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Role of membrane mimetics on biophysical EPR studies of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184138. [PMID: 36764474 DOI: 10.1016/j.bbamem.2023.184138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Biological membranes are essential in providing the stability of membrane proteins in a functional state. Functionally stable homogeneous sample is required for biophysical electron paramagnetic resonance (EPR) studies of membrane proteins for obtaining pertinent structural dynamics of the protein. Significant progresses have been made for the optimization of the suitable membrane environments required for biophysical EPR measurements. However, no universal membrane mimetic system is available that can solubilize all membrane proteins suitable for biophysical EPR studies while maintaining the functional integrity. Great efforts are needed to optimize the sample condition to obtain better EPR data quality of membrane proteins that can provide meaningful information on structural dynamics. In this mini-review, we will discuss important aspects of membrane mimetics for biophysical EPR measurements and current progress with some of the recent examples.
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2
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Davies JS, Currie MJ, Wright JD, Newton-Vesty MC, North RA, Mace PD, Allison JR, Dobson RCJ. Selective Nutrient Transport in Bacteria: Multicomponent Transporter Systems Reign Supreme. Front Mol Biosci 2021; 8:699222. [PMID: 34268334 PMCID: PMC8276074 DOI: 10.3389/fmolb.2021.699222] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
Multicomponent transporters are used by bacteria to transport a wide range of nutrients. These systems use a substrate-binding protein to bind the nutrient with high affinity and then deliver it to a membrane-bound transporter for uptake. Nutrient uptake pathways are linked to the colonisation potential and pathogenicity of bacteria in humans and may be candidates for antimicrobial targeting. Here we review current research into bacterial multicomponent transport systems, with an emphasis on the interaction at the membrane, as well as new perspectives on the role of lipids and higher oligomers in these complex systems.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Joshua D Wright
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jane R Allison
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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3
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Tookmanian EM, Belin BJ, Sáenz JP, Newman DK. The role of hopanoids in fortifying rhizobia against a changing climate. Environ Microbiol 2021; 23:2906-2918. [PMID: 33989442 DOI: 10.1111/1462-2920.15594] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Bacteria are a globally sustainable source of fixed nitrogen, which is essential for life and crucial for modern agriculture. Many nitrogen-fixing bacteria are agriculturally important, including bacteria known as rhizobia that participate in growth-promoting symbioses with legume plants throughout the world. To be effective symbionts, rhizobia must overcome multiple environmental challenges: from surviving in the soil, to transitioning to the plant environment, to maintaining high metabolic activity within root nodules. Climate change threatens to exacerbate these challenges, especially through fluctuations in soil water potential. Understanding how rhizobia cope with environmental stress is crucial for maintaining agricultural yields in the coming century. The bacterial outer membrane is the first line of defence against physical and chemical environmental stresses, and lipids play a crucial role in determining the robustness of the outer membrane. In particular, structural remodelling of lipid A and sterol-analogues known as hopanoids are instrumental in stress acclimation. Here, we discuss how the unique outer membrane lipid composition of rhizobia may underpin their resilience in the face of increasing osmotic stress expected due to climate change, illustrating the importance of studying microbial membranes and highlighting potential avenues towards more sustainable soil additives.
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Affiliation(s)
- Elise M Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Brittany J Belin
- Department of Embryology, The Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - James P Sáenz
- B CUBE Center for Molecular Bioengineering, Tatzberg 41, Technische Universität Dresden, Dresden, 01307, Germany
| | - Dianne K Newman
- Division of Biology & Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
- Division of Geology & Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
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4
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Inhibition of the Lysophosphatidylinositol Transporter ABCC1 Reduces Prostate Cancer Cell Growth and Sensitizes to Chemotherapy. Cancers (Basel) 2020; 12:cancers12082022. [PMID: 32718079 PMCID: PMC7465469 DOI: 10.3390/cancers12082022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022] Open
Abstract
Expression of ATP-binding cassette (ABC) transporters has long been implicated in cancer chemotherapy resistance. Increased expression of the ABCC subfamily transporters has been reported in prostate cancer, especially in androgen-resistant cases. ABCC transporters are known to efflux drugs but, recently, we have demonstrated that they can also have a more direct role in cancer progression. The pharmacological potential of targeting ABCC1, however, remained to be assessed. In this study, we investigated whether the blockade of ABCC1 affects prostate cancer cell proliferation using both in vitro and in vivo models. Our data demonstrate that pharmacological inhibition of ABCC1 reduced prostate cancer cell growth in vitro and potentiated the effects of Docetaxel in vitro and in mouse models of prostate cancer in vivo. Collectively, these data identify ABCC1 as a novel and promising target in prostate cancer therapy.
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5
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
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6
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Immadisetty K, Hettige J, Moradi M. Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter. ACS CENTRAL SCIENCE 2019; 5:43-56. [PMID: 30693324 PMCID: PMC6346382 DOI: 10.1021/acscentsci.8b00480] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 06/09/2023]
Abstract
By undergoing conformational changes, active membrane transporters alternate between an inward-facing (IF) and an outward-facing (OF) state to transport their substrates across cellular membrane. The conformational landscape of membrane transporters, however, could be influenced by their environment, and the dependence of the alternating access mechanism on the lipid composition has not been understood at the molecular level. We have performed an extensive set of microsecond-level all-atom molecular dynamics (MD) simulations on bacterial ATP binding cassette (ABC) exporter Sav1866 in six different phosphocholine (PC) and phosphoethanolamine (PE) lipid membrane environments. This study mainly focuses on the energetically downhill OF-to-IF conformational transition of Sav1866 upon the ATP hydrolysis. We observe that the transporter undergoes large-scale conformational changes in the PE environment, particularly in the POPE lipids, resulting in an IF-occluded conformation, a transition that does not occur when the transporter is embedded in any of the PC lipid bilayers. We propose that the PE lipids facilitate the closing of the protein on the periplasmic side due to their highly polar headgroups that mediate the interaction of the two transmembrane (TM) bundles by a network of lipid-lipid and lipid-protein hydrogen bonds. POPE lipids in particular facilitate the closure of periplasmic gate by promoting a hinge formation in TM helices and an interbundle salt bridge formation. This study explains how the alternating access mechanism and the flippase activity in ABC exporters could be lipid-dependent.
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7
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Thonghin N, Collins RF, Barbieri A, Shafi T, Siebert A, Ford RC. Novel features in the structure of P-glycoprotein (ABCB1) in the post-hydrolytic state as determined at 7.9 Å resolution. BMC STRUCTURAL BIOLOGY 2018; 18:17. [PMID: 30545335 PMCID: PMC6293506 DOI: 10.1186/s12900-018-0098-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND P-glycoprotein (ABCB1) is an ATP-binding cassette transporter that plays an important role in the clearance of drugs and xenobiotics and is associated with multi-drug resistance in cancer. Although several P-glycoprotein structures are available, these are either at low resolution, or represent mutated and/or quiescent states of the protein. RESULTS In the post-hydrolytic state the structure of the wild-type protein has been resolved at about 8 Å resolution. The cytosolic nucleotide-binding domains (NBDs) are separated but ADP remains bound, especially at the first NBD. Gaps in the transmembrane domains (TMDs) that connect to an inner hydrophilic cavity are filled by density emerging from the annular detergent micelle. The NBD-TMD linker is partly resolved, being located between the NBDs and close to the Signature regions involved in cooperative NBD dimerization. This, and the gap-filling detergent suggest steric impediment to NBD dimerization in the post-hydrolytic state. Two central regions of density lie in two predicted drug-binding sites, implying that the protein may adventitiously bind hydrophobic substances even in the post-hydrolytic state. The previously unresolved N-terminal extension was observed, and the data suggests these 30 residues interact with the headgroup region of the lipid bilayer. CONCLUSION The structural data imply that (i) a low basal ATPase activity is ensured by steric blockers of NBD dimerization and (ii) allocrite access to the central cavity may be structurally linked to NBD dimerization, giving insights into the mechanism of drug-stimulation of P-glycoprotein activity.
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Affiliation(s)
- Nopnithi Thonghin
- School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Richard F Collins
- School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Alessandro Barbieri
- School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Talha Shafi
- School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Alistair Siebert
- eBIC, Diamond Light Source Ltd, Diamond House, Harwell Science & Innovation Campus, Oxfordshire, Didcot, OX11 0DE, UK
| | - Robert C Ford
- School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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8
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Godinho CP, Prata CS, Pinto SN, Cardoso C, Bandarra NM, Fernandes F, Sá-Correia I. Pdr18 is involved in yeast response to acetic acid stress counteracting the decrease of plasma membrane ergosterol content and order. Sci Rep 2018; 8:7860. [PMID: 29777118 PMCID: PMC5959924 DOI: 10.1038/s41598-018-26128-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/04/2018] [Indexed: 11/11/2022] Open
Abstract
Saccharomyces cerevisiae has the ability to become less sensitive to a broad range of chemically and functionally unrelated cytotoxic compounds. Among multistress resistance mechanisms is the one mediated by plasma membrane efflux pump proteins belonging to the ABC superfamily, questionably proposed to enhance the kinetics of extrusion of all these compounds. This study provides new insights into the biological role and impact in yeast response to acetic acid stress of the multistress resistance determinant Pdr18 proposed to mediate ergosterol incorporation in plasma membrane. The described coordinated activation of the transcription of PDR18 and of several ergosterol biosynthetic genes (ERG2-4, ERG6, ERG24) during the period of adaptation to acetic acid inhibited growth provides further support to the involvement of Pdr18 in yeast response to maintain plasma membrane ergosterol content in stressed cells. Pdr18 role in ergosterol homeostasis helps the cell to counteract acetic acid-induced decrease of plasma membrane lipid order, increase of the non-specific membrane permeability and decrease of transmembrane electrochemical potential. Collectively, our results support the notion that Pdr18-mediated multistress resistance is closely linked to the status of plasma membrane lipid environment related with ergosterol content and the associated plasma membrane properties.
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Affiliation(s)
- Cláudia P Godinho
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Catarina S Prata
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Sandra N Pinto
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.,Centro de Química-Física Molecular, Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Carlos Cardoso
- DivAV, IPMA - Instituto Português do Mar e da Atmosfera, Rua Alfredo Magalhães Ramalho 6, 1495-006, Lisbon, Portugal
| | - Narcisa M Bandarra
- DivAV, IPMA - Instituto Português do Mar e da Atmosfera, Rua Alfredo Magalhães Ramalho 6, 1495-006, Lisbon, Portugal
| | - Fábio Fernandes
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.,Centro de Química-Física Molecular, Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
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9
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Thonghin N, Collins RF, Barbieri A, Shafi T, Siebert A, Ford. RC. Novel features in the structure of P-glycoprotein (ABCB1) in the post-hydrolytic state as determined at 7.9Å resolution.. [DOI: 10.1101/308114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractP-glycoprotein (ABCB1) is a ATP-binding cassette transporter that plays an important role in the removal of drugs and xenobiotic compounds from the cell. It is also associated with multi-drug resistance in cancer. Here we report novel features of the cryo-EM-derived structure of P-glycoprotein in the post-hydrolytic state: The cytosolic nucleotide-binding domains (NBDs) are separated despite ADP remaining bound to the NBDs. Gaps in the TMDs that connect to the inner hydrophilic cavity are back-filled by detergent head-groups from the annular detergent micelle and are close to two regions predicted to delineate two pseudo-symmetry-related drug-binding sites. In this conformation, the (newly-resolved) N-terminal extension, NBD-TMD linker region and gap-filling detergents all appear to impede NBD dimerisation. We propose a model for the mechanism of action of the exporter where ATP will be bound to the protein for most of the time, consistent with the high physiological ATP concentrationsin vivo.
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10
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The Synergetic Effects of Combining Structural Biology and EPR Spectroscopy on Membrane Proteins. CRYSTALS 2017. [DOI: 10.3390/cryst7040117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.
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11
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Neumann J, Rose-Sperling D, Hellmich UA. Diverse relations between ABC transporters and lipids: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:605-618. [PMID: 27693344 DOI: 10.1016/j.bbamem.2016.09.023] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 12/19/2022]
Abstract
It was first discovered in 1992 that P-glycoprotein (Pgp, ABCB1), an ATP binding cassette (ABC) transporter, can transport phospholipids such as phosphatidylcholine, -ethanolamine and -serine as well as glucosylceramide and glycosphingolipids. Subsequently, many other ABC transporters were identified to act as lipid transporters. For substrate transport by ABC transporters, typically a classic, alternating access model with an ATP-dependent conformational switch between a high and a low affinity substrate binding site is evoked. Transport of small hydrophilic substrates can easily be imagined this way, as the molecule can in principle enter and exit the transporter in the same orientation. Lipids on the other hand need to undergo a 180° degree turn as they translocate from one membrane leaflet to the other. Lipids and lipidated molecules are highly diverse, so there may be various ways how to achieve their flipping and flopping. Nonetheless, an increase in biophysical, biochemical and structural data is beginning to shed some light on specific aspects of lipid transport by ABC transporters. In addition, there is now abundant evidence that lipids affect ABC transporter conformation, dynamics as well as transport and ATPase activity in general. In this review, we will discuss different ways in which lipids and ABC transporters interact and how lipid translocation may be achieved with a focus on the techniques used to investigate these processes. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Jennifer Neumann
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dania Rose-Sperling
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Ute A Hellmich
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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12
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Lu Y, Zhang H, Niedzwiedzki DM, Jiang J, Blankenship RE, Gross ML. Fast Photochemical Oxidation of Proteins Maps the Topology of Intrinsic Membrane Proteins: Light-Harvesting Complex 2 in a Nanodisc. Anal Chem 2016; 88:8827-34. [PMID: 27500903 PMCID: PMC5201186 DOI: 10.1021/acs.analchem.6b01945] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although membrane proteins are crucial participants in photosynthesis and other biological processes, many lack high-resolution structures. Prior to achieving a high-resolution structure, we are investigating whether MS-based footprinting can provide coarse-grained protein structure by following structural changes that occur upon ligand binding, pH change, and membrane binding. Our platform probes topology and conformation of membrane proteins by combining MS-based footprinting, specifically fast photochemical oxidation of proteins (FPOP), and lipid Nanodiscs, which are more similar to the native membrane environment than are the widely used detergent micelles. We describe here results that show a protein's outer membrane regions are more heavily footprinted by OH radicals whereas the regions spanning the lipid bilayer remain inert to the labeling. Nanodiscs generally exhibit more protection of membrane proteins compared to detergent micelles and less shielding to those protein residues that exist outside the membrane. The combination of immobilizing the protein in Nanodiscs and footprinting with FPOP is a feasible approach to map extra-membrane protein surfaces, even at the amino-acid level, and to illuminate intrinsic membrane protein topology.
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Affiliation(s)
- Yue Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Dariusz M. Niedzwiedzki
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jing Jiang
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E. Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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13
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Lee CP, Millar AH. The Plant Mitochondrial Transportome: Balancing Metabolic Demands with Energetic Constraints. TRENDS IN PLANT SCIENCE 2016; 21:662-676. [PMID: 27162080 DOI: 10.1016/j.tplants.2016.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
In plants, mitochondrial function is associated with hundreds of metabolic reactions. To facilitate these reactions, charged substrates and cofactors move across the charge-impermeable inner mitochondrial membrane via specialized transporters and must work cooperatively with the electrochemical gradient which is essential for mitochondrial function. The regulatory framework for mitochondrial metabolite transport is expected to be more complex in plants than in mammals owing to the close metabolic association between mitochondrial, plastids, and peroxisome metabolism, as well as to the major diurnal fluctuations in plant metabolic function. We propose here how recent advances can be integrated towards defining the mitochondrial transportome in plants. We also discuss what this reveals about sustaining cooperativity between bioenergetics, metabolism, and transport in typical and challenging environments.
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Affiliation(s)
- Chun Pong Lee
- Australian Reseach Council (ARC) Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
| | - A Harvey Millar
- Australian Reseach Council (ARC) Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia.
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