1
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Mitra S, Chen MT, Stedman F, Hernandez J, Kumble G, Kang X, Zhang C, Tang G, Daugherty I, Liu W, Ocloo J, Klucznik KR, Li AA, Heinrich F, Deslouches B, Tristram-Nagle S. How Unnatural Amino Acids in Antimicrobial Peptides Change Interactions with Lipid Model Membranes. J Phys Chem B 2024. [PMID: 39328031 DOI: 10.1021/acs.jpcb.4c04152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
This study investigates the potential of antimicrobial peptides (AMPs) as alternatives to combat antibiotic resistance, with a focus on two AMPs containing unnatural amino acids (UAAs), E2-53R (16 AAs) and LE-54R (14 AAs). In both peptides, valine is replaced by norvaline (Nva), and tryptophan is replaced by 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic). Microbiological studies reveal their potent activity against both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria without any toxicity to eukaryotic cells at test concentrations up to 32 μM. Circular dichroism (CD) spectroscopy indicates that these peptides maintain α-helical structures when interacting with G(-) and G(+) lipid model membranes (LMMs), a feature linked to their efficacy. X-ray diffuse scattering (XDS) demonstrates a softening of G(-), G(+) and eukaryotic (Euk33) LMMs and a nonmonotonic decrease in chain order as a potential determinant for bacterial membrane destabilization. Additionally, XDS finds a significant link between both peptides' interfacial location in G(-) and G(+) LMMs and their efficacy. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Lack of toxicity in eukaryotic cells may be related to their loss of α-helicity and their hydrocarbon location in Euk33 LMMs. Both AMPs with UAAs offer a novel strategy to wipe out antibiotic-resistant strains while maintaining human cells. These findings are compared with previously published data on E2-35, which consists of the natural amino acids arginine, tryptophan, and valine.
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Affiliation(s)
- Saheli Mitra
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Mei-Tung Chen
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Francisca Stedman
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jedidiah Hernandez
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Grace Kumble
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xi Kang
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Churan Zhang
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Grace Tang
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Ian Daugherty
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wanqing Liu
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jeremy Ocloo
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kevin Raphael Klucznik
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Alexander Anzhi Li
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Frank Heinrich
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Berthony Deslouches
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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2
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Mitra S, Chandersekhar B, Li Y, Coopershlyak M, Mahoney ME, Evans B, Koenig R, Hall SCL, Klösgen B, Heinrich F, Deslouches B, Tristram-Nagle S. Novel non-helical antimicrobial peptides insert into and fuse lipid model membranes. SOFT MATTER 2024; 20:4088-4101. [PMID: 38712559 PMCID: PMC11109824 DOI: 10.1039/d4sm00220b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024]
Abstract
This research addresses the growing menace of antibiotic resistance by exploring antimicrobial peptides (AMPs) as alternatives to conventional antibiotics. Specifically, we investigate two linear amphipathic AMPs, LE-53 (12-mer) and LE-55 (16-mer), finding that the shorter LE-53 exhibits greater bactericidal activity against both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria. Remarkably, both AMPs are non-toxic to eukaryotic cells. The heightened effectiveness of LE-53 is attributed to its increased hydrophobicity (H) compared to LE-55. Circular dichroism (CD) reveals that LE-53 and LE-55 both adopt β-sheet and random coil structures in lipid model membranes (LMMs) mimicking G(-) and G(+) bacteria, so secondary structure is not the cause of the potency difference. X-ray diffuse scattering (XDS) reveals increased lipid chain order in LE-53, a potential key distinction. Additionally, XDS study uncovers a significant link between LE-53's upper hydrocarbon location in G(-) and G(+) LMMs and its efficacy. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Solution small angle X-ray scattering (SAXS) demonstrates LE-53's ability to induce vesicle fusion in bacterial LMMs without affecting eukaryotic LMMs, offering a promising strategy to combat antibiotic-resistant strains while preserving human cell integrity, whereas LE-55 has a smaller ability to induce fusion.
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Affiliation(s)
- Saheli Mitra
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Bhairavi Chandersekhar
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Yunshu Li
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Mark Coopershlyak
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Margot E Mahoney
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Brandt Evans
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Rachel Koenig
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Stephen C L Hall
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Beate Klösgen
- University of Southern Denmark, Dept. Physics, Chemistry & Pharmacy, PhyLife, Campusvej 55, Odense M5230, Denmark
| | - Frank Heinrich
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Berthony Deslouches
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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3
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Aguilella-Arzo M, Hoogerheide DP, Doucet M, Wang H, Aguilella VM. Charged Biological Membranes Repel Large Neutral Molecules by Surface Dielectrophoresis and Counterion Pressure. J Am Chem Soc 2024; 146:2701-2710. [PMID: 38291994 PMCID: PMC10835712 DOI: 10.1021/jacs.3c12348] [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: 11/05/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/01/2024]
Abstract
Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein-protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.
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Affiliation(s)
- Marcel Aguilella-Arzo
- Laboratory
of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071, Castellón, Spain
| | - David P. Hoogerheide
- Center
for Neutron Research, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Mathieu Doucet
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hanyu Wang
- Center
for Nanophase Materials Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Vicente M. Aguilella
- Laboratory
of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071, Castellón, Spain
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4
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Armstrong AJ, Apóstolo RFG, McCoy TM, Allen FJ, Doutch J, Cattoz BN, Dowding PJ, Welbourn RJL, Routh AF, Camp PJ. Experimental and simulation study of self-assembly and adsorption of glycerol monooleate in n-dodecane with varying water content onto iron oxide. NANOSCALE 2024; 16:1952-1970. [PMID: 38175178 DOI: 10.1039/d3nr05080g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The self-assembly and surface adsorption of glycerol monooleate (GMO) in n-dodecane are studied using a combination of experimental and molecular dynamics simulation techniques. The self-assembly of GMO to form reverse micelles, with and without added water, is studied using small-angle neutron scattering and simulations. A large-scale simulation is also used to investigate the self-assembly kinetics. GMO adsorption onto iron oxide is studied using depletion isotherms, neutron reflectometry, and simulations. The adsorbed amounts of GMO, and any added water, are determined experimentally, and the structures of the adsorbed films are investigated using reflectometry. Detailed fitting and analysis of the reflectometry measurements are presented, taking into account various factors such as surface roughness, and the presence of impurities. The reflectometry measurements are complemented by molecular dynamics simulations, and good consistency between both approaches is demonstrated by direct comparison of measured and simulated reflectivity and scattering length density profiles. The results of this analysis are that in dry systems, GMO adsorbs as self-assembled reverse micelles with some molecules adsorbing directly to the surface through the polar head groups, while in wet systems, the GMO is adsorbed onto a thin layer of water. Only at high surface coverage is some water trapped inside a reverse-micelle structure; at lower surface coverages, the GMO molecules associate primarily with the water layer, rather than self-assemble.
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Affiliation(s)
- Alexander J Armstrong
- ISIS Neutron and Muon Source, Didcot, UK
- Institute for Energy & Environmental Flows and Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Rui F G Apóstolo
- EPCC, Bayes Centre, 47 Potterrow, Edinburgh EH8 9BT, Scotland, UK
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, Scotland, UK.
| | - Thomas M McCoy
- Institute for Energy & Environmental Flows and Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Alexander F Routh
- Institute for Energy & Environmental Flows and Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Philip J Camp
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, Scotland, UK.
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5
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Zhang Y, Soubias O, Pant S, Heinrich F, Vogel A, Li J, Li Y, Clifton LA, Daum S, Bacia K, Huster D, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA. Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. Nat Commun 2023; 14:7570. [PMID: 37989735 PMCID: PMC10663523 DOI: 10.1038/s41467-023-43008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
ADP-ribosylation factor 1 (Arf1) interacts with multiple cellular partners and membranes to regulate intracellular traffic, organelle structure and actin dynamics. Defining the dynamic conformational landscape of Arf1 in its active form, when bound to the membrane, is of high functional relevance and key to understanding how Arf1 can alter diverse cellular processes. Through concerted application of nuclear magnetic resonance (NMR), neutron reflectometry (NR) and molecular dynamics (MD) simulations, we show that, while Arf1 is anchored to the membrane through its N-terminal myristoylated amphipathic helix, the G domain explores a large conformational space, existing in a dynamic equilibrium between membrane-associated and membrane-distal conformations. These configurational dynamics expose different interfaces for interaction with effectors. Interaction with the Pleckstrin homology domain of ASAP1, an Arf-GTPase activating protein (ArfGAP), restricts motions of the G domain to lock it in what seems to be a conformation exposing functionally relevant regions.
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Affiliation(s)
- Yue Zhang
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Ring Therapeutics, Inc., Cambridge, MA, USA
| | - Olivier Soubias
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Loxo Oncology at Lilly, Louisville, CO, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Jess Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Yifei Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Vonsun Pharmatech Co., Ltd., Suzhou, China
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK
| | - Sebastian Daum
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Kirsten Bacia
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA.
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6
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Pham KG, Thompson BR, Wang T, Samaddar S, Qian KK, Liu Y, Wagner NJ. Interfacial Pressure and Viscoelasticity of Antibodies and Their Correlation to Long-Term Stability in Formulation. J Phys Chem B 2023; 127:9724-9733. [PMID: 37917554 DOI: 10.1021/acs.jpcb.3c05900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Monoclonal antibodies (mAbs) form viscoelastic gel-like layers at the air-water interface due to their amphiphilic nature, and this same protein characteristic can lead to undesired aggregation of proteins in therapeutic formulations. We hypothesize that the interfacial viscoelasticity and surface pressure of mAbs at the air-water interface will correlate with their long-term stability. To test this hypothesis, the interfacial viscoelastic rheology and surface pressure of five different antibodies with varying visible particle counts from a three-year stability study were measured. We find that both the surface pressures and interfacial elastic moduli correlate well with the long-time mAb solution stability within a class of mAbs with the interfacial elastic moduli being particularly sensitive to discriminate between stable and unstable mAbs across a range of formulations. Furthermore, X-ray reflectivity was used to gain insight into the interfacial structure of mAbs at the air-water interface, providing a possible molecular mechanism to explain the relationship between interfacial elastic moduli and the long-term stability.
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Affiliation(s)
- Kiet G Pham
- Department of Chemical & Biomolecular Engineering, Center for Neutron Science, University of Delaware, Delaware 19716, United States
| | - Benjamin R Thompson
- Department of Chemical & Biomolecular Engineering, Center for Neutron Science, University of Delaware, Delaware 19716, United States
| | - Tingting Wang
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | - Shayak Samaddar
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | - Ken K Qian
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | - Yun Liu
- Department of Chemical & Biomolecular Engineering, Center for Neutron Science, University of Delaware, Delaware 19716, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Norman J Wagner
- Department of Chemical & Biomolecular Engineering, Center for Neutron Science, University of Delaware, Delaware 19716, United States
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7
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Andersson J, Kleinheinz D, Ramach U, Kiesenhofer N, Ashenden A, Valtiner M, Holt S, Koeper I, Schmidpeter PAM, Knoll W. Native Function of the Bacterial Ion Channel SthK in a Sparsely Tethered Lipid Bilayer Membrane Architecture. J Phys Chem B 2023; 127:3641-3650. [PMID: 37072125 PMCID: PMC10150356 DOI: 10.1021/acs.jpcb.2c07252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The plasma membrane protects the interiors of cells from their surroundings and also plays a critical role in communication, sensing, and nutrient import. As a result, the cell membrane and its constituents are among the most important drug targets. Studying the cell membrane and the processes it facilitates is therefore crucial, but it is a highly complex environment that is difficult to access experimentally. Various model membrane systems have been developed to provide an environment in which membrane proteins can be studied in isolation. Among them, tethered bilayer lipid membranes (tBLMs) are a promising model system providing a solvent-free membrane environment which can be prepared by self-assembly, is resistant to mechanical disturbances and has a high electrical resistance. tBLMs are therefore uniquely suitable to study ion channels and charge transport processes. However, ion channels are often large, complex, multimeric structures and their function requires a particular lipid environment. In this paper, we show that SthK, a bacterial cyclic nucleotide gated (CNG) ion channel that is strongly dependent on the surrounding lipid composition, functions normally when embedded into a sparsely tethered lipid bilayer. As SthK has been very well characterized in terms of structure and function, it is well-suited to demonstrate the utility of tethered membrane systems. A model membrane system suitable for studying CNG ion channels would be useful, as this type of ion channel performs a wide range of physiological functions in bacteria, plants, and mammals and is therefore of fundamental scientific interest as well as being highly relevant to medicine.
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Affiliation(s)
- Jakob Andersson
- Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - David Kleinheinz
- Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ulrich Ramach
- Technische Universität Wien, Wiedner Hauptstr. 8-10/134, 1040 Wien, Austria
- CEST Kompetenzzentrum für Oberflächentechnologie, Viktor Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | | | - Alex Ashenden
- Flinders University of South Australia, Bedford Park SA, 5042 Adelaide, Australia
| | - Markus Valtiner
- Technische Universität Wien, Wiedner Hauptstr. 8-10/134, 1040 Wien, Austria
- CEST Kompetenzzentrum für Oberflächentechnologie, Viktor Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | - Stephen Holt
- Australian Nuclear Science and Technology Organization, New Illawarra Rd, Lucas Heights, NSW 2234, Australia
| | - Ingo Koeper
- Flinders University of South Australia, Bedford Park SA, 5042 Adelaide, Australia
| | - Philipp A M Schmidpeter
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, New York 10065, United States
| | - Wolfgang Knoll
- Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
- Danube Private University, Steiner Landstraße 124, 3500 Krems an der Donau, Austria
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8
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Nagle JF, Jennings N, Qin W, Yan D, Tristram-Nagle S, Heinrich F. Structure of the gel phase of diC22:1PC lipid bilayers determined by x-ray diffraction. Biophys J 2023; 122:1033-1042. [PMID: 36566351 PMCID: PMC10111270 DOI: 10.1016/j.bpj.2022.12.030] [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: 09/13/2022] [Revised: 11/21/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
High-resolution x-ray data are reported for the ordered phases of long-chain di-monounsaturated C22:1 phosphocholine lipid bilayers. Similar to PC lipids that have saturated chains, diC22:1PC has a subgel phase and a gel phase, but dissimilarly, we find no ripple phase. Our quantitative focus is on the structure of the gel phase. We have recorded 17 lamellar orders, indicating a very well-ordered structure. Fitting to a model provides the phases of the orders. The Fourier construction of the electron density profile has two well-defined headgroup peaks and a very sharp and deep methyl trough. The wide-angle scattering exhibits two Bragg rods that provide the area per molecule. They have an intensity pattern quite different than that of lipids with saturated chains. Models of chain packing indicate that ground state chain configurations are tilted primarily toward next nearest neighbors with an angle that is also consistent with the modeling of the electron density profile. Wide-angle modeling also indicates broken mirror symmetry between the monolayers. Our wide-angle results and our electron density profile together leads to the hypothesis that the sn-1 and sn-2 chains have equivalent penetration depths in contrast to the gel phase structure of lipids with saturated hydrocarbon chains.
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Affiliation(s)
- John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
| | - Nathaniel Jennings
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Weiheng Qin
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Daniel Yan
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | | | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
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9
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Thorsen MK, Lai A, Lee MW, Hoogerheide DP, Wong GCL, Freed JH, Heldwein EE. Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering. mBio 2021; 12:e0154821. [PMID: 34425706 PMCID: PMC8406295 DOI: 10.1128/mbio.01548-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/28/2021] [Indexed: 02/01/2023] Open
Abstract
During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro, providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding. IMPORTANCE Herpesviruses are large viruses that infect nearly all vertebrates and some invertebrates and cause lifelong infections in most of the world's population. During replication, herpesviruses export their capsids from the nucleus into the cytoplasm by an unusual mechanism in which the viral nuclear egress complex (NEC) deforms the nuclear membrane around the capsid. However, how membrane deformation is achieved is unclear. Here, we show that the NEC from herpes simplex virus 1, a prototypical herpesvirus, uses clusters of positive charges to bind membranes and order membrane lipids. Reducing the positive charge or introducing negative charges weakens the membrane deforming ability of the NEC. We propose that the virus employs electrostatics to deform nuclear membrane around the capsid and can control this process by changing the NEC charge through phosphorylation. Blocking NEC-membrane interactions could be exploited as a therapeutic strategy.
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Affiliation(s)
- Michael K. Thorsen
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alex Lai
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Michelle W. Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Gerard C. L. Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Ekaterina E. Heldwein
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
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10
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Frewein MPK, Doktorova M, Heberle FA, Scott HL, Semeraro EF, Porcar L, Pabst G. Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase. Symmetry (Basel) 2021; 13:1441. [PMID: 35530371 PMCID: PMC9075682 DOI: 10.3390/sym13081441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center, we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, previously reported for gel phase structures, also extend to the more relevant physiological fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementarily performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. The extent of this back-bending was similar to that in chain symmetric bilayers. For both cases of adaptation to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.
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Affiliation(s)
- Moritz P. K. Frewein
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- Institut Laue-Langevin, 38043 Grenoble, France
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Haden L. Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Enrico F. Semeraro
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | | | - Georg Pabst
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
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11
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Silin VI, Hoogerheide DP. pH dependent electrical properties of the inner- and outer- leaflets of biomimetic cell membranes. J Colloid Interface Sci 2021; 594:279-289. [PMID: 33765647 DOI: 10.1016/j.jcis.2021.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
Composition and asymmetry of lipid membranes provide a means for regulation of trans-membrane permeability of ions and small molecules. The pH dependence of these processes plays an important role in the functioning and survival of cells. In this work, we study the pH dependence of membrane electrical resistance and capacitance using electrochemical impedance spectroscopy (EIS), surface plasmon resonance (SPR) and neutron reflectometry (NR) measurements of biomimetic tethered bilayer lipid membranes (tBLMs). tBLMs were prepared with single-component phospholipid compositions, as well as mixtures of phospholipids (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingomyelin and cholesterol) that mimic the inner- and outer- leaflets of plasma cell membranes. We found that all studied tBLMs have a resistance maximum at pHs near the pKas of the phospholipids. SPR and NR indicated that surface concentration of phospholipids and the thickness of the hydrophobic part of the membrane did not change versus pH. We postulate that these maxima are the result of protonation of the phosphate oxygen of the phospholipids and that hydronium ions play a major role in the conductance at pHs < pKas while sodium ions play the major role at pHs > pKas. An additional sharp resistance maximum of the PE tBLMs found at pH 5.9 and most likely represents the phosphatidylethanolamine's isoelectric point. The data show the key roles of the characteristic parts of phospholipid molecules: terminal group (choline, carboxyl, amine), phosphate, glycerol and ester oxygens on the permeability and selectivity of ions through the membrane. The interactions between these groups lead to significant differences in the electrical properties of biomimetic models of inner- and outer- leaflets of the plasma cell membranes.
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Affiliation(s)
- Vitalii I Silin
- University of Maryland, Institute for Bioscience and Biotechnology Research, Rockville MD 20850, USA.
| | - David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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12
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Rostovtseva TK, Bezrukov SM, Hoogerheide DP. Regulation of Mitochondrial Respiration by VDAC Is Enhanced by Membrane-Bound Inhibitors with Disordered Polyanionic C-Terminal Domains. Int J Mol Sci 2021; 22:7358. [PMID: 34298976 PMCID: PMC8306229 DOI: 10.3390/ijms22147358] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) is the primary regulating pathway of water-soluble metabolites and ions across the mitochondrial outer membrane. When reconstituted into lipid membranes, VDAC responds to sufficiently large transmembrane potentials by transitioning to gated states in which ATP/ADP flux is reduced and calcium flux is increased. Two otherwise unrelated cytosolic proteins, tubulin, and α-synuclein (αSyn), dock with VDAC by a novel mechanism in which the transmembrane potential draws their disordered, polyanionic C-terminal domains into and through the VDAC channel, thus physically blocking the pore. For both tubulin and αSyn, the blocked state is observed at much lower transmembrane potentials than VDAC gated states, such that in the presence of these cytosolic docking proteins, VDAC's sensitivity to transmembrane potential is dramatically increased. Remarkably, the features of the VDAC gated states relevant for bioenergetics-reduced metabolite flux and increased calcium flux-are preserved in the blocked state induced by either docking protein. The ability of tubulin and αSyn to modulate mitochondrial potential and ATP production in vivo is now supported by many studies. The common physical origin of the interactions of both tubulin and αSyn with VDAC leads to a general model of a VDAC inhibitor, facilitates predictions of the effect of post-translational modifications of known inhibitors, and points the way toward the development of novel therapeutics targeting VDAC.
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Affiliation(s)
- Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
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13
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Kinnun JJ, Scott HL, Ashkar R, Katsaras J. Biomembrane Structure and Material Properties Studied With Neutron Scattering. Front Chem 2021; 9:642851. [PMID: 33987167 PMCID: PMC8110834 DOI: 10.3389/fchem.2021.642851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA, United States.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
| | - John Katsaras
- Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States.,Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, United States
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14
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Michalak DJ, Lösche M, Hoogerheide DP. Charge Effects Provide Ångström-Level Control of Lipid Bilayer Morphology on Titanium Dioxide Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3970-3981. [PMID: 33761262 PMCID: PMC10995910 DOI: 10.1021/acs.langmuir.1c00214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Interfaces between molecular organic architectures and oxidic substrates are a central feature of biosensors and applications of biomimetics in science and technology. For phospholipid bilayers, the large range of pH- and ionic strength-dependent surface charge densities adopted by titanium dioxide and other oxidic surfaces leads to a rich landscape of phenomena that provides exquisite control of membrane interactions with such substrates. Using neutron reflectometry measurements, we report sharp, reversible transitions that occur between closely surface-associated and weakly coupled states. We show that these states arise from a complex interplay of the tunable length scale of electrostatic interactions with the length scale arising from other forces that are independent of solution conditions. A generalized free energy potential, with its inputs only derived from established measurements of surface and bilayer properties, quantitatively describes these and previously reported observations concerning the unbinding of bilayers from supporting substrates.
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Affiliation(s)
- Dennis J Michalak
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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15
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Semeraro EF, Marx L, Frewein MPK, Pabst G. Increasing complexity in small-angle X-ray and neutron scattering experiments: from biological membrane mimics to live cells. SOFT MATTER 2021; 17:222-232. [PMID: 32104874 DOI: 10.1039/c9sm02352f] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Small-angle X-ray and neutron scattering are well-established, non-invasive experimental techniques to interrogate global structural properties of biological membrane mimicking systems under physiologically relevant conditions. Recent developments, both in bottom-up sample preparation techniques for increasingly complex model systems, and in data analysis techniques have opened the path toward addressing long standing issues of biological membrane remodelling processes. These efforts also include emerging quantitative scattering studies on live cells, thus enabling a bridging of molecular to cellular length scales. Here, we review recent progress in devising compositional models for joint small-angle X-ray and neutron scattering studies on diverse membrane mimics - with a specific focus on membrane structural coupling to amphiphatic peptides and integral proteins - and live Escherichia coli. In particular, we outline the present state-of-the-art in small-angle scattering methods applied to complex membrane systems, highlighting how increasing system complexity must be followed by an advance in compositional modelling and data-analysis tools.
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Affiliation(s)
- Enrico F Semeraro
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria
| | - Lisa Marx
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria
| | - Moritz P K Frewein
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria and Institut Laue-Langevin, 38000 Grenoble, France
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria
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16
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Van QN, López CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Esposito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane. Proc Natl Acad Sci U S A 2020; 117:24258-24268. [PMID: 32913056 PMCID: PMC7533834 DOI: 10.1073/pnas.2006504117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as "membrane-distal" and estimate to comprise ∼90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.
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Affiliation(s)
- Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Troy Taylor
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Ben Niu
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Debsindhu Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Simon Messing
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Patrick Alexander
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Daniel Scott
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Xiaoying Ye
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Matt Drew
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Oleg Chertov
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Mathias Lösche
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Michael L Gross
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - William K Gillette
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dominic Esposito
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Frank McCormick
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
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17
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Soubias O, Pant S, Heinrich F, Zhang Y, Roy NS, Li J, Jian X, Yohe ME, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA. Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1. SCIENCE ADVANCES 2020; 6:6/40/eabd1882. [PMID: 32998886 PMCID: PMC7527224 DOI: 10.1126/sciadv.abd1882] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/04/2020] [Indexed: 05/05/2023]
Abstract
Adenosine diphosphate-ribosylation factor (Arf) guanosine triphosphatase-activating proteins (GAPs) are enzymes that need to bind to membranes to catalyze the hydrolysis of guanosine triphosphate (GTP) bound to the small GTP-binding protein Arf. Binding of the pleckstrin homology (PH) domain of the ArfGAP With SH3 domain, ankyrin repeat and PH domain 1 (ASAP1) to membranes containing phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is key for maximum GTP hydrolysis but not fully understood. By combining nuclear magnetic resonance, neutron reflectometry, and molecular dynamics simulation, we show that binding of multiple PI(4,5)P2 molecules to the ASAP1 PH domain (i) triggers a functionally relevant allosteric conformational switch and (ii) maintains the PH domain in a well-defined orientation, allowing critical contacts with an Arf1 mimic to occur. Our model provides a framework to understand how binding of the ASAP1 PH domain to PI(4,5)P2 at the membrane may play a role in the regulation of ASAP1.
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Affiliation(s)
- Olivier Soubias
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- NIST Center for Neutron Research, Gaithersburg, MD 20878, USA
| | - Yue Zhang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Neeladri Sekhar Roy
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jess Li
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
- NIST Center for Neutron Research, Gaithersburg, MD 20878, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
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18
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Doktorova M, Kučerka N, Kinnun JJ, Pan J, Marquardt D, Scott HL, Venable RM, Pastor RW, Wassall SR, Katsaras J, Heberle FA. Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data. J Phys Chem B 2020; 124:5186-5200. [PMID: 32468822 DOI: 10.1021/acs.jpcb.0c03389] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.
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Affiliation(s)
- Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.,Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 814 99 Bratislava, Slovakia
| | - Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen R Wassall
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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19
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Heinrich F, Kienzle PA, Hoogerheide DP, Lösche M. Information gain from isotopic contrast variation in neutron reflectometry on protein-membrane complex structures. J Appl Crystallogr 2020; 53:800-810. [PMID: 32684895 PMCID: PMC7312142 DOI: 10.1107/s1600576720005634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022] Open
Abstract
A framework is applied to quantify information gain from neutron or X-ray reflectometry experiments [Treece, Kienzle, Hoogerheide, Majkrzak, Lösche & Heinrich (2019). J. Appl. Cryst. 52, 47-59], in an in-depth investigation into the design of scattering contrast in biological and soft-matter surface architectures. To focus the experimental design on regions of interest, the marginalization of the information gain with respect to a subset of model parameters describing the structure is implemented. Surface architectures of increasing complexity from a simple model system to a protein-lipid membrane complex are simulated. The information gain from virtual surface scattering experiments is quantified as a function of the scattering length density of molecular components of the architecture and the surrounding aqueous bulk solvent. It is concluded that the information gain is mostly determined by the local scattering contrast of a feature of interest with its immediate molecular environment, and experimental design should primarily focus on this region. The overall signal-to-noise ratio of the measured reflectivity modulates the information gain globally and is a second factor to be taken into consideration.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899-6102, USA
| | - Paul A. Kienzle
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899-6102, USA
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899-6102, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899-6102, USA
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
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20
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Treece BW, Heinrich F, Ramanathan A, Lösche M. Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results. J Chem Theory Comput 2020; 16:3408-3419. [DOI: 10.1021/acs.jctc.0c00136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bradley W. Treece
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- The NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Arvind Ramanathan
- Data Science and Learning, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- The NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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21
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Josey BP, Heinrich F, Silin V, Lösche M. Association of Model Neurotransmitters with Lipid Bilayer Membranes. Biophys J 2020; 118:1044-1057. [PMID: 32032504 DOI: 10.1016/j.bpj.2020.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 11/15/2022] Open
Abstract
Aimed at reproducing the results of electrophysiological studies of synaptic signal transduction, conventional models of neurotransmission are based on the specific binding of neurotransmitters to ligand-gated receptor ion channels. However, the complex kinetic behavior observed in synaptic transmission cannot be reproduced in a standard kinetic model without the ad hoc postulation of additional conformational channel states. On the other hand, if one invokes unspecific neurotransmitter adsorption to the bilayer-a process not considered in the established models-the electrophysiological data can be rationalized with only the standard set of three conformational receptor states that also depend on this indirect coupling of neurotransmitters via their membrane interaction. Experimental verification has been difficult because binding affinities of neurotransmitters to the lipid bilayer are low. We quantify this interaction with surface plasmon resonance to measure equilibrium dissociation constants in neurotransmitter membrane association. Neutron reflection measurements on artificial membranes, so-called sparsely tethered bilayer lipid membranes, reveal the structural aspects of neurotransmitters' association with zwitterionic and anionic bilayers. We thus establish that serotonin interacts nonspecifically with the membrane at physiologically relevant concentrations, whereas γ-aminobutyric acid does not. Surface plasmon resonance shows that serotonin adsorbs with millimolar affinity, and neutron reflectometry shows that it penetrates the membrane deeply, whereas γ-aminobutyric is excluded from the bilayer.
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Affiliation(s)
- Brian P Josey
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland
| | - Vitalii Silin
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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22
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Hoogerheide DP, Forsyth VT, Brown KA. Neutron scattering for STRUCTURAL BIOLOGY: Modern neutron sources illuminate the complex functions of living systems. PHYSICS TODAY 2020; 73:10.1063/pt.3.4498. [PMID: 38487716 PMCID: PMC10938470 DOI: 10.1063/pt.3.4498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Modern neutron sources illuminate the complex functions of living systems.
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Affiliation(s)
- David P Hoogerheide
- National Institute of Standards and Technology Center for Neutron Research in Gaithersburg, Maryland
| | - V Trevor Forsyth
- Institut Laue-Langevin in Grenoble, France; he also holds a chair in biophysics at Keele University in the UK
| | - Katherine A Brown
- Cavendish Laboratory at Cambridge University in the UK and at the University of Texas at Austin
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23
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Kumari H, Eisenhart A, Pajoubpong J, Heinrich F, Beck TL. Investigating partitioning of free versus macrocycle bound guest into a model POPC lipid bilayer. RSC Adv 2020; 10:15148-15153. [PMID: 35495443 PMCID: PMC9052308 DOI: 10.1039/d0ra02850a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
We report on the permeation of free and macrocycle-bound avobenzone across a POPC lipid bilayer through combined neutron reflectometry experiments and molecular dynamics simulations. Results indicate that the p-phosphonated calix[8]arene macrocycle limits the avobenzone penetration into the upper leaflet of the membrane. Hence, it could serve as a useful vehicle for safer formulations. We report on the permeation of free and macrocycle-bound avobenzone across a POPC lipid bilayer through combined neutron reflectometry experiments and molecular dynamics simulations.![]()
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Affiliation(s)
- Harshita Kumari
- James L. Winkle College of Pharmacy
- University of Cincinnati
- Cincinnati
- USA
| | | | | | - Frank Heinrich
- Department of Physics
- Carnegie Mellon University
- Pittsburgh
- USA
- Center for Neutron Research
| | - Thomas L. Beck
- Department of Chemistry
- University of Cincinnati
- Cincinnati
- USA
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24
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Pond MP, Eells R, Treece BW, Heinrich F, Lösche M, Roux B. Membrane Anchoring of Hck Kinase via the Intrinsically Disordered SH4-U and Length Scale Associated with Subcellular Localization. J Mol Biol 2019; 432:2985-2997. [PMID: 31877324 DOI: 10.1016/j.jmb.2019.11.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/21/2022]
Abstract
Src family kinases (SFKs) are a group of nonreceptor tyrosine kinases that are characterized by their involvement in critical signal transduction pathways. SFKs are often found attached to membranes, but little is known about the conformation of the protein in this environment. Here, solution nuclear magnetic resonance (NMR), neutron reflectometry (NR), and molecular dynamics (MD) simulations were employed to study the membrane interactions of the intrinsically disordered SH4 and Unique domains of the Src family kinase Hck. Through development of a procedure to combine the information from the different techniques, we were able produce a first-of-its-kind atomically detailed structural ensemble of a membrane-bound intrinsically disordered protein. Evaluation of the model demonstrated its consistency with previous work and provided insight into how SFK Unique domains act to differentiate the family members from one another. Fortuitously, the position of the ensemble on the membrane allowed the model to be combined with configurations of the multidomain Hck kinase previously determined from small-angle solution X-ray scattering to produce full-length models of membrane-anchored Hck. The resulting models allowed us to estimate that the kinase active site is positioned about 65 ± 35 Å away from the membrane surface, offering the first estimations of the length scale associated with the concept of SFK subcellular localization.
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Affiliation(s)
- Matthew P Pond
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, IL, 60637, USA
| | - Rebecca Eells
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Bradley W Treece
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA; Center for Neutron Research, NIST, Gaithersburg, MD, 20899, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA; Center for Neutron Research, NIST, Gaithersburg, MD, 20899, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, IL, 60637, USA.
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25
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Chattrakun K, Hoogerheide DP, Mao C, Randall LL, King GM. Protein Translocation Activity in Surface-Supported Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:12246-12256. [PMID: 31448613 PMCID: PMC10906442 DOI: 10.1021/acs.langmuir.9b01928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Surface-supported lipid bilayers are used widely throughout the nanoscience community as cellular membrane mimics. For example, they are frequently employed in single-molecule atomic force microscopy (AFM) studies to shed light on membrane protein conformational dynamics and folding. However, in AFM as well as in other surface-sensing techniques, the close proximity of the supporting surface raises questions about preservation of the biochemical activity. Employing the model translocase from the general secretory (Sec) system of Escherichia coli, here we quantify the activity via two biochemical assays in surface-supported bilayers. The first assesses ATP hydrolysis and the second assesses polypeptide translocation across the membrane via protection from added protease. Hydrolysis assays revealed distinct levels of activation ranging from medium (translocase-activated) to high (translocation-associated) that were similar to traditional solution experiments and further identified an adenosine triphosphatase population exhibiting characteristics of conformational hysteresis. Translocation assays revealed turn over numbers that were comparable to solution but with a 10-fold reduction in apparent rate constant. Despite differences in kinetics, the chemomechanical coupling (ATP hydrolyzed per residue translocated) only varied twofold on glass compared to solution. The activity changed with the topographic complexity of the underlying surface. Rough glass coverslips were favored over atomically flat mica, likely due to differences in frictional coupling between the translocating polypeptide and surface. Neutron reflectometry and AFM corroborated the biochemical measurements and provided structural characterization of the submembrane space and upper surface of the bilayer. Overall, the translocation activity was maintained for the surface-adsorbed Sec system, albeit with a slower rate-limiting step. More generally, polypeptide translocation activity measurements yield valuable quantitative metrics to assess the local environment about surface-supported lipid bilayers.
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Affiliation(s)
- Kanokporn Chattrakun
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Chunfeng Mao
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Gavin M. King
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
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26
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Zhang P, Villanueva V, Kalkowski J, Liu C, Donovan AJ, Bu W, Schlossman ML, Lin B, Liu Y. Molecular interactions of phospholipid monolayers with a model phospholipase. SOFT MATTER 2019; 15:4068-4077. [PMID: 30958491 DOI: 10.1039/c8sm01154k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The intrinsic overexpression of secretory phospholipase A2 (sPLA2) in various pro-inflammatory diseases and cancers has the potential to be exploited as a therapeutic strategy for diagnostics and treatment. To explore this potential and advance our knowledge of the role of sPLA2 in related diseases, it is necessary to systematically investigate the molecular interaction of the enzyme with lipids. By employing a Langmuir trough integrated with X-ray reflectivity and grazing incidence X-ray diffraction techniques, this study examined the molecular packing structure of 1,2-palmitoyl-sn-glycero-3-phosphocholine (DPPC) films before and after enzyme adsorption and enzyme-catalyzed degradation. Molecular interaction of sPLA2 (from bee venom) with the DPPC monolayer exhibited Ca2+ dependence. DPPC molecules at the interface without Ca2+ retained a monolayer organization; upon adsorption of sPLA2 to the monolayer the packing became tighter. In contrast, sPLA2-catalyzed degradation of DPPC occurred in the presence of Ca2+, leading to disruption of the ordered monolayer structure of DPPC. The interfacial film became a mixture of highly ordered multilayer domains of palmitic acid (PA) and loosely packed monolayer phase of 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (lysoPC) that potentially contained the remaining un-degraded DPPC. The redistribution of lipid degradation products into the third dimension, which produced multilayer PA domains, damaged the structural integrity of the original lipid layer and may explain the bursting of liposomes observed in other studies after a latency period of mixing liposomes with sPLA2. A quantitative understanding of the lipid packing and lipid-enzyme interaction provides an intuitive means of designing and optimizing lipid-related drug delivery systems.
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Affiliation(s)
- Pin Zhang
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA.
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27
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Jadhav V, Hoogerheide DP, Korlach J, Wanunu M. Porous Zero-Mode Waveguides for Picogram-Level DNA Capture. NANO LETTERS 2019; 19:921-929. [PMID: 30484321 PMCID: PMC9701543 DOI: 10.1021/acs.nanolett.8b04170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have recently shown that nanopore zero-mode waveguides are effective tools for capturing picogram levels of long DNA fragments for single-molecule DNA sequencing. Despite these key advantages, the manufacturing of large arrays is not practical due to the need for serial nanopore fabrication. To overcome this challenge, we have developed an approach for the wafer-scale fabrication of waveguide arrays on low-cost porous membranes, which are deposited using molecular-layer deposition. The membrane at each waveguide base contains a network of serpentine pores that allows for efficient electrophoretic DNA capture at picogram levels while eliminating the need for prohibitive serial pore milling. Here, we show that the loading efficiency of these porous waveguides is up to 2 orders of magnitude greater than their nanopore predecessors. This new device facilitates the scaling-up of the process, greatly reducing the cost and effort of manufacturing. Furthermore, the porous zero-mode waveguides can be used for applications that benefit from low-input single-molecule real-time sequencing.
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Affiliation(s)
- Vivek Jadhav
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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28
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Clifton LA, Hall SCL, Mahmoudi N, Knowles TJ, Heinrich F, Lakey JH. Structural Investigations of Protein-Lipid Complexes Using Neutron Scattering. Methods Mol Biol 2019; 2003:201-251. [PMID: 31218621 DOI: 10.1007/978-1-4939-9512-7_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Neutron scattering has significant benefits for examining the structure of protein-lipid complexes. Cold (slow) neutrons are nondamaging and predominantly interact with the atomic nucleus, meaning that neutron beams can penetrate deeply into samples, which allows for flexibility in the design of samples studied. Most importantly, there is a strong difference in neutron scattering length (i.e., scattering power) between protium ([Formula: see text], 99.98% natural abundance) and deuterium ([Formula: see text] or D, 0.015%). Through the mixing of H2O and D2O in the samples and in some cases the deuterium labeling of the biomolecules, components within a complex can be hidden or enhanced in the scattering signal. This enables both the overall structure and the relative distribution of components within a complex to be resolved. Lipid-protein complexes are most commonly studied using neutron reflectometry (NR) and small angle neutron scattering (SANS). In this review the methodologies to produce and examine a variety of model biological membrane systems using SANS and NR are detailed. These systems include supported lipid bilayers derived from vesicle dispersions or Langmuir-Blodgett deposition, tethered bilayer systems, membrane protein-lipid complexes and polymer wrapped lipid nanodiscs. The three key stages of any SANS/NR study on model membrane systems-sample preparation, data collection, and analysis-are described together with some background on the techniques themselves.
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Affiliation(s)
- Luke A Clifton
- Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, Oxfordshire, UK.
| | - Stephen C L Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Najet Mahmoudi
- Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, Oxfordshire, UK
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- National Institute of Standards and Technology Centre for Neutron Research, Gaithersburg, MD, USA
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK.
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29
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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30
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Hoogerheide DP, Noskov SY, Kuszak AJ, Buchanan SK, Rostovtseva TK, Nanda H. Structure of voltage-dependent anion channel-tethered bilayer lipid membranes determined using neutron reflectivity. Acta Crystallogr D Struct Biol 2018; 74:1219-1232. [PMID: 30605136 PMCID: PMC6317592 DOI: 10.1107/s2059798318011749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/20/2018] [Indexed: 01/05/2023] Open
Abstract
Neutron reflectivity (NR) has emerged as a powerful technique to study the structure and behavior of membrane proteins at planar lipid interfaces. Integral membrane proteins (IMPs) remain a significant challenge for NR owing to the difficulty of forming complete bilayers with sufficient protein density for scattering techniques. One strategy to achieve high protein density on a solid substrate is the capture of detergent-stabilized, affinity-tagged IMPs on a nitrilotriacetic acid (NTA)-functionalized self-assembled monolayer (SAM), followed by reconstitution into the lipids of interest. Such protein-tethered bilayer lipid membranes (ptBLMs) have the notable advantage of a uniform IMP orientation on the substrate. Here, NR is used to provide a structural characterization of the ptBLM process from formation of the SAM to capture of the detergent-stabilized IMP and lipid reconstitution. The mitochondrial outer-membrane voltage-dependent anion channel (VDAC), which controls the exchange of bioenergetic metabolites between mitochondria and the cytosol, was used as a model β-barrel IMP. Molecular dynamics simulations were used for comparison with the experimental results and to inform the parameters of the physical models describing the NR data. The detailed structure of the SAM is shown to depend on the density of the NTA chelating groups. The relative content of detergent and protein in surface-immobilized, detergent-stabilized VDAC is measured, while the reconstituted lipid bilayer is shown to be complete to within a few percent, using the known atomic structure of VDAC. Finally, excess lipid above the reconstituted bilayer, which is of consequence for more indirect structural and functional studies, is shown to be present.
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Affiliation(s)
- David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA
| | - Sergei Yu. Noskov
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Adam J. Kuszak
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatiana K. Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirsh Nanda
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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31
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Vanegas JM, Heinrich F, Rogers DM, Carson BD, La Bauve S, Vernon BC, Akgun B, Satija S, Zheng A, Kielian M, Rempe SB, Kent MS. Insertion of Dengue E into lipid bilayers studied by neutron reflectivity and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1216-1230. [PMID: 29447917 DOI: 10.1016/j.bbamem.2018.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 02/01/2023]
Abstract
The envelope (E) protein of Dengue virus rearranges to a trimeric hairpin to mediate fusion of the viral and target membranes, which is essential for infectivity. Insertion of E into the target membrane serves to anchor E and possibly also to disrupt local order within the membrane. Both aspects are likely to be affected by the depth of insertion, orientation of the trimer with respect to the membrane normal, and the interactions that form between trimer and membrane. In the present work, we resolved the depth of insertion, the tilt angle, and the fundamental interactions for the soluble portion of Dengue E trimers (sE) associated with planar lipid bilayer membranes of various combinations of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-glycerol (POPG), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), and cholesterol (CHOL) by neutron reflectivity (NR) and by molecular dynamics (MD) simulations. The results show that the tip of E containing the fusion loop (FL) is located at the interface of the headgroups and acyl chains of the outer leaflet of the lipid bilayers, in good agreement with prior predictions. The results also indicate that E tilts with respect to the membrane normal upon insertion, promoted by either the anionic lipid POPG or CHOL. The simulations show that tilting of the protein correlates with hydrogen bond formation between lysines and arginines located on the sides of the trimer close to the tip (K246, K247, and R73) and nearby lipid headgroups. These hydrogen bonds provide a major contribution to the membrane anchoring and may help to destabilize the target membrane.
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Affiliation(s)
- Juan M Vanegas
- Sandia National Laboratories, Albuquerque, NM, United States
| | - Frank Heinrich
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, MD, United States; Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
| | - David M Rogers
- Sandia National Laboratories, Albuquerque, NM, United States
| | - Bryan D Carson
- Sandia National Laboratories, Albuquerque, NM, United States
| | - Sadie La Bauve
- Sandia National Laboratories, Albuquerque, NM, United States
| | - Briana C Vernon
- Sandia National Laboratories, Albuquerque, NM, United States
| | - Bulent Akgun
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, MD, United States
| | - Sushil Satija
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, MD, United States
| | - Aihua Zheng
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Susan B Rempe
- Sandia National Laboratories, Albuquerque, NM, United States
| | - Michael S Kent
- Sandia National Laboratories, Albuquerque, NM, United States.
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32
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Neumann BM, Kenney D, Wen Q, Gericke A. Microfluidic device as a facile in vitro tool to generate and investigate lipid gradients. Chem Phys Lipids 2017; 210:109-121. [PMID: 29102758 DOI: 10.1016/j.chemphyslip.2017.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 01/13/2023]
Abstract
This work describes a method that utilizes a microfluidic gradient generator to develop lateral lipid gradients in supported lipid bilayers (SLB). The new methodology provides freedom of choice with respect to the lipid composition of the SLB. In addition, the device has the ability to create a protein or bivalent cation gradient in the aqueous phase above the lipid bilayer which can elicit a gradient specific response in the SLB. To highlight these features we demonstrate that we can create a phosphoinositide gradient on various length scales, ranging from 2mm to 50μm. We further show that a Ca2+ gradient in the aqueous phase above the SLB causes anionic lipid clustering mirroring the cation gradient. We demonstrate this effect for mixed phosphatidylcholine/phosphatidylinositol-4,5-bisphosphate bilayers and fora mixed phosphatidylcholine/phosphatidylserine bilayers. The biomimetic platform can be combined with a Total Internal Reflection Fluorescence (TIRF) microscopy setup, which allows for the convenient observation of the time evolution of the gradient and the interaction of ligands with the lipid bilayer. The method provides unprecedented access to study the dynamics and mechanics of protein-lipid interactions on membranes with micron level gradients, mimicking plasma membrane gradients observed in organisms such as Dictyostelium discodeum and neutrophils.
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Affiliation(s)
- Brittany M Neumann
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, USA
| | - Devin Kenney
- Bridgewater State University, Department of Chemical Sciences, USA
| | - Qi Wen
- Worcester Polytechnic Institute, Department of Physics, USA
| | - Arne Gericke
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, USA.
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33
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Zimmermann K, Eells R, Heinrich F, Rintoul S, Josey B, Shekhar P, Lösche M, Stern LJ. The cytosolic domain of T-cell receptor ζ associates with membranes in a dynamic equilibrium and deeply penetrates the bilayer. J Biol Chem 2017; 292:17746-17759. [PMID: 28893902 PMCID: PMC5663876 DOI: 10.1074/jbc.m117.794370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/21/2017] [Indexed: 11/06/2022] Open
Abstract
Interactions between lipid bilayers and the membrane-proximal regions of membrane-associated proteins play important roles in regulating membrane protein structure and function. The T-cell antigen receptor is an assembly of eight single-pass membrane-spanning subunits on the surface of T lymphocytes that initiates cytosolic signaling cascades upon binding antigens presented by MHC-family proteins on antigen-presenting cells. Its ζ-subunit contains multiple cytosolic immunoreceptor tyrosine-based activation motifs involved in signal transduction, and this subunit by itself is sufficient to couple extracellular stimuli to intracellular signaling events. Interactions of the cytosolic domain of ζ (ζcyt) with acidic lipids have been implicated in the initiation and regulation of transmembrane signaling. ζcyt is unstructured in solution. Interaction with acidic phospholipids induces structure, but its disposition when bound to lipid bilayers is controversial. Here, using surface plasmon resonance and neutron reflection, we characterized the interaction of ζcyt with planar lipid bilayers containing mixtures of acidic and neutral lipids. We observed two binding modes of ζcyt to the bilayers in dynamic equilibrium: one in which ζcyt is peripherally associated with lipid headgroups and one in which it penetrates deeply into the bilayer. Such an equilibrium between the peripherally bound and embedded forms of ζcyt apparently controls accessibility of the immunoreceptor tyrosine-based activation signal transduction pathway. Our results reconcile conflicting findings of the ζ structure reported in previous studies and provide a framework for understanding how lipid interactions regulate motifs to tyrosine kinases and may regulate the T-cell antigen receptor biological activities for this cell-surface receptor system.
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Affiliation(s)
| | | | - Frank Heinrich
- the Departments of Physics and
- the National Institute of Standards and Technology (NIST) Center for Neutron Research, Gaithersburg, Maryland 20899
| | | | | | | | - Mathias Lösche
- the Departments of Physics and
- the National Institute of Standards and Technology (NIST) Center for Neutron Research, Gaithersburg, Maryland 20899
- Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and
| | - Lawrence J Stern
- From the Departments of Pathology and
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
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34
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Eells R, Barros M, Scott KM, Karageorgos I, Heinrich F, Lösche M. Structural characterization of membrane-bound human immunodeficiency virus-1 Gag matrix with neutron reflectometry. Biointerphases 2017; 12:02D408. [PMID: 28511544 PMCID: PMC5433906 DOI: 10.1116/1.4983155] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/22/2017] [Accepted: 04/26/2017] [Indexed: 12/29/2022] Open
Abstract
The structural characterization of peripheral membrane proteins represents a tremendous challenge in structural biology due to their transient interaction with the membrane and the potential multitude of protein conformations during this interaction. Neutron reflectometry is uniquely suited to address this problem because of its ability to structurally characterize biological model systems nondestructively and under biomimetic conditions that retain full protein functionality. Being sensitive to only the membrane-bound fraction of a water-soluble peripheral protein, neutron reflectometry obtains a low-resolution average structure of the protein-membrane complex that is further refined using integrative modeling strategies. Here, the authors review the current technological state of biological neutron reflectometry exemplified by a detailed report on the structure determination of the myristoylated human immunodeficiency virus-1 (HIV-1) Gag matrix associated with phosphoserine-containing model membranes. The authors found that the HIV-1 Gag matrix is able to adopt different configurations at the membrane in a pH-dependent manner and that the myristate group orients the protein in a way that is conducive to PIP2-binding.
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Affiliation(s)
- Rebecca Eells
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Marilia Barros
- Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kerry M Scott
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899 and Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Ioannis Karageorgos
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899 and Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 and NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Mathias Lösche
- Departments of Physics and Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 and NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
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35
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Hoogerheide DP, Noskov SY, Jacobs D, Bergdoll L, Silin V, Worcester DL, Abramson J, Nanda H, Rostovtseva TK, Bezrukov SM. Structural features and lipid binding domain of tubulin on biomimetic mitochondrial membranes. Proc Natl Acad Sci U S A 2017; 114:E3622-E3631. [PMID: 28420794 PMCID: PMC5422764 DOI: 10.1073/pnas.1619806114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dimeric tubulin, an abundant water-soluble cytosolic protein known primarily for its role in the cytoskeleton, is routinely found to be associated with mitochondrial outer membranes, although the structure and physiological role of mitochondria-bound tubulin are still unknown. There is also no consensus on whether tubulin is a peripheral membrane protein or is integrated into the outer mitochondrial membrane. Here the results of five independent techniques-surface plasmon resonance, electrochemical impedance spectroscopy, bilayer overtone analysis, neutron reflectometry, and molecular dynamics simulations-suggest that α-tubulin's amphipathic helix H10 is responsible for peripheral binding of dimeric tubulin to biomimetic "mitochondrial" membranes in a manner that differentiates between the two primary lipid headgroups found in mitochondrial membranes, phosphatidylethanolamine and phosphatidylcholine. The identification of the tubulin dimer orientation and membrane-binding domain represents an essential step toward our understanding of the complex mechanisms by which tubulin interacts with integral proteins of the mitochondrial outer membrane and is important for the structure-inspired design of tubulin-targeting agents.
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Affiliation(s)
- David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899;
| | - Sergei Y Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4;
| | - Daniel Jacobs
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Lucie Bergdoll
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Vitalii Silin
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - David L Worcester
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
| | - Hirsh Nanda
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;
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36
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Preta G, Jankunec M, Heinrich F, Griffin S, Sheldon IM, Valincius G. Tethered bilayer membranes as a complementary tool for functional and structural studies: The pyolysin case. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2070-2080. [PMID: 27211243 DOI: 10.1016/j.bbamem.2016.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/27/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
We demonstrate the use of tethered bilayer lipid membranes (tBLMs) as an experimental platform for functional and structural studies of membrane associated proteins by electrochemical techniques. The reconstitution of the cholesterol-dependent cytolysin (CDC) pyolysin (PLO) from Trueperella pyogenes into tBLMs was followed in real-time by electrochemical impedance spectroscopy (EIS). Changes of the EIS parameters of the tBLMs upon exposure to PLO solutions were consistent with the dielectric barrier damage occurring through the formation of water-filled pores in membranes. Parallel experiments involving a mutant version of PLO, which is able to bind to the membranes but does not form oligomer pores, strengthen the reliability of this methodology, since no change in the electrochemical impedance was observed. Complementary atomic force microscopy (AFM) and neutron reflectometry (NR) measurements revealed structural details of the membrane bound PLO, consistent with the structural transformations of the membrane bound toxins found for other cholesterol dependent cytolysins. In this work, using the tBLMs platform we also observed a protective effect of the dynamin inhibitor Dynasore against pyolysin as well as pneumolysin. An effect of Dynasore in tBLMs, which was earlier observed in experiments with live cells, confirms the biological relevance of the tBLMs models, as well as demonstrates the potential of the electrochemical impedance spectroscopy to quantify membrane damage by the pore forming toxins. In conclusion, tBLMs are a reliable and complementary method to explore the activity of CDCs in eukaryotic cells and to develop strategies to limit the toxic effects of CDCs.
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Affiliation(s)
- Giulio Preta
- Department of Bioelectrochemistry and Biospectroscopy, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Marija Jankunec
- Department of Bioelectrochemistry and Biospectroscopy, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Frank Heinrich
- NIST Center for Neutron Research, Gaithersburg, MD 20899, USA
| | - Sholeem Griffin
- Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, United Kingdom
| | - Iain Martin Sheldon
- Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, United Kingdom
| | - Gintaras Valincius
- Department of Bioelectrochemistry and Biospectroscopy, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania.
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37
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Shen Y, Barros M, Vennemann T, Gallagher DT, Yin Y, Linden SB, Heselpoth RD, Spencer DJ, Donovan DM, Moult J, Fischetti VA, Heinrich F, Lösche M, Nelson DC. A bacteriophage endolysin that eliminates intracellular streptococci. eLife 2016; 5. [PMID: 26978792 PMCID: PMC4848087 DOI: 10.7554/elife.13152] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/14/2016] [Indexed: 12/25/2022] Open
Abstract
PlyC, a bacteriophage-encoded endolysin, lyses Streptococcus pyogenes (Spy) on contact. Here, we demonstrate that PlyC is a potent agent for controlling intracellular Spy that often underlies refractory infections. We show that the PlyC holoenzyme, mediated by its PlyCB subunit, crosses epithelial cell membranes and clears intracellular Spy in a dose-dependent manner. Quantitative studies using model membranes establish that PlyCB interacts strongly with phosphatidylserine (PS), whereas its interaction with other lipids is weak, suggesting specificity for PS as its cellular receptor. Neutron reflection further substantiates that PlyC penetrates bilayers above a PS threshold concentration. Crystallography and docking studies identify key residues that mediate PlyCB–PS interactions, which are validated by site-directed mutagenesis. This is the first report that a native endolysin can traverse epithelial membranes, thus substantiating the potential of PlyC as an antimicrobial for Spy in the extracellular and intracellular milieu and as a scaffold for engineering other functionalities. DOI:http://dx.doi.org/10.7554/eLife.13152.001 Streptococcus pyogenes is the bacterium that causes throat infections and other serious infections in humans. Antibiotics such as penicillin are used to treat active infections, but so-called “strep throat infections” often return after treatment. This is because S. pyogenes can enter the cells that line the throat and hide from the antibiotics, which cannot enter the throat cells. Endolysins are enzymes produced by viruses that attack bacteria, and these enzymes target and destroy the bacterial cell wall. A previous study revealed that an endolysin known as PlyC could destroy S. pyogenes bacteria on contact. PlyC and other endolysins have the potential to act as alternatives to common antibiotics, but before these enzymes can be developed as therapeutics, it is important to understand how they interact with human host cells. Like antibiotics, the PlyC endolysin was not expected to enter throat cells. However, Shen, Barros et al. have now discovered that not only can PlyC enter throat cells, it can essentially chase down and kill S. pyogenes that are hiding inside. Other similar enzymes could not act in this way, and further studies confirmed that PlyC could move around inside a throat cell without causing it damage. Shen, Barros et al. also determined that PlyC has a pocket on its surface that binds with a specific component of the throat cell membrane, a molecule called phosphatidylserine. This interaction – which is a bit like a lock and key – grants PlyC access into the cell. While it is clear that PlyC eventually kills S. pyogenes hiding inside throat cells, future experiments will aim to determine how PlyC moves around once inside an infected throat cell. Together, an understanding of how an endolysin enters cells and destroys hiding S. pyogenes will contribute to the development of endolysins with broader activity, which can be used as alternatives to common antibiotics. DOI:http://dx.doi.org/10.7554/eLife.13152.002
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Affiliation(s)
- Yang Shen
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Marilia Barros
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - Tarek Vennemann
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - D Travis Gallagher
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States.,National Institute of Standards and Technology, Gaithersburg, United States
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Sara B Linden
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Ryan D Heselpoth
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States
| | - Dennis J Spencer
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, United States
| | - David M Donovan
- Animal Biosciences and Biotechnology Lab, Agricultural Research Service, USDA, Beltsville, United States
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Rockville, United States
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, United States
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States.,Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, United States
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States.,Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, United States.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States
| | - Daniel C Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States.,Department of Veterinary Medicine, University of Maryland, College Park, College Park, United States
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39
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Belička M, Gerelli Y, Kučerka N, Fragneto G. The component group structure of DPPC bilayers obtained by specular neutron reflectometry. SOFT MATTER 2015; 11:6275-6283. [PMID: 26160133 DOI: 10.1039/c5sm00274e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Specular neutron reflectometry was measured on a floating bilayer system consisting of 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine deposited over a 1,2-dibehenoyl-sn-glycero-3-phosphocholine bilayer at 25 and 55 °C. The internal structure of lipid bilayers was described by a one-dimensional neutron scattering length density profile model, originally developed for the evaluation of small-angle scattering data. The reflectivity data from the supported bilayer were evaluated separately and used further as constraints in modeling the floating bilayer reflectivity curves. The model reflectivity curves successfully describe the experimental reflectivities of the supported bilayer in the gel phase and the floating bilayer system in the liquid-crystalline phase. The results yield an internal structure of a deposited bilayer and a floating bilayer on the level of component groups of lipid molecules. The obtained structure of the floating d62-diC16:0PC bilayer displays high resemblance of the bilayer structure in the form of unilamellar vesicles. At the same time, however, the results show differences in comparison to unilamellar vesicle bilayers, most likely due to the undulations of supported bilayers.
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Affiliation(s)
- Michal Belička
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
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40
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Hydrodynamic and Membrane Binding Properties of Purified Rous Sarcoma Virus Gag Protein. J Virol 2015; 89:10371-82. [PMID: 26246573 DOI: 10.1128/jvi.01628-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/28/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Previously, no retroviral Gag protein has been highly purified in milligram quantities and in a biologically relevant and active form. We have purified Rous sarcoma virus (RSV) Gag protein and in parallel several truncation mutants of Gag and have studied their biophysical properties and membrane interactions in vitro. RSV Gag is unusual in that it is not naturally myristoylated. From its ability to assemble into virus-like particles in vitro, we infer that RSV Gag is biologically active. By size exclusion chromatography and small-angle X-ray scattering, Gag in solution appears extended and flexible, in contrast to previous reports on unmyristoylated HIV-1 Gag, which is compact. However, by neutron reflectometry measurements of RSV Gag bound to a supported bilayer, the protein appears to adopt a more compact, folded-over conformation. At physiological ionic strength, purified Gag binds strongly to liposomes containing acidic lipids. This interaction is stimulated by physiological levels of phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] and by cholesterol. However, unlike HIV-1 Gag, RSV Gag shows no sensitivity to acyl chain saturation. In contrast with full-length RSV Gag, the purified MA domain of Gag binds to liposomes only weakly. Similarly, both an N-terminally truncated version of Gag that is missing the MA domain and a C-terminally truncated version that is missing the NC domain bind only weakly. These results imply that NC contributes to membrane interaction in vitro, either by directly contacting acidic lipids or by promoting Gag multimerization. IMPORTANCE Retroviruses like HIV assemble at and bud from the plasma membrane of cells. Assembly requires the interaction between thousands of Gag molecules to form a lattice. Previous work indicated that lattice formation at the plasma membrane is influenced by the conformation of monomeric HIV. We have extended this work to the more tractable RSV Gag. Our results show that RSV Gag is highly flexible and can adopt a folded-over conformation on a lipid bilayer, implicating both the N and C termini in membrane binding. In addition, binding of Gag to membranes is diminished when either terminal domain is truncated. RSV Gag membrane association is significantly less sensitive than HIV Gag membrane association to lipid acyl chain saturation. These findings shed light on Gag assembly and membrane binding, critical steps in the viral life cycle and an untapped target for antiretroviral drugs.
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41
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Perevozchikova T, Nanda H, Nesta DP, Roberts CJ. Protein Adsorption, Desorption, and Aggregation Mediated by Solid-Liquid Interfaces. J Pharm Sci 2015; 104:1946-1959. [DOI: 10.1002/jps.24429] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 02/19/2015] [Accepted: 02/26/2015] [Indexed: 01/13/2023]
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42
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Yap TL, Jiang Z, Heinrich F, Gruschus JM, Pfefferkorn CM, Barros M, Curtis JE, Sidransky E, Lee JC. Structural features of membrane-bound glucocerebrosidase and α-synuclein probed by neutron reflectometry and fluorescence spectroscopy. J Biol Chem 2014; 290:744-54. [PMID: 25429104 DOI: 10.1074/jbc.m114.610584] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations in glucocerebrosidase (GCase), the enzyme deficient in Gaucher disease, are a common genetic risk factor for the development of Parkinson disease and related disorders, implicating the role of this lysosomal hydrolase in the disease etiology. A specific physical interaction exists between the Parkinson disease-related protein α-synuclein (α-syn) and GCase both in solution and on the lipid membrane, resulting in efficient enzyme inhibition. Here, neutron reflectometry was employed as a first direct structural characterization of GCase and α-syn·GCase complex on a sparsely-tethered lipid bilayer, revealing the orientation of the membrane-bound GCase. GCase binds to and partially inserts into the bilayer with its active site most likely lying just above the membrane-water interface. The interaction was further characterized by intrinsic Trp fluorescence, circular dichroism, and surface plasmon resonance spectroscopy. Both Trp fluorescence and neutron reflectometry results suggest a rearrangement of loops surrounding the catalytic site, where they extend into the hydrocarbon chain region of the outer leaflet. Taking advantage of contrasting neutron scattering length densities, the use of deuterated α-syn versus protiated GCase showed a large change in the membrane-bound structure of α-syn in the complex. We propose a model of α-syn·GCase on the membrane, providing structural insights into inhibition of GCase by α-syn. The interaction displaces GCase away from the membrane, possibly impeding substrate access and perturbing the active site. GCase greatly alters membrane-bound α-syn, moving helical residues away from the bilayer, which could impact the degradation of α-syn in the lysosome where these two proteins interact.
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Affiliation(s)
| | - Zhiping Jiang
- From the Laboratory of Molecular Biophysics, NHLBI, and
| | - Frank Heinrich
- the Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and the Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899
| | | | | | - Marilia Barros
- the Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and
| | - Joseph E Curtis
- the Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899
| | - Ellen Sidransky
- the Medical Genetics Branch, NHGRI, National Institutes of Health, Bethesda, Maryland 20892
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43
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Nanda H, Heinrich F, Lösche M. Membrane association of the PTEN tumor suppressor: neutron scattering and MD simulations reveal the structure of protein-membrane complexes. Methods 2014; 77-78:136-46. [PMID: 25461777 DOI: 10.1016/j.ymeth.2014.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/10/2014] [Accepted: 10/14/2014] [Indexed: 12/31/2022] Open
Abstract
Neutron reflection (NR) from planar interfaces is an emerging technology that provides unique and otherwise inaccessible structural information on disordered molecular systems such as membrane proteins associated with fluid bilayers, thus addressing one of the remaining challenges of structural biology. Although intrinsically a low-resolution technique, using structural information from crystallography or NMR allows the construction of NR models that describe the architecture of protein-membrane complexes at high resolution. In addition, a combination of these methods with molecular dynamics (MD) simulations has the potential to reveal the dynamics of protein interactions with the bilayer in atomistic detail. We review recent advances in this area by discussing the application of these techniques to the complex formed by the PTEN phosphatase with the plasma membrane. These studies provide insights in the cellular regulation of PTEN, its interaction with PI(4,5)P2 in the inner plasma membrane and the pathway by which its substrate, PI(3,4,5)P3, accesses the PTEN catalytic site.
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Affiliation(s)
- Hirsh Nanda
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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44
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Benedetto A, Heinrich F, Gonzalez MA, Fragneto G, Watkins E, Ballone P. Structure and Stability of Phospholipid Bilayers Hydrated by a Room-Temperature Ionic Liquid/Water Solution: A Neutron Reflectometry Study. J Phys Chem B 2014; 118:12192-206. [DOI: 10.1021/jp507631h] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Antonio Benedetto
- School
of Physics, University College Dublin−UCD, Belfield Campus, Dublin 4, Ireland
| | - Frank Heinrich
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | | | | | - Erik Watkins
- Institute Laue-Langevin, Grenoble, France
- Lujan
Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Pietro Ballone
- Center
for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia (IIT), 00161 Roma, Italy
- Department
of Physics, Universita’ di Roma “La Sapienza”, 00185 Roma, Italy
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45
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Heinrich F, Lösche M. Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:2341-9. [PMID: 24674984 PMCID: PMC4082750 DOI: 10.1016/j.bbamem.2014.03.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/13/2014] [Accepted: 03/17/2014] [Indexed: 11/23/2022]
Abstract
Neutron reflectometry (NR) is an emerging experimental technique for the structural characterization of proteins interacting with fluid bilayer membranes under conditions that mimic closely the cellular environment. Thus, cellular processes can be emulated in artificial systems and their molecular basis studied by adding cellular components one at a time in a well-controlled environment while the resulting structures, or structural changes in response to external cues, are monitored with neutron reflection. In recent years, sample environments, data collection strategies and data analysis were continuously refined. The combination of these improvements increases the information which can be obtained from NR to an extent that enables structural characterization of protein-membrane complexes at a length scale that exceeds the resolution of the measurement by far. Ultimately, the combination of NR with molecular dynamics (MD) simulations can be used to cross-validate the results of the two techniques and provide atomic-scale structural models. This review discusses these developments in detail and demonstrates how they provide new windows into relevant biomedical problems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Frank Heinrich
- Physics Department, Carnegie Mellon University, Pittsburgh, PA, U.S.A.; NIST Center for Neutron Research, Gaithersburg, MD, U.S.A
| | - Mathias Lösche
- Physics Department, Carnegie Mellon University, Pittsburgh, PA, U.S.A.; NIST Center for Neutron Research, Gaithersburg, MD, U.S.A..
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46
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Heinrich F, Nanda H, Goh HZ, Bachert C, Lösche M, Linstedt AD. Myristoylation restricts orientation of the GRASP domain on membranes and promotes membrane tethering. J Biol Chem 2014; 289:9683-91. [PMID: 24505136 DOI: 10.1074/jbc.m113.543561] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian Golgi reassembly stacking protein (GRASP) proteins are Golgi-localized homotypic membrane tethers that organize Golgi stacks into a long, contiguous ribbon-like structure. It is unknown how GRASPs undergo trans pairing given that cis interactions between the proteins in the plane of the membrane are intrinsically favored. To test the hypothesis that myristoylation of the self-interacting GRASP domain restricts its orientation on the membrane to favor trans pairing, we established an in vitro assay that recapitulates GRASP-dependent membrane tethering and used neutron reflection under similar conditions to determine the orientation of the GRASP domain. In vivo, the membrane association of GRASP proteins is conferred by the simultaneous insertion of an N-terminal myristic acid and binding to a Golgi-associated binding partner. In our assay, the latter contact was replaced using a C-terminal hexa-His moiety, which bound to Ni(2+)-conjugated lipids incorporated into a substrate-supported bilayer lipid membrane. Nonmyristoylated protein lacked a fixed orientation on the membrane and inefficiently tethered liposomes. In contrast, myristoylated GRASP promoted tethering and exhibited a unique membrane complex. Thus, myristoylation restricts the membrane orientation of the GRASP domain favoring interactions in trans for membrane tethering.
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47
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Budvytyte R, Valincius G, Niaura G, Voiciuk V, Mickevicius M, Stauffer H, Goh HZ, Shekhar P, Heinrich F, Shenoy S, Lösche M, Vanderah DJ. Structure and properties of tethered bilayer lipid membranes with unsaturated anchor molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8645-56. [PMID: 23745652 PMCID: PMC3753044 DOI: 10.1021/la401132c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The self-assembled monolayers (SAMs) of new lipidic anchor molecule HC18 [Z-20-(Z-octadec-9-enyloxy)-3,6,9,12,15,18,22-heptaoxatetracont-31-ene-1-thiol] and mixed HC18/β-mercaptoethanol (βME) SAMs were studied by spectroscopic ellipsometry, contact angle measurements, reflection-absorption infrared spectroscopy, and electrochemical impedance spectroscopy (EIS) and were evaluated in tethered bilayer lipid membranes (tBLMs). Our data indicate that HC18, containing a double bond in the alkyl segments, forms highly disordered SAMs up to anchor/βME molar fraction ratios of 80/20 and result in tBLMs that exhibit higher lipid diffusion coefficients relative to those of previous anchor compounds with saturated alkyl chains, as determined by fluorescence correlation spectroscopy. EIS data shows the HC18 tBLMs, completed by rapid solvent exchange or vesicle fusion, form more easily than with saturated lipidic anchors, exhibit excellent electrical insulating properties indicating low defect densities, and readily incorporate the pore-forming toxin α-hemolysin. Neutron reflectivity measurements on HC18 tBLMs confirm the formation of complete tBLMs, even at low tether compositions and high ionic lipid compositions. Our data indicate that HC18 results in tBLMs with improved physical properties for the incorporation of integral membrane proteins (IMPs) and that 80% HC18 tBLMs appear to be optimal for practical applications such as biosensors where high electrical insulation and IMP/peptide reconstitution are imperative.
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Affiliation(s)
- Rima Budvytyte
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | - Gintaras Valincius
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | - Gediminas Niaura
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | - Vladislava Voiciuk
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | | | - Hilary Stauffer
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Hood College, Frederick, MD 21701
| | - Haw-Zan Goh
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | | | - Frank Heinrich
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Siddharth Shenoy
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Mathias Lösche
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - David J. Vanderah
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850
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48
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Budvytyte R, Mickevicius M, Vanderah DJ, Heinrich F, Valincius G. Modification of tethered bilayers by phospholipid exchange with vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4320-4327. [PMID: 23445262 DOI: 10.1021/la304613a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phosphatidylcholine and cholesterol exchange between vesicles and planar tethered bilayer lipid membranes (tBLMs) was demonstrated from electrochemical impedance spectroscopy (EIS), fluorescence microscopy (FM), and neutron reflectometry (NR) data. Cholesterol is incorporated into the tBLMs, as determined by the functional reconstitution of the pore forming toxin α-hemolysin (EIS data), attaining cholesterol concentrations nearly equal to that in the donor vesicles. Using fluorescently labeled lipids and cholesterol, FM indicates that the vesicle-tBLM exchange is homogeneous for the lipids but not for cholesterol. NR data with perdeuterated lipids indicates lipid exchange asymmetry with two lipids exchanged in the outer leaflet for every lipid in the inner leaflet. NR and EIS data further show different exchange rates for cholesterol (t1/2 < 60 min) and phosphatidylcholine (t1/2 > 4 h). This work lays the foundation for the preparation of robust, lower defect, more biologically relevant tBLMs by essentially combining the two methods of tBLM formation-rapid solvent exchange and vesicle fusion.
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Affiliation(s)
- Rima Budvytyte
- Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
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Gericke A, Leslie NR, Lösche M, Ross AH. PtdIns(4,5)P2-mediated cell signaling: emerging principles and PTEN as a paradigm for regulatory mechanism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 991:85-104. [PMID: 23775692 DOI: 10.1007/978-94-007-6331-9_6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PtdIns(4,5)P2 (phosphatidylinositol 4,5-bisphosphate) is a relatively common anionic lipid that regulates cellular functions by multiple mechanisms. Hydrolysis of PtdIns(4,5)P2 by phospholipase C yields inositol trisphosphate and diacylglycerol. Phosphorylation by phosphoinositide 3-kinase yields PtdIns(3,4,5)P3, which is a potent signal for survival and proliferation. Also, PtdIns(4,5)P2 can bind directly to integral and peripheral membrane proteins. As an example of regulation by PtdIns(4,5)P2, we discuss phosphatase and tensin homologue deleted on chromosome 10 (PTEN) in detail. PTEN is an important tumor suppressor and hydrolyzes PtdIns(3,4,5)P3. PtdIns(4,5)P2 enhances PTEN association with the plasma membrane and activates its phosphatase activity. This is a critical regulatory mechanism, but a detailed description of this process from a structural point of view is lacking. The disordered lipid bilayer environment hinders structural determinations of membrane-bound PTEN. A new method to analyze membrane-bound protein measures neutron reflectivity for proteins bound to tethered phospholipid membranes. These methods allow determination of the orientation and shape of membrane-bound proteins. In combination with molecular dynamics simulations, these studies will provide crucial structural information that can serve as a foundation for our understanding of PTEN regulation in normal and pathological processes.
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Affiliation(s)
- Arne Gericke
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609, USA
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50
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Membrane association of the PTEN tumor suppressor: electrostatic interaction with phosphatidylserine-containing bilayers and regulatory role of the C-terminal tail. J Struct Biol 2012; 180:394-408. [PMID: 23073177 DOI: 10.1016/j.jsb.2012.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 10/03/2012] [Accepted: 10/05/2012] [Indexed: 01/23/2023]
Abstract
The phosphatidylinositolphosphate phosphatase PTEN is the second most frequently mutated protein in human tumors. Its membrane association, allosteric activation and membrane dissociation are poorly understood. We recently reported PTEN binding affinities to membranes of different compositions (Shenoy et al., 2012, PLoS ONE 7, e32591) and a preliminary investigation of the protein-membrane complex with neutron reflectometry (NR). Here we use NR to validate molecular dynamics (MD) simulations of the protein and study conformational differences of the protein in solution and on anionic membranes. NR shows that full-length PTEN binds to such membranes roughly in the conformation and orientation suggested by the crystal structure of a truncated PTEN protein, in contrast with a recently presented model which suggested that membrane binding depends critically on the SUMOylation of the CBR3 loop of PTEN's C2 domain. Our MD simulations confirm that PTEN is peripherally bound to the bilayer surface and show slight differences of the protein structure in solution and in the membrane-bound state, where the protein body flattens against the bilayer surface. PTEN's C2 domain binds phosphatidylserine (PS) tightly through its CBR3 loop, and its phosphatase domain also forms electrostatic interactions with PS. NR and MD results show consistently that PTEN's unstructured, anionic C-terminal tail is repelled from the bilayer surface. In contrast, this tail is tightly tugged against the C2 domain in solution, partially obstructing the membrane-binding interface of the protein. Arresting the C-terminal tail in this conformation by phosphorylation may provide a control mechanism for PTEN's membrane binding and activity.
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