellular metabolic demand. Protein-protein interaction was evaluated using reciprocal co-immunoprecipitation and in situ proximity ligation assay. KD of ANT2 and UCP2 was performed by siRNA in human embryonic kidney cells 293A (HEK293A) cells. Mitochondrial and cellular respiration was measured by high-resolution respirometry. ANT2-UCP2 interaction was demonstrated, and this was dependent on cellular metabolism. Inhibition of ATP synthase promoted ANT2-UCP2 interaction whereas high cellular respiration, induced by adding the mitochondrial uncoupler FCCP, prevented interaction. UCP2 KD contributed to increased carboxyatractyloside (CATR) sensitive proton leak, whereas ANT2 and UCP2 double KD reduced CATR sensitive proton leak, compared to UCP2 KD. Furthermore, proton leak was reduced in double KD compared to UCP2 KD. In conclusion, our results show that there is an interaction between ANT2-UCP2, which appears to be dynamically regulated by mitochondrial respiratory activity. This may have implications in the regulation of mitochondrial efficiency or cellular substrate utilization as increased activity of UCP2 may promote a switch from glucose to fatty acid metabolism.
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Affiliation(s)
- Tomas A. Schiffer
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
- *Correspondence: Tomas A. Schiffer,
| | - Liza Löf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Radiosa Gallini
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mattias Carlström
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Fredrik Palm
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
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5
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Sowlati-Hashjin S, Gandhi A, Garton M. Dawn of a New Era for Membrane Protein Design. BIODESIGN RESEARCH 2022; 2022:9791435. [PMID: 37850134 PMCID: PMC10521746 DOI: 10.34133/2022/9791435] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/20/2022] [Indexed: 10/19/2023] Open
Abstract
A major advancement has recently occurred in the ability to predict protein secondary structure from sequence using artificial neural networks. This new accessibility to high-quality predicted structures provides a big opportunity for the protein design community. It is particularly welcome for membrane protein design, where the scarcity of solved structures has been a major limitation of the field for decades. Here, we review the work done to date on the membrane protein design and set out established and emerging tools that can be used to most effectively exploit this new access to structures.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Aanshi Gandhi
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
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6
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Uncoupling Proteins and Regulated Proton Leak in Mitochondria. Int J Mol Sci 2022; 23:ijms23031528. [PMID: 35163451 PMCID: PMC8835771 DOI: 10.3390/ijms23031528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022] Open
Abstract
Higher concentration of protons in the mitochondrial intermembrane space compared to the matrix results in an electrochemical potential causing the back flux of protons to the matrix. This proton transport can take place through ATP synthase complex (leading to formation of ATP) or can occur via proton transporters of the mitochondrial carrier superfamily and/or membrane lipids. Some mitochondrial proton transporters, such as uncoupling proteins (UCPs), transport protons as their general regulating function; while others are symporters or antiporters, which use the proton gradient as a driving force to co-transport other substrates across the mitochondrial inner membrane (such as phosphate carrier, a symporter; or aspartate/glutamate transporter, an antiporter). Passage (or leakage) of protons across the inner membrane to matrix from any route other than ATP synthase negatively impacts ATP synthesis. The focus of this review is on regulated proton transport by UCPs. Recent findings on the structure and function of UCPs, and the related research methodologies, are also critically reviewed. Due to structural similarity of members of the mitochondrial carrier superfamily, several of the known structural features are potentially expandable to all members. Overall, this report provides a brief, yet comprehensive, overview of the current knowledge in the field.
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Ardalan A, Sowlati-Hashjin S, Oduwoye H, Uwumarenogie SO, Karttunen M, Smith MD, Jelokhani-Niaraki M. Biphasic Proton Transport Mechanism for Uncoupling Proteins. J Phys Chem B 2021; 125:9130-9144. [PMID: 34365794 DOI: 10.1021/acs.jpcb.1c04766] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It has been suggested that uncoupling proteins (UCPs) transport protons via interconversion between two conformational states: one in the "cytoplasmic state" and the other in the "matrix state". Matrix and cytoplasmic salt-bridge networks are key controllers of these states. This study proposes a mechanism for proton transport in tetrameric UCP2, with focus on the role of the matrix network. Eleven mutants were prepared to disrupt (K → Q or D → N mutations) or alter (K → D and D → K mutations) the salt-bridges in the matrix network. Proteins were recombinantly expressed in Escherichia coli membrane, reconstituted in model lipid membranes, and their structures and functions were analyzed by gel electrophoresis, circular dichroism spectroscopy, fluorescence assays, as well as molecular dynamics simulations. It is shown that the UCP2 matrix network contains five salt-bridges (rather than the previously reported three), and the matrix network can regulate the proton transport by holding the protein's transmembrane helices in close proximity, limiting the movement of the activator fatty acid(s). A biphasic two-state molecular model is proposed for proton transport in tetrameric (a dimer of stable dimers) UCP2, in which all the monomers are functional, and monomers in each dimer are in the same transport mode. Purine nucleotide (e.g., ATP) can occlude the internal pore of the monomeric units of UCP tetramers via interacting with positive residues at or in the proximity of the matrix network (K38, K141, K239, R88, R185, and R279) and prevent switching between cytoplasmic and matrix states, thus inhibiting the proton transport. This study provides new insights into the mechanism of proton transport and regulation in UCPs.
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Affiliation(s)
- Afshan Ardalan
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada.,The Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario N6K 3K7, Canada
| | - Habib Oduwoye
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Stephanie O Uwumarenogie
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada.,The Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario N6K 3K7, Canada.,Department of Physics and Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Masoud Jelokhani-Niaraki
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
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8
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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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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