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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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2
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Spreacker PJ, Brousseau M, Hisao GS, Soltani M, Davis JH, Henzler-Wildman KA. Charge neutralization of the active site glutamates does not limit substrate binding and transport by small multidrug resistance transporter EmrE. J Biol Chem 2022; 299:102805. [PMID: 36529287 PMCID: PMC9860125 DOI: 10.1016/j.jbc.2022.102805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/30/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
EmrE, a small multidrug resistance transporter from Escherichia coli, confers broad-spectrum resistance to polyaromatic cations and quaternary ammonium compounds. Previous transport assays demonstrate that EmrE transports a +1 and a +2 substrate with the same stoichiometry of two protons:one cationic substrate. This suggests that EmrE substrate binding capacity is limited to neutralization of the two essential glutamates, E14A and E14B (one from each subunit in the antiparallel homodimer), in the primary binding site. Here, we explicitly test this hypothesis, since EmrE has repeatedly broken expectations for membrane protein structure and transport mechanism. We previously showed that EmrE can bind a +1 cationic substrate and proton simultaneously, with cationic substrate strongly associated with one E14 residue, whereas the other remains accessible to bind and transport a proton. Here, we demonstrate that EmrE can bind a +2 cation substrate and a proton simultaneously using NMR pH titrations of EmrE saturated with divalent substrates, for a net +1 charge in the transport pore. Furthermore, we find that EmrE can alternate access and transport a +2 substrate and proton at the same time. Together, these results lead us to conclude that E14 charge neutralization does not limit the binding and transport capacity of EmrE.
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Affiliation(s)
- Peyton J. Spreacker
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Merissa Brousseau
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Grant S. Hisao
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Mohammad Soltani
- Department of Chemistry, University of South Alabama, Mobile, Alabama, USA
| | - James H. Davis
- Department of Chemistry, University of South Alabama, Mobile, Alabama, USA
| | - Katherine A. Henzler-Wildman
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin, USA,For correspondence: Katherine A. Henzler-Wildman
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3
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Spreacker PJ, Thomas NE, Beeninga WF, Brousseau M, Porter CJ, Hibbs KM, Henzler-Wildman KA. Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility. Nat Commun 2022; 13:7655. [PMID: 36496486 PMCID: PMC9741644 DOI: 10.1038/s41467-022-35410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Small multidrug resistance (SMR) transporters contribute to antibiotic resistance through proton-coupled efflux of toxic compounds. Previous biophysical studies of the E. coli SMR transporter EmrE suggest that it should also be able to perform proton/toxin symport or uniport, leading to toxin susceptibility rather than resistance in vivo. Here we show EmrE does confer susceptibility to several previously uncharacterized small-molecule substrates in E. coli, including harmane. In vitro electrophysiology assays demonstrate that harmane binding triggers uncoupled proton flux through EmrE. Assays in E. coli are consistent with EmrE-mediated dissipation of the transmembrane pH gradient as the mechanism underlying the in vivo phenotype of harmane susceptibility. Furthermore, checkerboard assays show this alternative EmrE transport mode can synergize with some existing antibiotics, such as kanamycin. These results demonstrate that it is possible to not just inhibit multidrug efflux, but to activate alternative transport modes detrimental to bacteria, suggesting a strategy to address antibiotic resistance.
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Affiliation(s)
- Peyton J Spreacker
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53703, USA
| | - Nathan E Thomas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53703, USA
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, 92093, USA
| | - Will F Beeninga
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53703, USA
| | - Merissa Brousseau
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53703, USA
| | - Colin J Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53703, USA
| | - Kylie M Hibbs
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53703, USA
| | - Katherine A Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53703, USA.
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53703, USA.
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4
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Ceccon A, Kubatova N, Louis JM, Clore GM, Tugarinov V. Global Dynamics of a Protein on the Surface of Anisotropic Lipid Nanoparticles Derived from Relaxation-Based NMR Spectroscopy. J Phys Chem B 2022; 126:5646-5654. [PMID: 35877206 DOI: 10.1021/acs.jpcb.2c03519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The global motions of ubiquitin, a model protein, on the surface of anisotropically tumbling 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG):1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) bicelles are described. The shapes of POPG:DHPC bicelles prepared with high molar ratios q of POPG to DHPC can be approximated by prolate ellipsoids, with the ratio of ellipsoid dimensions and dimensions themselves increasing with higher values of q. Adaptation of the nuclear magnetic resonance (NMR) relaxation-based approach that we previously developed for interactions of ubiquitin with spherical POPG liposomes (Ceccon, A. J. Am. Chem. Soc. 2016, 138, 5789-5792) allowed us to quantitatively analyze the variation in lifetime line broadening of NMR signals (ΔR2) measured for ubiquitin in the presence of q = 2 POPG:DHPC bicelles and the associated transverse spin relaxation rates (R2,B) of bicelle-bound ubiquitin. Ubiquitin, transiently bound to POPG:DHPC bicelles, undergoes internal rotation about an axis orthogonal to the surface of the bicelle and perpendicular to the principal axis of its rotational diffusion tensor on the low microsecond time scale (∼3 μs), while the rotation axis itself wobbles in a cone on a submicrosecond time scale (≤ 500 ns).
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Nina Kubatova
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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5
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Role of a bacterial glycolipid in Sec-independent membrane protein insertion. Sci Rep 2022; 12:12231. [PMID: 35851412 PMCID: PMC9293918 DOI: 10.1038/s41598-022-16304-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/07/2022] [Indexed: 11/08/2022] Open
Abstract
Non-proteinaceous components in membranes regulate membrane protein insertion cooperatively with proteinaceous translocons. An endogenous glycolipid in the Escherichia coli membrane called membrane protein integrase (MPIase) is one such component. Here, we focused on the Sec translocon-independent pathway and examined the mechanisms of MPIase-facilitated protein insertion using physicochemical techniques. We determined the membrane insertion efficiency of a small hydrophobic protein using solid-state nuclear magnetic resonance, which showed good agreement with that determined by the insertion assay using an in vitro translation system. The observed insertion efficiency was strongly correlated with membrane physicochemical properties measured using fluorescence techniques. Diacylglycerol, a trace component of E. coli membrane, reduced the acyl chain mobility in the core region and inhibited the insertion, whereas MPIase restored them. We observed the electrostatic intermolecular interactions between MPIase and the side chain of basic amino acids in the protein, suggesting that the negatively charged pyrophosphate of MPIase attracts the positively charged residues of a protein near the membrane surface, which triggers the insertion. Thus, this study demonstrated the ingenious approach of MPIase to support membrane insertion of proteins by using its unique molecular structure in various ways.
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6
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High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport. Nat Commun 2022; 13:991. [PMID: 35181664 PMCID: PMC8857205 DOI: 10.1038/s41467-022-28556-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/27/2022] [Indexed: 12/20/2022] Open
Abstract
The homo-dimeric bacterial membrane protein EmrE effluxes polyaromatic cationic substrates in a proton-coupled manner to cause multidrug resistance. We recently determined the structure of substrate-bound EmrE in phospholipid bilayers by measuring hundreds of protein-ligand HN–F distances for a fluorinated substrate, 4-fluoro-tetraphenylphosphonium (F4-TPP+), using solid-state NMR. This structure was solved at low pH where one of the two proton-binding Glu14 residues is protonated. Here, to understand how substrate transport depends on pH, we determine the structure of the EmrE-TPP complex at high pH, where both Glu14 residues are deprotonated. The high-pH complex exhibits an elongated and hydrated binding pocket in which the substrate is similarly exposed to the two sides of the membrane. In contrast, the low-pH complex asymmetrically exposes the substrate to one side of the membrane. These pH-dependent EmrE conformations provide detailed insights into the alternating-access model, and suggest that the high-pH conformation may facilitate proton binding in the presence of the substrate, thus accelerating the conformational change of EmrE to export the substrate. EmrE transporter effluxes cationic substrates across lipid membranes in a pH-coupled manner. Here, the authors solve the structure of ligand-bound EmrE at high pH by NMR, with insights into the transport mechanism.
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7
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Lewis A, Kurauskas V, Tonelli M, Henzler-Wildman K. Ion-dependent structure, dynamics, and allosteric coupling in a non-selective cation channel. Nat Commun 2021; 12:6225. [PMID: 34711838 PMCID: PMC8553846 DOI: 10.1038/s41467-021-26538-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
The selectivity filter (SF) determines which ions are efficiently conducted through ion channel pores. NaK is a non-selective cation channel that conducts Na+ and K+ with equal efficiency. Crystal structures of NaK suggested a rigid SF structure, but later solid-state NMR and MD simulations questioned this interpretation. Here, we use solution NMR to characterize how bound Na+ vs. K+ affects NaK SF structure and dynamics. We find that the extracellular end of the SF is flexible on the ps-ns timescale regardless of bound ion. On a slower timescale, we observe a structural change between the Na+ and K+-bound states, accompanied by increased structural heterogeneity in Na+. We also show direct evidence that the SF structure is communicated to the pore via I88 on the M2 helix. These results support a dynamic SF with multiple conformations involved in non-selective conduction. Our data also demonstrate allosteric coupling between the SF and pore-lining helices in a non-selective cation channel that is analogous to the allosteric coupling previously demonstrated for K+-selective channels, supporting the generality of this model. NaK is a bacterial non-selective cation channel. Here, the authors use solution NMR to show that selectivity filter (SF) in NaK is dynamic, with structural differences between the Na+ and K + -bound states. The conformation of the SF is communicated to the pore-lining helices similarly as in the K + -selective channels.
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Affiliation(s)
- Adam Lewis
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Vilius Kurauskas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA. .,National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, 53706, USA.
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8
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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9
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Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles. Molecules 2021; 26:molecules26123607. [PMID: 34204651 PMCID: PMC8231226 DOI: 10.3390/molecules26123607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The driving forces and conformational pathways leading to amphitropic protein-membrane binding and in some cases also to protein misfolding and aggregation is the subject of intensive research. In this study, a chimeric polypeptide, A-Cage-C, derived from α-Lactalbumin is investigated with the aim of elucidating conformational changes promoting interaction with bilayers. From previous studies, it is known that A-Cage-C causes membrane leakages associated with the sporadic formation of amorphous aggregates on solid-supported bilayers. Here we express and purify double-labelled A-Cage-C and prepare partially deuterated bicelles as a membrane mimicking system. We investigate A-Cage-C in the presence and absence of these bicelles at non-binding (pH 7.0) and binding (pH 4.5) conditions. Using in silico analyses, NMR, conformational clustering, and Molecular Dynamics, we provide tentative insights into the conformations of bound and unbound A-Cage-C. The conformation of each state is dynamic and samples a large amount of overlapping conformational space. We identify one of the clusters as likely representing the binding conformation and conclude tentatively that the unfolding around the central W23 segment and its reorientation may be necessary for full intercalation at binding conditions (pH 4.5). We also see evidence for an overall elongation of A-Cage-C in the presence of model bilayers.
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10
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Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers. Nat Commun 2021; 12:172. [PMID: 33420032 PMCID: PMC7794478 DOI: 10.1038/s41467-020-20468-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/01/2020] [Indexed: 01/29/2023] Open
Abstract
The dimeric transporter, EmrE, effluxes polyaromatic cationic drugs in a proton-coupled manner to confer multidrug resistance in bacteria. Although the protein is known to adopt an antiparallel asymmetric topology, its high-resolution drug-bound structure is so far unknown, limiting our understanding of the molecular basis of promiscuous transport. Here we report an experimental structure of drug-bound EmrE in phospholipid bilayers, determined using 19F and 1H solid-state NMR and a fluorinated substrate, tetra(4-fluorophenyl) phosphonium (F4-TPP+). The drug-binding site, constrained by 214 protein-substrate distances, is dominated by aromatic residues such as W63 and Y60, but is sufficiently spacious for the tetrahedral drug to reorient at physiological temperature. F4-TPP+ lies closer to the proton-binding residue E14 in subunit A than in subunit B, explaining the asymmetric protonation of the protein. The structure gives insight into the molecular mechanism of multidrug recognition by EmrE and establishes the basis for future design of substrate inhibitors to combat antibiotic resistance.
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11
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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12
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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13
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Versatile formation of supported lipid bilayers from bicellar mixtures of phospholipids and capric acid. Sci Rep 2020; 10:13849. [PMID: 32796898 PMCID: PMC7427796 DOI: 10.1038/s41598-020-70872-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/29/2020] [Indexed: 01/07/2023] Open
Abstract
Originally developed for the structural biology field, lipid bicelle nanostructures composed of long- and short-chain phospholipid molecules have emerged as a useful interfacial science tool to fabricate two-dimensional supported lipid bilayers (SLBs) on hydrophilic surfaces due to ease of sample preparation, scalability, and versatility. To improve SLB fabrication prospects, there has been recent interest in replacing the synthetic, short-chain phospholipid component of bicellar mixtures with naturally abundant fatty acids and monoglycerides, i.e., lauric acid and monocaprin. Such options have proven successful under specific conditions, however, there is room for devising more versatile fabrication options, especially in terms of overcoming lipid concentration-dependent SLB formation limitations. Herein, we investigated SLB fabrication by using bicellar mixtures consisting of long-chain phospholipid and capric acid, the latter of which has similar headgroup and chain length properties to lauric acid and monocaprin, respectively. Quartz crystal microbalance-dissipation, epifluorescence microscopy, and fluorescence recovery after photobleaching experiments were conducted to characterize lipid concentration-dependent bicelle adsorption onto silicon dioxide surfaces. We identified that uniform-phase SLB formation occurred independently of total lipid concentration when the ratio of long-chain phospholipid to capric acid molecules ("q-ratio") was 0.25 or 2.5, which is superior to past results with lauric acid- and monocaprin-containing bicelles in which cases lipid concentration-dependent behavior was observed. Together, these findings demonstrate that capric acid-containing bicelles are versatile tools for SLB fabrication and highlight how the molecular structure of bicelle components can be rationally finetuned to modulate self-assembly processes at solid-liquid interfaces.
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14
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Danmaliki GI, Hwang PM. Solution NMR spectroscopy of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183356. [PMID: 32416193 DOI: 10.1016/j.bbamem.2020.183356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/06/2023]
Abstract
Integral membrane proteins (IMPs) perform unique and indispensable functions in the cell, making them attractive targets for fundamental research and drug discovery. Developments in protein production, isotope labeling, sample preparation, and pulse sequences have extended the utility of solution NMR spectroscopy for studying IMPs with multiple transmembrane segments. Here we review some recent applications of solution NMR for studying structure, dynamics, and interactions of polytopic IMPs, emphasizing strategies used to overcome common technical challenges.
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Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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15
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Sut TN, Park S, Yoon BK, Jackman JA, Cho NJ. Supported Lipid Bilayer Formation from Phospholipid-Fatty Acid Bicellar Mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5021-5029. [PMID: 32308002 DOI: 10.1021/acs.langmuir.0c00675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Supported lipid bilayers (SLBs) are versatile cell membrane-mimicking biointerfaces for various applications such as biosensors and drug delivery systems, and there is broad interest in developing simple, cost-effective methods to achieve SLB fabrication. One promising approach involves the deposition of quasi-two-dimensional bicelle nanostructures that are composed of long-chain phospholipids and either short-chain phospholipids or detergent molecules. While a variety of long-chain phospholipids have been used to prepare bicelles for SLB fabrication applications, only two short-chain phospholipids, 1,2-dihexanoyl-sn-glycero-3-phosphocholine and 1,2-diheptanoyl-sn-glycero-3-phosphocholine (collectively referred to as DHPC), have been investigated. There remains an outstanding need to identify natural alternatives to DHPC, especially ones that are more affordable, to improve fabrication prospects and application opportunities. Herein, we explored the potential to fabricate SLBs from bicellar mixtures composed of long-chain phospholipids and lauric acid (LA), which is a low-cost, naturally abundant fatty acid that is widely used in soapmaking and various industrial applications. Quartz crystal microbalance-dissipation (QCM-D) experiments were conducted to track bicelle adsorption onto silica surfaces as a function of bicelle composition and lipid concentration, along with time-lapse fluorescence microscopy imaging and fluorescence recovery after photobleaching (FRAP) experiments to further characterize lipid adlayer properties. The results identified optimal conditions where it is possible to efficiently form SLBs from LA-containing bicelles at low lipid concentrations while also unraveling mechanistic insights into the bicelle-mediated SLB formation process and verifying that LA-containing bicelles are biocompatible with human cells for surface coating applications.
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Affiliation(s)
- Tun Naw Sut
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Soohyun Park
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Bo Kyeong Yoon
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Joshua A Jackman
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
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16
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Gao YG, My Le LT, Zhai X, Boldyrev IA, Mishra SK, Tischer A, Murayama T, Nishida A, Molotkovsky JG, Alam A, Brown RE. Measuring Lipid Transfer Protein Activity Using Bicelle-Dilution Model Membranes. Anal Chem 2020; 92:3417-3425. [PMID: 31970977 DOI: 10.1021/acs.analchem.9b05523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In vitro assessment of lipid intermembrane transfer activity by cellular proteins typically involves measurement of either radiolabeled or fluorescently labeled lipid trafficking between vesicle model membranes. Use of bilayer vesicles in lipid transfer assays usually comes with inherent challenges because of complexities associated with the preparation of vesicles and their rather short "shelf life". Such issues necessitate the laborious task of fresh vesicle preparation to achieve lipid transfer assays of high quality, precision, and reproducibility. To overcome these limitations, we have assessed model membrane generation by bicelle dilution for monitoring the transfer rates and specificity of various BODIPY-labeled sphingolipids by different glycolipid transfer protein (GLTP) superfamily members using a sensitive fluorescence resonance energy transfer approach. Robust, protein-selective sphingolipid transfer is observed using donor and acceptor model membranes generated by dilution of 0.5 q-value mixtures. The sphingolipid transfer rates are comparable to those observed between small bilayer vesicles produced by sonication or ethanol injection. Among the notable advantages of using bicelle-generated model membranes are (i) easy and straightforward preparation by means that avoid lipid fluorophore degradation and (ii) long "shelf life" after production (≥6 days) and resilience to freeze-thaw storage. The bicelle-dilution-based assay is sufficiently robust, sensitive, and stable for application, not only to purified LTPs but also for LTP activity detection in crude cytosolic fractions of cell homogenates.
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Affiliation(s)
- Yong-Guang Gao
- The Hormel Institute , University of Minnesota , 801 16th Avenue NE , Austin , Minnesota 55912 , United States
| | - Le Thi My Le
- The Hormel Institute , University of Minnesota , 801 16th Avenue NE , Austin , Minnesota 55912 , United States
| | - Xiuhong Zhai
- The Hormel Institute , University of Minnesota , 801 16th Avenue NE , Austin , Minnesota 55912 , United States
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , 117997 Moscow , Russian Federation
| | - Shrawan K Mishra
- The Hormel Institute , University of Minnesota , 801 16th Avenue NE , Austin , Minnesota 55912 , United States
| | - Alexander Tischer
- Mayo Clinic Division of Hematology , 150 Third Street SW , Stabile Building, Rochester , Minnesota 55905 , United States
| | - Toshihiko Murayama
- Graduate School of Pharmaceutical Sciences , Chiba University , Inohana 1-8-1 , Chuo-ku, Chiba 260-8675 , Japan
| | - Atsushi Nishida
- Graduate School of Pharmaceutical Sciences , Chiba University , Inohana 1-8-1 , Chuo-ku, Chiba 260-8675 , Japan
| | - Julian G Molotkovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , 117997 Moscow , Russian Federation
| | - Amer Alam
- The Hormel Institute , University of Minnesota , 801 16th Avenue NE , Austin , Minnesota 55912 , United States
| | - Rhoderick E Brown
- The Hormel Institute , University of Minnesota , 801 16th Avenue NE , Austin , Minnesota 55912 , United States
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17
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F Dudás E, Wacha A, Bóta A, Bodor A. Peptide-bicelle interaction: Following variations in size and morphology by a combined NMR-SAXS approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183095. [PMID: 31672542 DOI: 10.1016/j.bbamem.2019.183095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
Abstract
Changes in membrane properties occurring upon protein interaction are key questions in understanding membrane protein function. To report on the occurring size and shape variation we present here a combined NMR-SAXS method performed under physiological conditions using the same samples, enabling determination of a global parameter, the hydration radius (rH) and estimating the bicelle shape. We use zwitterionic (DMPC/DHPC) and negatively charged (DMPC/DHPC/DMPG) bicelles and investigate the interaction with model transmembrane and surface active peptides (KALP23 and melittin). 1H NMR measurements based mostly on the translational diffusion coefficient D determination are used to characterize cmc values of DHPC micelles under the investigated conditions, to describe DHPC distribution with exact determination of the q (long chain/short chain) lipid ratio, to estimate aggregation numbers and effective rH values. The scattering curve is used to fit a lenticular core-shell model enabling us to describe the bicelle shape in terms of ellipsoidal axis length parameters. For all studied systems formation of oblate ellipsoids is found. Even though the rG/rH ratio would be an elegant way to characterize shape variations, we show that changes occurring upon peptide-bicelle interaction in the "effective" size and in the measure on the anisometry - morphology - of the objects can be described by using rH and the simplistic ellipsoidal core-shell model. While the influence of the transmembrane KALP peptide is significant, effects upon addition of surface active melittin peptide seem negligible. This synergy of techniques under controlled conditions can provide information about bicellar shape modulation occurring during peptide-bicelle interactions.
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Affiliation(s)
- E F Dudás
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - A Wacha
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bóta
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary.
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18
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Barniol-Xicota M, Verhelst SHL. Isolation of intramembrane proteases in membrane-like environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183193. [PMID: 31945321 DOI: 10.1016/j.bbamem.2020.183193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/24/2022]
Abstract
Intramembrane proteases (IMPs) are proteolytic enzymes embedded in the lipid bilayer, where they cleave transmembrane substrates. The importance of IMPs relies on their role in a wide variety of cellular processes and diseases. In order to study the activity and function of IMPs, their purified form is often desired. The production of pure and active IMPs has proven to be a challenging task. This process unavoidably requires the use of solubilizing agents that will, to some extent, alter the native environment of these proteases. In this review we present the current solubilization and reconstitution techniques that have been applied to IMPs. In addition, we describe how these techniques had an influence on the activity and structural studies of IMPs, focusing on rhomboid proteases and γ-secretase.
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Affiliation(s)
- Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium.
| | - Steven H L Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium; Leibniz Institute for Analytical Sciences, ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
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19
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Schmidpeter PAM, Sukomon N, Nimigean CM. Reconstitution of Membrane Proteins into Platforms Suitable for Biophysical and Structural Analyses. Methods Mol Biol 2020; 2127:191-205. [PMID: 32112324 PMCID: PMC9288841 DOI: 10.1007/978-1-0716-0373-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Integral membrane proteins have historically been challenging targets for biophysical research due to their low solubility in aqueous solution. Their importance for chemical and electrical signaling between cells, however, makes them fascinating targets for investigators interested in the regulation of cellular and physiological processes. Since membrane proteins shunt the barrier imposed by the cell membrane, they also serve as entry points for drugs, adding pharmaceutical research and development to the interests. In recent years, detailed understanding of membrane protein function has significantly increased due to high-resolution structural information obtained from single-particle cryo-EM, X-ray crystallography, and NMR. In order to further advance our mechanistic understanding on membrane proteins as well as foster drug development, it is crucial to generate more biophysical and functional data on these proteins under defined conditions. To that end, different techniques have been developed to stabilize integral membrane proteins in native-like environments that allow both structural and biophysical investigations-amphipols, lipid bicelles, and lipid nanodiscs. In this chapter, we provide detailed protocols for the reconstitution of membrane proteins according to these three techniques. We also outline some of the possible applications of each technique and discuss their advantages and possible caveats.
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Affiliation(s)
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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20
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Bhaduri S, Zhang H, Erramilli S, Cramer WA. Structural and functional contributions of lipids to the stability and activity of the photosynthetic cytochrome b 6 f lipoprotein complex. J Biol Chem 2019; 294:17758-17767. [PMID: 31597701 DOI: 10.1074/jbc.ra119.009331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 10/08/2019] [Indexed: 11/06/2022] Open
Abstract
The photosynthetic cytochrome b 6 f complex, a homodimer containing eight distinct subunits and 26 transmembrane helices per monomer, catalyzes proton-coupled electron transfer across the thylakoid membrane. The 2.5-Å-resolution structure of the complex from the cyanobacterium Nostoc sp. revealed the presence of 23 lipid-binding sites per monomer. Although the crystal structure of the cytochrome b 6 f from a plant source has not yet been solved, the identities of the lipids present in a plant b 6 f complex have previously been determined, indicating that the predominant lipid species are monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), phosphatidylglycerol (PG), and sulfoquinovosyldiacylglycerol (SQDG). Despite the extensive structural analyses of b 6 f-lipid interactions, the basis of the stabilization by lipids remains poorly understood. In the present study, we report on the effect of individual lipids on the structural and functional integrity of the b 6 f complex, purified from Spinacea oleracea It was found that (i) galactolipids (MGDG, DGDG, and SQDG) and phospholipids dilinolenoyl-phosphatidylglycerol (DLPG), 1,2-dioleoylphosphatidylglycerol (DOPG), and 1,2-dioleoyl-sn-glycerol-3-phosphatidylcholine (DOPC) structurally stabilize the complex to varying degrees; (ii) SQDG has a major role in stabilizing the dimeric complex; (iii) the b 6 f complex is stabilized by incorporation into nanodiscs or bicelles; (iv) removal of bound phospholipid by phospholipase A2 inactivates the cytochrome complex; and (v) activity can be restored significantly by the addition of the anionic lipid PG, which is attributed to stabilization of the quinone portal and the hinge region of the iron-sulfur protein.
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Affiliation(s)
- Satarupa Bhaduri
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47906
| | - Huamin Zhang
- SSCI, a Division of Albany Molecular Research Inc., West Lafayette, Indiana 47906
| | - Satchal Erramilli
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois 60637
| | - William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47906
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21
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Tsopelas F, Tsantili-Kakoulidou A. Advances with weak affinity chromatography for fragment screening. Expert Opin Drug Discov 2019; 14:1125-1135. [DOI: 10.1080/17460441.2019.1648425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fotios Tsopelas
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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22
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Wu C, Wynne SA, Thomas NE, Uhlemann EM, Tate CG, Henzler-Wildman KA. Identification of an Alternating-Access Dynamics Mutant of EmrE with Impaired Transport. J Mol Biol 2019; 431:2777-2789. [PMID: 31158365 PMCID: PMC6599891 DOI: 10.1016/j.jmb.2019.05.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 11/25/2022]
Abstract
Proteins that perform active transport must alternate the access of a binding site, first to one side of a membrane and then to the other, resulting in the transport of bound substrates across the membrane. To better understand this process, we sought to identify mutants of the small multidrug resistance transporter EmrE with reduced rates of alternating access. We performed extensive scanning mutagenesis by changing every amino acid residue to Val, Ala, or Gly, and then screening the drug resistance phenotypes of the resulting mutants. We identified EmrE mutants that had impaired transport activity but retained the ability to bind substrate and further tested their alternating access rates using NMR. Ultimately, we were able to identify a single mutation, S64V, which significantly reduced the rate of alternating access but did not impair substrate binding. Six other transport-impaired mutants did not have reduced alternating access rates, highlighting the importance of other aspects of the transport cycle to achieve drug resistance activity in vivo. To better understand the transport cycle of EmrE, efforts are now underway to determine a high-resolution structure using the S64V mutant identified here.
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Affiliation(s)
- Chao Wu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, MO 63110, USA
| | | | - Nathan E Thomas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eva-Maria Uhlemann
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, MO 63110, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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23
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Chen H, Pan J, Gandhi DM, Dockendorff C, Cui Q, Chanda B, Henzler-Wildman KA. NMR Structural Analysis of Isolated Shaker Voltage-Sensing Domain in LPPG Micelles. Biophys J 2019; 117:388-398. [PMID: 31301804 DOI: 10.1016/j.bpj.2019.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/20/2019] [Indexed: 11/25/2022] Open
Abstract
The voltage-sensing domain (VSD) is a conserved structural module that regulates the gating of voltage-dependent ion channels in response to a change in membrane potential. Although the structures of many VSD-containing ion channels are now available, our understanding of the structural dynamics associated with gating transitions remains limited. To probe dynamics with site-specific resolution, we utilized NMR spectroscopy to characterize the VSD derived from Shaker potassium channel in 1-palmitoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) (LPPG) micelles. The backbone dihedral angles predicted based on secondary chemical shifts using torsion angle likeliness obtained from shift (TALOS+) showed that the Shaker-VSD shares many structural features with the homologous Kv1.2/2.1 chimera, including a transition from α-helix to 310 helix in the C-terminal portion of the fourth transmembrane helix. Nevertheless, there are clear differences between the Shaker-VSD and Kv1.2/2.1 chimera in the S2-S3 linker and S3 transmembrane region, where the organization of secondary structure elements in Shaker-VSD appears to more closely resemble the KvAP-VSD. Comparison of microsecond-long molecular dynamics simulations of Kv 1.2-VSD in LPPG micelles and a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayer showed that LPPG micelles do not induce significant structural distortion in the isolated voltage sensor. To assess the integrity of the tertiary fold, we directly probed the binding of BrMT analog 2-[2-({[3-(2-amino-ethyl)-6-bromo-1H-indol-2-yl]methoxy}k7methyl)-6-bromo-1H-indol-3-yl]ethan-1-amine (BrET), a gating modifier toxin, and identified the location of the putative binding site. Our results suggest that the Shaker-VSD in LPPG micelles is in a native-like fold and is likely to provide valuable insights into the dynamics of voltage-gating and its regulation.
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Affiliation(s)
- Hongbo Chen
- Graduate Program in Biophysics, Madison, Wisconsin; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Junkun Pan
- Department of Neuroscience, Madison, Wisconsin; Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
| | - Disha M Gandhi
- Departments of Chemistry, Marquette University, Milwaukee, Wisconsin
| | - Chris Dockendorff
- Departments of Chemistry, Marquette University, Milwaukee, Wisconsin
| | - Qiang Cui
- Departments of Chemistry, Physics, Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Baron Chanda
- Graduate Program in Biophysics, Madison, Wisconsin; Department of Neuroscience, Madison, Wisconsin; Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin.
| | - Katherine A Henzler-Wildman
- Graduate Program in Biophysics, Madison, Wisconsin; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin.
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24
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Sut TN, Jackman JA, Cho NJ. Understanding How Membrane Surface Charge Influences Lipid Bicelle Adsorption onto Oxide Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8436-8444. [PMID: 31141663 DOI: 10.1021/acs.langmuir.9b00570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The adsorption of two-dimensional bicellar disks onto solid supports is an emerging fabrication technique to form supported lipid bilayers (SLBs) that is efficient and requires minimal sample preparation. To date, nearly all relevant studies have focused on zwitterionic lipid compositions and silica-based surfaces, and extending the scope of investigation to other lipid compositions and surfaces would improve our understanding of application possibilities and underpinning formation processes. Herein, using the quartz crystal microbalance-dissipation technique, we systematically investigated the adsorption of charged lipid bicelles onto silicon dioxide, titanium oxide, and aluminum oxide surfaces. Depending on the lipid composition and substrate, we observed different adsorption pathways, including (i) SLB formation via one- or two-step adsorption kinetics, (ii) monotonic adsorption without SLB formation, and (iii) negligible adsorption. On each substrate, SLB formation could be achieved with particular lipid compositions, whereas the trend in adsorption pathways varied according to the substrate and could be controlled by adjusting the bicelle?substrate interaction strength. To rationalize these findings, we discuss how electrostatic and hydration forces affect bicelle?substrate interactions on different oxide surfaces. Collectively, our findings demonstrate the broad utility of lipid bicelles for SLB formation while revealing physicochemical insights into the role of interfacial forces in controlling bicelle adsorption pathways.
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Affiliation(s)
- Tun Naw Sut
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue 639798 , Singapore
| | - Joshua A Jackman
- School of Chemical Engineering , Sungkyunkwan University , Suwon 16419 , Republic of Korea
| | - Nam-Joon Cho
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue 639798 , Singapore
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive 637459 , Singapore
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25
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Bada Juarez JF, Harper AJ, Judge PJ, Tonge SR, Watts A. From polymer chemistry to structural biology: The development of SMA and related amphipathic polymers for membrane protein extraction and solubilisation. Chem Phys Lipids 2019; 221:167-175. [PMID: 30940445 DOI: 10.1016/j.chemphyslip.2019.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 12/13/2022]
Abstract
Nanoparticles assembled with poly(styrene-maleic acid) copolymers, identified in the literature as Lipodisq, SMALPs or Native Nanodisc, are routinely used as membrane mimetics to stabilise protein structures in their native conformation. To date, transmembrane proteins of varying complexity (up to 8 beta strands or 48 alpha helices) and of a range of molecular weights (from 27 kDa up to 500 kDa) have been incorporated into this particle system for structural and functional studies. SMA and related amphipathic polymers have become versatile components of the biochemist's tool kit for the stabilisation, extraction and structural characterization of membrane proteins by techniques including cryo-EM and X-ray crystallography. Lipodisq formation does not require the use of conventional detergents and thus avoids their associated detrimental consequences. Here the development of this technology, from its fundamental concept and design to the diverse range of experimental methodologies to which it can now be applied, will be reviewed.
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Affiliation(s)
| | - Andrew J Harper
- Malvern Cosmeceutics Ltd, Malvern Hills Science Park, Geraldine Road, Malvern, WR14 3SZ, UK
| | - Peter J Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Stephen R Tonge
- Malvern Cosmeceutics Ltd, Malvern Hills Science Park, Geraldine Road, Malvern, WR14 3SZ, UK
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK.
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26
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Thomas NE, Wu C, Morrison EA, Robinson AE, Werner JP, Henzler-Wildman KA. The C terminus of the bacterial multidrug transporter EmrE couples drug binding to proton release. J Biol Chem 2018; 293:19137-19147. [PMID: 30287687 DOI: 10.1074/jbc.ra118.005430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/25/2018] [Indexed: 01/16/2023] Open
Abstract
Ion-coupled transporters must regulate access of ions and substrates into and out of the binding site to actively transport substrates and minimize dissipative leak of ions. Within the single-site alternating access model, competitive substrate binding forms the foundation of ion-coupled antiport. Strict competition between substrates leads to stoichiometric antiport without slippage. However, recent NMR studies of the bacterial multidrug transporter EmrE have demonstrated that this multidrug transporter can simultaneously bind drug and proton, which will affect the transport stoichiometry and efficiency of coupled antiport. Here, we investigated the nature of substrate competition in EmrE using multiple methods to measure proton release upon the addition of saturating concentrations of drug as a function of pH. The resulting proton-release profile confirmed simultaneous binding of drug and proton, but suggested that a residue outside EmrE's Glu-14 binding site may release protons upon drug binding. Using NMR-monitored pH titrations, we trace this drug-induced deprotonation event to His-110, EmrE's C-terminal residue. Further NMR experiments disclosed that the C-terminal tail is strongly coupled to EmrE's drug-binding domain. Consideration of our results alongside those from previous studies of EmrE suggests that this conserved tail participates in secondary gating of EmrE-mediated proton/drug transport, occluding the binding pocket of fully protonated EmrE in the absence of drug to prevent dissipative proton transport.
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Affiliation(s)
- Nathan E Thomas
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Chao Wu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Emma A Morrison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Anne E Robinson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Josephine P Werner
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Katherine A Henzler-Wildman
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and .,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
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27
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Caldwell TA, Baoukina S, Brock AT, Oliver RC, Root KT, Krueger JK, Glover KJ, Tieleman DP, Columbus L. Low- q Bicelles Are Mixed Micelles. J Phys Chem Lett 2018; 9:4469-4473. [PMID: 30024762 PMCID: PMC6353637 DOI: 10.1021/acs.jpclett.8b02079] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bicelles are used in many membrane protein studies because they are thought to be more bilayer-like than micelles. We investigated the properties of "isotropic" bicelles by small-angle neutron scattering, small-angle X-ray scattering, fluorescence anisotropy, and molecular dynamics. All data suggest that bicelles with a q value below 1 deviate from the classic bicelle that contains lipids in the core and detergent in the rim. Thus not all isotropic bicelles are bilayer-like.
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Affiliation(s)
- Tracy A. Caldwell
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Svetlana Baoukina
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ashton T. Brock
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ryan C. Oliver
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kyle T. Root
- Department of Chemistry, Lock Haven University, Lock Haven, Pennsylvania 17745, United States
| | - Joanna K. Krueger
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kerney Jebrell Glover
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - D. Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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28
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Robinson AE, Henderson JP, Henzler-Wildman KA. A mass spectrometry based transport assay for studying EmrE transport of unlabeled substrates. Anal Biochem 2018; 549:130-135. [PMID: 29559333 PMCID: PMC5938110 DOI: 10.1016/j.ab.2018.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/22/2022]
Abstract
Membrane transporters are an important class of proteins which remain challenging to study. Transport assays are crucial to developing our understanding of such proteins as they allow direct measurement of their transport activity. However, currently available methods for monitoring liposomal loading of organic substrates primarily rely on detection of radioactively or fluorescently labeled substrates. The requirement of a labeled substrate significantly restricts the systems and substrates that can be studied. Here we present a mass spectrometry based detection method for liposomal uptake assays that eliminates the need for labeled substrates. We demonstrate the efficacy of the assay with EmrE, a small multidrug resistance transporter found in E. coli that has become a model transport system for the study of secondary active transport. Furthermore, we develop a method for differentiation between bound and transported substrate, enhancing the information gained from the liposomal uptake assay. The transport assay presented here is readily applicable to other transport systems and substrates.
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Affiliation(s)
- Anne E Robinson
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States; Center for Women's Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Jeffrey P Henderson
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States; Center for Women's Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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Gruenhagen TC, Ziarek JJ, Schlebach JP. Bicelle size modulates the rate of bacteriorhodopsin folding. Protein Sci 2018; 27:1109-1112. [PMID: 29604129 DOI: 10.1002/pro.3414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 11/09/2022]
Abstract
The conformational equilibria of integral membrane proteins have proven extremely difficult to characterize within native lipid bilayers. To circumvent technical issues, investigations of the structure and stability of α-helical membrane proteins are often carried out in mixed micelle or bicelle solvents that mimic the membrane and facilitate measurements of reversible folding. Under these conditions, the energetics of membrane protein folding are typically proportional to the mole fraction of an anionic detergent in the micelle. However, investigations of the folding and unfolding of bacteriorhodopsin (bR) surprisingly revealed that the folding rate is also highly sensitive to the bulk molar concentration of lipids and detergents. We show here that this rate enhancement coincides with changes in bicelle size and suggest this effect arises through restriction of the conformational search space during folding. In conjunction with previous mutagenic studies, these results provide additional evidence that a topological search limits the rate of bR folding. Furthermore, this finding provides insights into the manner by which micellar and bicellar environments influence the conformational stability of polytopic membrane proteins.
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Affiliation(s)
| | - Joshua J Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, 47405-7102
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30
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Abstract
EmrE is a small multidrug resistance transporter found in Escherichia coli that confers resistance to toxic polyaromatic cations due to its proton-coupled antiport of these substrates. Here we show that EmrE breaks the rules generally deemed essential for coupled antiport. NMR spectra reveal that EmrE can simultaneously bind and cotransport proton and drug. The functional consequence of this finding is an exceptionally promiscuous transporter: not only can EmrE export diverse drug substrates, it can couple antiport of a drug to either one or two protons, performing both electrogenic and electroneutral transport of a single substrate. We present a free-exchange model for EmrE antiport that is consistent with these results and recapitulates ∆pH-driven concentrative drug uptake. Kinetic modeling suggests that free exchange by EmrE sacrifices coupling efficiency but boosts initial transport speed and drug release rate, which may facilitate efficient multidrug efflux.
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31
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Kolahdouzan K, Jackman JA, Yoon BK, Kim MC, Johal MS, Cho NJ. Optimizing the Formation of Supported Lipid Bilayers from Bicellar Mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5052-5064. [PMID: 28457139 DOI: 10.1021/acs.langmuir.7b00210] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Supported lipid bilayers (SLBs) are widely studied model membrane platforms that are compatible with various surface-sensitive measurement techniques. SLBs are typically formed on silica-based materials, and there are numerous possible fabrication routes involving either bottom-up molecular self-assembly or vesicle adsorption and rupture. In between these two classes of fabrication strategies lies an emerging approach based on depositing quasi-two-dimensional lamellar, bicellar disks composed of a mixture of long-chain and short-chain phospholipids to promote the formation of SLBs. This approach takes advantage of the thermodynamic preference of long-chain phospholipids to form planar SLBs, whereas short-chain phospholipids have brief residence times. Although a few studies have shown that SLBs can be formed on silica-based materials from bicellar mixtures, outstanding questions remain about the self-assembly mechanism as well as the influence of the total phospholipid concentration, ratio of the two phospholipids (termed the "q-ratio"), and process of sample preparation. Herein, we address these questions through comprehensive quartz crystal microbalance-dissipation, fluorescence microscopy, and fluorescence recovery after photobleaching experiments. Our findings identify that optimal SLB formation occurs at lower total concentrations of phospholipids than previously used as short-chain phospholipids behave like membrane-destabilizing detergents at higher concentrations. Using lower phospholipid concentrations, we also discovered that the formation of SLBs proceeds through a two-step mechanism involving a critical coverage of bicellar disks akin to vesicle fusion. In addition, the results indicate that at least one cycle of freeze-thaw-vortexing is useful during the sample preparation process to produce SLBs. Taken together, the findings in this work identify optimal routes for fabricating SLBs from bicellar mixtures and reveal mechanistic details about the bicelle-mediated SLB formation process, which will aid further exploration of bicellar mixtures as tools for model membrane fabrication.
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Affiliation(s)
- Kavoos Kolahdouzan
- Department of Chemistry, Pomona College , 645 North College Avenue, Claremont, California 91711, United States
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
| | - Bo Kyeong Yoon
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
| | - Min Chul Kim
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
| | - Malkiat S Johal
- Department of Chemistry, Pomona College , 645 North College Avenue, Claremont, California 91711, United States
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University , 62 Nanyang Drive, 637459, Singapore
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32
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From Nanodiscs to Isotropic Bicelles: A Procedure for Solution Nuclear Magnetic Resonance Studies of Detergent-Sensitive Integral Membrane Proteins. Structure 2016; 24:1830-1841. [PMID: 27618661 DOI: 10.1016/j.str.2016.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/25/2016] [Accepted: 07/25/2016] [Indexed: 01/04/2023]
Abstract
Nanodiscs and isotropic bicelles are promising membrane mimetics in the field of solution nuclear magnetic resonance (NMR) spectroscopy of integral membrane proteins (IMPs). Despite varied challenges to solution NMR studies of IMPs, we attribute the paucity of solution NMR structures in these environments to the inability of diverse IMPs to withstand detergent treatment during standard nanodisc and bicelle preparations. Here, we present a strategy that creates small isotropic bicelles from IMPs co-translationally embedded in large nanodiscs using cell-free expression. Our results demonstrate appreciable gains in NMR spectral quality while preserving lipid-IMP contacts. We validate the approach on the detergent-sensitive LspA, which finally allowed us to perform high-quality triple-resonance NMR experiments for structural studies. Our strategy of producing bicelles from nanodiscs comprehensively avoids detergent during expression and preparation and is suitable for solution NMR spectroscopy of lipid-IMP complexes.
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33
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Kim DM, Dikiy I, Upadhyay V, Posson DJ, Eliezer D, Nimigean CM. Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles. J Gen Physiol 2016; 148:119-32. [PMID: 27432996 PMCID: PMC4969796 DOI: 10.1085/jgp.201611602] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/27/2016] [Indexed: 12/27/2022] Open
Abstract
The process of ion channel gating-opening and closing-involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Igor Dikiy
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065
| | - Vikrant Upadhyay
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
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34
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Kiselev MA, Lombardo D. Structural characterization in mixed lipid membrane systems by neutron and X-ray scattering. Biochim Biophys Acta Gen Subj 2016; 1861:3700-3717. [PMID: 27138452 DOI: 10.1016/j.bbagen.2016.04.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 01/13/2023]
Abstract
Lipids membranes, the primary component of the living cell, involve collective behaviour of numerous interacting molecules. The rich morphology and complex phase diagram of the lipid systems require different strategies in describing bio-membranes in order to capture the essential properties of self-assembly processes as well as the underling molecular collective phenomena involved in biological functions. Among the experimental methods used, the scattering techniques such as small angle neutrons and X-rays scattering (SANS and SAXS) are probably the most important experimental approaches for the structural investigation of bio-membranes and mixed lipids complex systems. In this tutorial review we describe the main approaches employed in the investigation of lipid bio-membranes by means of the neutron and x-ray scattering techniques. While introducing the main structural properties of lipid bio-membranes we highlight the important role of lipid components in different biological functions of living organisms. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Mikhail A Kiselev
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Ulica Joliot-Curie 6, Dubna, Moscow 141980, Russia
| | - Domenico Lombardo
- CNR-IPCF, Consiglio Nazionale delle Ricerche. Istituto per i Processi Chimico Fisici, Viale F.S. D'Alcontres, No. 37, 98158 Messina, Italy.
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35
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Mercredi PY, Bucca N, Loeliger B, Gaines CR, Mehta M, Bhargava P, Tedbury PR, Charlier L, Floquet N, Muriaux D, Favard C, Sanders CR, Freed EO, Marchant J, Summers MF. Structural and Molecular Determinants of Membrane Binding by the HIV-1 Matrix Protein. J Mol Biol 2016; 428:1637-55. [PMID: 26992353 DOI: 10.1016/j.jmb.2016.03.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Assembly of HIV-1 particles is initiated by the trafficking of viral Gag polyproteins from the cytoplasm to the plasma membrane, where they co-localize and bud to form immature particles. Membrane targeting is mediated by the N-terminally myristoylated matrix (MA) domain of Gag and is dependent on the plasma membrane marker phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. Recent studies revealed that PI(4,5)P2 molecules containing truncated acyl chains [tr-PI(4,5)P2] are capable of binding MA in an "extended lipid" conformation and promoting myristoyl exposure. Here we report that tr-PI(4,5)P2 molecules also readily bind to non-membrane proteins, including HIV-1 capsid, which prompted us to re-examine MA-PI(4,5)P2 interactions using native lipids and membrane mimetic liposomes and bicelles. Liposome binding trends observed using a recently developed NMR approach paralleled results of flotation assays, although the affinities measured under the equilibrium conditions of NMR experiments were significantly higher. Native PI(4,5)P2 enhanced MA binding to liposomes designed to mimic non-raft-like regions of the membrane, suggesting the possibility that binding of the protein to disordered domains may precede Gag association with, or nucleation of, rafts. Studies with bicelles revealed a subset of surface and myr-associated MA residues that are sensitive to native PI(4,5)P2, but cleft residues that interact with the 2'-acyl chains of tr-PI(4,5)P2 molecules in aqueous solution were insensitive to native PI(4,5)P2 in bicelles. Our findings call to question extended-lipid MA:membrane binding models, and instead support a model put forward from coarse-grained simulations indicating that binding is mediated predominantly by dynamic, electrostatic interactions between conserved basic residues of MA and multiple PI(4,5)P2 and phosphatidylserine molecules.
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Affiliation(s)
- Peter Y Mercredi
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Nadine Bucca
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Burk Loeliger
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Christy R Gaines
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Mansi Mehta
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Pallavi Bhargava
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Philip R Tedbury
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, National Cancer Institute at Fredrick, Fredrick, MD 21702-1201, USA
| | - Landry Charlier
- Institut des Biomolécules Max Mousseron, CNRS UMR5247, Université Montpellier, Faculté de Pharmacie, Montpellier Cedex 05, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron, CNRS UMR5247, Université Montpellier, Faculté de Pharmacie, Montpellier Cedex 05, France
| | - Delphine Muriaux
- Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé CNRS-UMR 5236, Université Montpellier, Montpellier Cedex 5, France
| | - Cyril Favard
- Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé CNRS-UMR 5236, Université Montpellier, Montpellier Cedex 5, France
| | - Charles R Sanders
- Department of Biochemistry, Center for Structural Biology, and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37240-7917, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, National Cancer Institute at Fredrick, Fredrick, MD 21702-1201, USA.
| | - Jan Marchant
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
| | - Michael F Summers
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
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36
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Duong-Thi MD, Bergström M, Edwards K, Eriksson J, Ohlson S, To Yiu Ying J, Torres J, Agmo Hernández V. Lipodisks integrated with weak affinity chromatography enable fragment screening of integral membrane proteins. Analyst 2016; 141:981-8. [DOI: 10.1039/c5an02105g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Membrane proteins constitute the largest class of drug targets but they present many challenges in drug discovery.
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Affiliation(s)
- Minh-Dao Duong-Thi
- Linnaeus University
- Department of Chemistry and Biomedical Sciences
- SE-39182 Kalmar
- Sweden
| | - Maria Bergström
- Linnaeus University
- Department of Chemistry and Biomedical Sciences
- SE-39182 Kalmar
- Sweden
| | - Katarina Edwards
- Uppsala University
- Department of Chemistry-BMC
- SE-75123 Uppsala
- Sweden
| | - Jonny Eriksson
- Uppsala University
- Department of Chemistry-BMC
- SE-75123 Uppsala
- Sweden
| | - Sten Ohlson
- Nanyang Technological University
- School of Biological Sciences
- Singapore 637551
- Republic of Singapore
| | - Janet To Yiu Ying
- Nanyang Technological University
- School of Biological Sciences
- Singapore 637551
- Republic of Singapore
| | - Jaume Torres
- Nanyang Technological University
- School of Biological Sciences
- Singapore 637551
- Republic of Singapore
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37
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Brettmann JB, Urusova D, Tonelli M, Silva JR, Henzler-Wildman KA. Role of protein dynamics in ion selectivity and allosteric coupling in the NaK channel. Proc Natl Acad Sci U S A 2015; 112:15366-71. [PMID: 26621745 PMCID: PMC4687598 DOI: 10.1073/pnas.1515965112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flux-dependent inactivation that arises from functional coupling between the inner gate and the selectivity filter is widespread in ion channels. The structural basis of this coupling has only been well characterized in KcsA. Here we present NMR data demonstrating structural and dynamic coupling between the selectivity filter and intracellular constriction point in the bacterial nonselective cation channel, NaK. This transmembrane allosteric communication must be structurally different from KcsA because the NaK selectivity filter does not collapse under low-cation conditions. Comparison of NMR spectra of the nonselective NaK and potassium-selective NaK2K indicates that the number of ion binding sites in the selectivity filter shifts the equilibrium distribution of structural states throughout the channel. This finding was unexpected given the nearly identical crystal structure of NaK and NaK2K outside the immediate vicinity of the selectivity filter. Our results highlight the tight structural and dynamic coupling between the selectivity filter and the channel scaffold, which has significant implications for channel function. NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating.
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Affiliation(s)
- Joshua B Brettmann
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Darya Urusova
- Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO 63130
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Jonathan R Silva
- Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO 63130
| | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
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38
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Morrison EA, Robinson AE, Liu Y, Henzler-Wildman KA. Asymmetric protonation of EmrE. J Gen Physiol 2015; 146:445-61. [PMID: 26573622 PMCID: PMC4664823 DOI: 10.1085/jgp.201511404] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 10/13/2015] [Indexed: 01/26/2023] Open
Abstract
The small multidrug resistance transporter EmrE is a homodimer that uses energy provided by the proton motive force to drive the efflux of drug substrates. The pKa values of its "active-site" residues--glutamate 14 (Glu14) from each subunit--must be poised around physiological pH values to efficiently couple proton import to drug export in vivo. To assess the protonation of EmrE, pH titrations were conducted with (1)H-(15)N TROSY-HSQC nuclear magnetic resonance (NMR) spectra. Analysis of these spectra indicates that the Glu14 residues have asymmetric pKa values of 7.0 ± 0.1 and 8.2 ± 0.3 at 45°C and 6.8 ± 0.1 and 8.5 ± 0.2 at 25°C. These pKa values are substantially increased compared with typical pKa values for solvent-exposed glutamates but are within the range of published Glu14 pKa values inferred from the pH dependence of substrate binding and transport assays. The active-site mutant, E14D-EmrE, has pKa values below the physiological pH range, consistent with its impaired transport activity. The NMR spectra demonstrate that the protonation states of the active-site Glu14 residues determine both the global structure and the rate of conformational exchange between inward- and outward-facing EmrE. Thus, the pKa values of the asymmetric active-site Glu14 residues are key for proper coupling of proton import to multidrug efflux. However, the results raise new questions regarding the coupling mechanism because they show that EmrE exists in a mixture of protonation states near neutral pH and can interconvert between inward- and outward-facing forms in multiple different protonation states.
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Affiliation(s)
- Emma A Morrison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Anne E Robinson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Yongjia Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
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39
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Dutta S, Morrison EA, Henzler-Wildman KA. Blocking dynamics of the SMR transporter EmrE impairs efflux activity. Biophys J 2015; 107:613-620. [PMID: 25099800 DOI: 10.1016/j.bpj.2014.06.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/30/2014] [Accepted: 06/18/2014] [Indexed: 11/19/2022] Open
Abstract
EmrE is a small multidrug resistance transporter that has been well studied as a model for secondary active transport. Because transport requires the protein to convert between at least two states open to opposite sides of the membrane, it is expected that blocking these conformational transitions will prevent transport activity. We have previously shown that NMR can quantitatively measure the transition between the open-in and open-out states of EmrE in bicelles. Now, we have used the antiparallel EmrE crystal structure to design a cross-link to inhibit this conformational exchange process. We probed the structural, dynamic, and functional effects of this cross-link with NMR and in vivo efflux assays. Our NMR results show that our antiparallel cross-link performs as predicted: dramatically reducing conformational exchange while minimally perturbing the overall structure of EmrE and essentially trapping EmrE in a single state. The same cross-link also impairs ethidium efflux activity by EmrE in Escherichia coli. This confirms the hypothesis that transport can be inhibited simply by blocking conformational transitions in a properly folded transporter. The success of our cross-linker design also provides further evidence that the antiparallel crystal structure provides a good model for functional EmrE.
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Affiliation(s)
- Supratik Dutta
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Emma A Morrison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri.
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40
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Khakbaz P, Klauda JB. Probing the importance of lipid diversity in cell membranes via molecular simulation. Chem Phys Lipids 2015; 192:12-22. [PMID: 26260616 DOI: 10.1016/j.chemphyslip.2015.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 12/31/2022]
Abstract
Lipid membranes in prokaryotes and eukaryotes have a wide array of lipids that are necessary for proper membrane structure and function. In this paper, an introduction to lipid diversity in biology and a mini-review on how molecular simulations have been used to model biological membranes (primarily limited to one to three lipid types in most simulation-based models) is provided, which motivates the use of all-atom molecular dynamics (MD) simulations to study the effect of lipid diversity on properties of realistic membrane models of prokaryotes and eukaryotes. As an example, cytoplasmic membrane models of Escherichia coli were developed at different stages of the colony growth cycle (early-log, mid-log, stationary and overnight). The main difference between lipid compositions at each stage was the concentration of a cyclopropane-containing moiety on the sn-2 lipid acyl chain (cyC17:0). Triplicate MD simulations for each stage were run for 300 ns to study the influence of lipid diversity on the surface area per lipid, area compressibility modulus, deuterium order parameters, and electron density profiles. The overnight stage (also known as the death stage) had the highest average surface area per lipid, highest rigidity, and lowest bilayer thickness compare to other stages of E. coli cytoplasmic membrane. Although bilayer thickness did depend on the growth stage, the changes between these were small suggesting that the hydrophobic core of transmembrane proteins fit well with the membrane in all growth stages. Although it is still common practise in MD simulations of membrane proteins to use simple one- or two-component membranes, it can be important to use diverse lipid model membranes when membrane protein structure and function are influenced by changes in lipid membrane composition.
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Affiliation(s)
- Pouyan Khakbaz
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Biophysics Program, University of Maryland, College Park, MD 20742, USA.
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41
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Mehmood S, Allison TM, Robinson CV. Mass Spectrometry of Protein Complexes: From Origins to Applications. Annu Rev Phys Chem 2015; 66:453-74. [DOI: 10.1146/annurev-physchem-040214-121732] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Timothy M. Allison
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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42
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43
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Foo ACY, Harvey BGR, Metz JJ, Goto NK. Influence of hydrophobic mismatch on the catalytic activity of Escherichia coli GlpG rhomboid protease. Protein Sci 2014; 24:464-73. [PMID: 25307614 DOI: 10.1002/pro.2585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022]
Abstract
Rhomboids comprise a broad family of intramembrane serine proteases that are found in a wide range of organisms and participate in a diverse array of biological processes. High-resolution structures of the catalytic transmembrane domain of the Escherichia coli GlpG rhomboid have provided numerous insights that help explain how hydrolytic cleavage can be achieved below the membrane surface. Key to this are observations that GlpG hydrophobic domain dimensions may not be sufficient to completely span the native lipid bilayer. This formed the basis for a model where hydrophobic mismatch Induces thinning of the local membrane environment to promote access to transmembrane substrates. However, hydrophobic mismatch also has the potential to alter the functional properties of the rhomboid, a possibility we explore in the current work. For this purpose, we purified the catalytic transmembrane domain of GlpG into phosphocholine or maltoside detergent micelles of varying alkyl chain lengths, and assessed proteolytic function with a model water-soluble substrate. Catalytic turnover numbers were found to depend on detergent alkyl chain length, with saturated chains containing 10-12 carbon atoms supporting maximal activity. Similar results were obtained in phospholipid bicelles, with no proteolytic activity being detected in longer-chain lipids. Although differences in thermal stability and GlpG oligomerization could not explain these activity differences, circular dichroism spectra suggest that mismatch gives rise to a small change in structure. Overall, these results demonstrate that hydrophobic mismatch can exert an inhibitory effect on rhomboid activity, with the potential for changes in local membrane environment to regulate activity in vivo.
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Affiliation(s)
- Alexander C Y Foo
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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Vostrikov VV, Soller KJ, Ha KN, Gopinath T, Veglia G. Effects of naturally occurring arginine 14 deletion on phospholamban conformational dynamics and membrane interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:315-22. [PMID: 25251363 DOI: 10.1016/j.bbamem.2014.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/12/2014] [Accepted: 09/13/2014] [Indexed: 01/10/2023]
Abstract
Phospholamban (PLN) is a single-pass membrane protein that regulates the sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA). Phosphorylation of PLN at Ser16 reverses its inhibitory function under β-adrenergic stimulation, augmenting Ca²⁺ uptake in the sarcoplasmic reticulum and muscle contractility. PLN exists in two conformations; a T state, where the cytoplasmic domain is helical and adsorbed on the membrane surface, and an R state, where the cytoplasmic domain is unfolded and membrane detached. Previous studies have shown that the PLN conformational equilibrium is crucial to SERCA regulation. Here, we used a combination of solution and solid-state NMR to compare the structural topology and conformational dynamics of monomeric PLN (PLN(AFA)) with that of the PLN(R14del), a naturally occurring deletion mutant that is linked to the progression of dilated cardiomyopathy. We found that the behavior of the inhibitory transmembrane domain of PLN(R14del) is similar to that of the native sequence. Conversely, the conformational dynamics of R14del both in micelles and lipid membranes are enhanced. We conclude that the deletion of Arg14 in the cytoplasmic region weakens the interactions with the membrane and shifts the conformational equilibrium of PLN toward the disordered R state. This conformational transition is correlated with the loss-of-function character of this mutant and is corroborated by SERCA's activity assays. These findings support our hypothesis that SERCA function is fine-tuned by PLN conformational dynamics and begin to explain the aberrant regulation of SERCA by the R14del mutant.
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kailey J Soller
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kim N Ha
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemistry and Biochemistry, St. Catherine University, St. Paul, MN 55105, USA
| | - T Gopinath
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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Jaremko L, Jaremko M, Giller K, Becker S, Zweckstetter M. Structure of the mitochondrial translocator protein in complex with a diagnostic ligand. Science 2014; 343:1363-6. [PMID: 24653034 DOI: 10.1126/science.1248725] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The 18-kilodalton translocator protein TSPO is found in mitochondrial membranes and mediates the import of cholesterol and porphyrins into mitochondria. In line with the role of TSPO in mitochondrial function, TSPO ligands are used for a variety of diagnostic and therapeutic applications in animals and humans. We present the three-dimensional high-resolution structure of mammalian TSPO reconstituted in detergent micelles in complex with its high-affinity ligand PK11195. The TSPO-PK11195 structure is described by a tight bundle of five transmembrane α helices that form a hydrophobic pocket accepting PK11195. Ligand-induced stabilization of the structure of TSPO suggests a molecular mechanism for the stimulation of cholesterol transport into mitochondria.
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Affiliation(s)
- Lukasz Jaremko
- Max-Planck-Institut für Biophysikalische Chemie, 37077 Göttingen, Germany
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46
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EmrE dimerization depends on membrane environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1817-22. [PMID: 24680655 DOI: 10.1016/j.bbamem.2014.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 11/22/2022]
Abstract
The small multi-drug resistant (SMR) transporter EmrE functions as a homodimer. Although the small size of EmrE would seem to make it an ideal model system, it can also make it challenging to work with. As a result, a great deal of controversy has surrounded even such basic questions as the oligomeric state. Here we show that the purified protein is a homodimer in isotropic bicelles with a monomer-dimer equilibrium constant (KMD(2D)) of 0.002-0.009mol% for both the substrate-free and substrate-bound states. Thus, the dimer is stabilized in bicelles relative to detergent micelles where the KMD(2D) is only 0.8-0.95mol% (Butler et al. 2004). In dilauroylphosphatidylcholine (DLPC) liposomes KMD(2D) is 0.0005-0.0008mol% based on Förster resonance energy transfer (FRET) measurements, slightly tighter than bicelles. These results emphasize the importance of the lipid membrane in influencing dimer affinity.
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Morrison EA, Henzler-Wildman KA. Transported substrate determines exchange rate in the multidrug resistance transporter EmrE. J Biol Chem 2014; 289:6825-6836. [PMID: 24448799 DOI: 10.1074/jbc.m113.535328] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
EmrE, a small multidrug resistance transporter, serves as an ideal model to study coupling between multidrug recognition and protein function. EmrE has a single small binding pocket that must accommodate the full range of diverse substrates recognized by this transporter. We have studied a series of tetrahedral compounds, as well as several planar substrates, to examine multidrug recognition and transport by EmrE. Here we show that even within this limited series, the rate of interconversion between the inward- and outward-facing states of EmrE varies over 3 orders of magnitude. Thus, the identity of the bound substrate controls the rate of this critical step in the transport process. The binding affinity also varies over a similar range and is correlated with substrate hydrophobicity within the tetrahedral substrate series. Substrate identity influences both the ground-state and transition-state energies for the conformational exchange process, highlighting the coupling between substrate binding and transport required for alternating access antiport.
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Affiliation(s)
- Emma A Morrison
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis School of Medicine, St. Louis, Missouri 63110
| | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis School of Medicine, St. Louis, Missouri 63110.
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48
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Hopper JT, Yu YTC, Li D, Raymond A, Bostock M, Liko I, Mikhailov V, Laganowsky A, Benesch JL, Caffrey M, Nietlispach D, Robinson CV. Detergent-free mass spectrometry of membrane protein complexes. Nat Methods 2013; 10:1206-8. [PMID: 24122040 PMCID: PMC3868940 DOI: 10.1038/nmeth.2691] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/29/2013] [Indexed: 02/02/2023]
Abstract
We developed a method that allows release of intact membrane protein complexes from amphipols, bicelles and nanodiscs in the gas phase for observation by mass spectrometry (MS). Current methods involve release of membrane protein complexes from detergent micelles, which reveals subunit composition and lipid binding. We demonstrated that oligomeric complexes or proteins requiring defined lipid environments are stabilized to a greater extent in the absence of detergent.
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Affiliation(s)
- Jonathan T.S. Hopper
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Yvonne Ting-Chun Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Dianfan Li
- School of Medicine Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Alison Raymond
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Mark Bostock
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Victor Mikhailov
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Arthur Laganowsky
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Justin L.P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Martin Caffrey
- School of Medicine Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
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49
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Zhang W, Sun J, He Z. The application of open disk-like structures as model membrane and drug carriers. Asian J Pharm Sci 2013. [DOI: 10.1016/j.ajps.2013.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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50
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Dürr UH, Soong R, Ramamoorthy A. When detergent meets bilayer: birth and coming of age of lipid bicelles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:1-22. [PMID: 23465641 PMCID: PMC3741677 DOI: 10.1016/j.pnmrs.2013.01.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/30/2012] [Indexed: 05/12/2023]
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