1
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Neville GM, Morrison KA, Shilliday ER, Doutch J, Dalgliesh R, Price GJ, Edler KJ. The effect of polymer end-group on the formation of styrene - maleic acid lipid particles (SMALPs). SOFT MATTER 2023; 19:8507-8518. [PMID: 37889133 DOI: 10.1039/d3sm01180a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
A series of block copolymers comprising styrene and maleic acid (SMA) has been prepared using RAFT polymerisation. RAFT often results in a large hydrophobic alkylthiocarbonylthio end group and this work examines its effect on the solution behaviour of the copolymers. SMA variants with, and without, this end group were synthesised and their behaviour compared with a commercially-available random copolymer of similar molecular weight. Dynamic light scattering and surface tension measurements found the RAFT-copolymers preferentially self-assembled into higher-order aggregates in aqueous solution. Small angle neutron scattering using deuterated styrene varients add support to the accepted model that these agreggates comprise a solvent-protected styrenic core with an acid-rich shell. Replacing the hydrophobic RAFT end group with a more hydrophilic nitrile caused differences in the resulting surface activity, attributed to the ability of the adjoining styrene homoblock to drive aggregation. Each of the copolymers formed SMALP nanodiscs with DMPC lipids, which were found to encapsulate a model membrane protein, gramicidin. However, end group variation affected solubilisition of DPPC, a lipid with a higher phase transition temperature. When using RAFT-copolymers terminated with a hydrophobic group, swelling of the bilayer and greater penetration of the homoblock into the nanodisc core occurred with increasing homoblock length. Conversely, commercial and nitrile-terminated RAFT-copolymers produced nanodisc sizes that stayed constant, instead indicating interaction at the edge of the lipid patch. The results highlight how even minor changes to the copolymer can modify the amphiphilic balance between regions, knowledge useful towards optimising copolymer structure to enhance and control nanodisc formation.
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Affiliation(s)
- George M Neville
- Centre for Sustainable Chemical Technologies, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Kerrie A Morrison
- Centre for Sustainable Chemical Technologies, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Ella R Shilliday
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - James Doutch
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Robert Dalgliesh
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Gareth J Price
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Department of Chemistry, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Karen J Edler
- Centre for Sustainable Chemical Technologies, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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2
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Trinh TKH, Cabezas AJ, Joshi S, Catalano C, Siddique AB, Qiu W, Deshmukh S, des Georges A, Guo Y. pH-tunable membrane-active polymers, NCMNP2a- x, and their potential membrane protein applications. Chem Sci 2023; 14:7310-7326. [PMID: 37416719 PMCID: PMC10321531 DOI: 10.1039/d3sc01890c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Accurate 3D structures of membrane proteins are essential for comprehending their mechanisms of action and designing specific ligands to modulate their activities. However, these structures are still uncommon due to the involvement of detergents in the sample preparation. Recently, membrane-active polymers have emerged as an alternative to detergents, but their incompatibility with low pH and divalent cations has hindered their efficacy. Herein, we describe the design, synthesis, characterization, and application of a new class of pH-tunable membrane-active polymers, NCMNP2a-x. The results demonstrated that NCMNP2a-x could be used for high-resolution single-particle cryo-EM structural analysis of AcrB in various pH conditions and can effectively solubilize BcTSPO with the function preserved. Molecular dynamic simulation is consistent with experimental data that shed great insights into the working mechanism of this class of polymers. These results demonstrated that NCMNP2a-x might have broad applications in membrane protein research.
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Affiliation(s)
- Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Andres Jorge Cabezas
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
| | - Soumil Joshi
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Claudio Catalano
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Abu Bakkar Siddique
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
| | - Sanket Deshmukh
- Department of Chemical Engineering, Virginia Tech Blacksburg VA2 4060 USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York New York New York 10017 USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York New York New York 10017 USA
- Department of Chemistry & Biochemistry, City College of New York New York New York 10017 USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond VA 23298 USA
- Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University Richmond VA 23219 USA
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3
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Yu T, Omarova M, Zhang M, Hossain I, Chen J, Darvish O, John VT, Zhang D. Uncovering the Optimal Molecular Characteristics of Hydrophobe-Containing Polypeptoids to Induce Liposome or Cell Membrane Fragmentation. Biomacromolecules 2023; 24:1511-1521. [PMID: 36802533 PMCID: PMC10015453 DOI: 10.1021/acs.biomac.3c00028] [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] [Indexed: 02/23/2023]
Abstract
Cellular functions of membrane proteins are strongly coupled to their structures and aggregation states in the cellular membrane. Molecular agents that can induce the fragmentation of lipid membranes are highly sought after as they are potentially useful for extracting membrane proteins in their native lipid environment. Toward this goal, we investigated the fragmentation of synthetic liposome using hydrophobe-containing polypeptoids (HCPs), a class of facially amphiphilic pseudo-peptidic polymers. A series of HCPs with varying chain lengths and hydrophobicities have been designed and synthesized. The effects of polymer molecular characteristics on liposome fragmentation are systemically investigated by a combination of light scattering (SLS/DLS) and transmission electron microscopy (cryo-TEM and negative stained TEM) methods. We demonstrate that HCPs with a sufficient chain length (DPn ≈ 100) and intermediate hydrophobicity (PNDG mol % = 27%) can most effectively induce the fragmentation of liposomes into colloidally stable nanoscale HCP-lipid complexes owing to the high density of local hydrophobic contact between the HCP polymers and lipid membranes. The HCPs can also effectively induce the fragmentation of bacterial lipid-derived liposomes and erythrocyte ghost cells (i.e., empty erythrocytes) to form nanostructures, highlighting the potential of HCPs as novel macromolecular surfactants toward the application of membrane protein extraction.
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Affiliation(s)
- Tianyi Yu
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Marzhana Omarova
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Meng Zhang
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Istiak Hossain
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Jianqiang Chen
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Omead Darvish
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Vijay T. John
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Donghui Zhang
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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4
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Elbahnasawy MA, Nasr ML. DNA-nanostructure-templated assembly of planar and curved lipid-bilayer membranes. Front Chem 2023; 10:1047874. [PMID: 36844038 PMCID: PMC9944057 DOI: 10.3389/fchem.2022.1047874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 02/10/2023] Open
Abstract
Lipid-bilayer nanodiscs and liposomes have been developed to stabilize membrane proteins in order to study their structures and functions. Nanodiscs are detergent-free, water-soluble, and size-controlled planar phospholipid-bilayer platforms. On the other hand, liposomes are curved phospholipid-bilayer spheres with an aqueous core used as drug delivery systems and model membrane platforms for studying cellular activities. A long-standing challenge is the generation of a homogenous and monodispersed lipid-bilayer system with a very wide range of dimensions and curvatures (elongation, bending, and twisting). A DNA-origami template provides a way to control the shapes, sizes, and arrangements of lipid bilayers via enforcing the assembly of lipid bilayers within the cavities created by DNA nanostructures. Here, we provide a concise overview and discuss how to design planar and curved lipid-bilayer membranes by using DNA-origami nanostructures as templates. Finally, we will discuss the potential applications of DNA-origami nanostructures in the structural and functional studies of large membrane proteins and their complexes.
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Affiliation(s)
- Mostafa A. Elbahnasawy
- Immunology Laboratory, Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mahmoud L. Nasr
- Renal Division and Engineering in Medicine Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States,*Correspondence: Mahmoud L. Nasr,
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5
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van Walree CA. Intramolecular Hydrogen Bonding in DIBMA Model Compounds. MACROMOL THEOR SIMUL 2022. [DOI: 10.1002/mats.202200042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Cornelis A. van Walree
- Membrane Biochemistry and Biophysics Utrecht University Padualaan 8 Utrecht 3584 CH Netherlands
- University College Utrecht Campusplein 1 Utrecht 3584 ED the Netherlands
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6
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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7
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Khaojanta T, Kalaithong W, Somsunan R, Punyamoonwongsa P, Mahomed A, Topham PD, Tighe BJ, Molloy R. Synthesis and characterization of block copolymers of styrene‐maleic acid with acrylamide and
N
,
N
‐dimethylacrylamide. POLYM ENG SCI 2022. [DOI: 10.1002/pen.25986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thidarat Khaojanta
- Polymer Research Group, Department of Chemistry, Faculty of Science Chiang Mai University Chiang Mai Thailand
| | - Wichaya Kalaithong
- Polymer Research Group, Department of Chemistry, Faculty of Science Chiang Mai University Chiang Mai Thailand
| | - Runglawan Somsunan
- Polymer Research Group, Department of Chemistry, Faculty of Science Chiang Mai University Chiang Mai Thailand
| | | | - Anisa Mahomed
- Aston Institute of Materials Research, Aston University Birmingham UK
| | - Paul D. Topham
- Aston Institute of Materials Research, Aston University Birmingham UK
| | - Brian J. Tighe
- Aston Institute of Materials Research, Aston University Birmingham UK
| | - Robert Molloy
- Polymer Research Group, Department of Chemistry, Faculty of Science Chiang Mai University Chiang Mai Thailand
- Materials Science Research Center, Faculty of Science Chiang Mai University Chiang Mai Thailand
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8
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Catania R, Machin J, Rappolt M, Muench SP, Beales PA, Jeuken LJC. Detergent-Free Functionalization of Hybrid Vesicles with Membrane Proteins Using SMALPs. Macromolecules 2022; 55:3415-3422. [PMID: 35571225 PMCID: PMC9097535 DOI: 10.1021/acs.macromol.2c00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/08/2022] [Indexed: 11/28/2022]
Abstract
![]()
Hybrid
vesicles (HVs) that consist of mixtures of block copolymers
and lipids are robust biomimetics of liposomes, providing a valuable
building block in bionanotechnology, catalysis, and synthetic biology.
However, functionalization of HVs with membrane proteins remains laborious
and expensive, creating a significant current challenge in the field.
Here, using a new approach of extraction with styrene-maleic acid
(SMA), we show that a membrane protein (cytochrome bo3) directly transfers into HVs with an efficiency of 73.9
± 13.5% without the requirement of detergent, long incubation
times, or mechanical disruption. Direct transfer of membrane proteins
using this approach was not possible into liposomes, suggesting that
HVs are more amenable than liposomes to membrane protein incorporation
from a SMA lipid particle system. Finally, we show that this transfer
method is not limited to cytochrome bo3 and can also be performed with complex membrane protein mixtures.
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Affiliation(s)
- Rosa Catania
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Jonathan Machin
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
| | - Stephen P. Muench
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Paul A. Beales
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| | - Lars J. C. Jeuken
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Leiden Institute of Chemistry, University Leiden, Leiden 2300RA, The Netherlands
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9
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Neville GM, Edler KJ, Price GJ. Fluorescent styrene maleic acid copolymers to facilitate membrane protein studies in lipid nanodiscs. NANOSCALE 2022; 14:5689-5693. [PMID: 35315461 DOI: 10.1039/d1nr07230g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fluorescently-labelled variants of poly(styrene-co-maleic acid), SMA, have been synthesised by RAFT copolymerisation. We show that low ratios of vinyl fluorophores, analogous to styrene, can be successfully incorporated during polymerisation without detriment to nanodisc formation upon interaction with lipids. These novel copolymers are capable of encapuslating lipids and the model membrane protein, gramicidin, and hence have the potential to be applied in fluorescence-based biological studies. To demonstrate this, energy transfer is used to probe polymer-protein interactions in nanodiscs. The copolymers may also be used to monitor nanodisc self assembly by exploiting aggregation-caused-quenching (ACQ).
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Affiliation(s)
| | - Karen J Edler
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
| | - Gareth J Price
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
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10
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Wu W, Zhou Q, Xu B, Zhong Y, Xu H, Zhang L, Mao Z. Study on the dispersion mechanism of the polycarboxylic acid dispersant for disperse dyes. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Jeong C, Franklin R, Edler KJ, Vanommeslaeghe K, Krueger S, Curtis JE. Styrene-Maleic Acid Copolymer Nanodiscs to Determine the Shape of Membrane Proteins. J Phys Chem B 2022; 126:1034-1044. [PMID: 35089036 DOI: 10.1021/acs.jpcb.1c05050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipid nanodiscs can be used to solubilize functional membrane proteins (MPs) in nativelike environments. Thus, they are promising reagents that have been proven useful to characterize MPs. Both protein and non-protein molecular belts have shown promise to maintain the structural integrity of MPs in lipid nanodiscs. Small-angle neutron scattering (SANS) can be used to determine low-resolution structures of proteins in solution, which can be enhanced through the use of contrast variation methods. We present theoretical contrast variation SANS results for protein and styrene-maleic acid copolymer (SMA) belt 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) nanodiscs with and without additional bound or transmembrane proteins. The predicted scattering properties are derived from atomistic molecular dynamics simulations to account for conformational fluctuations, and we determine deuterium-labeling conditions such that SANS intensity profiles only include contributions from the scattering of the MP of interest. We propose strategies to tune the neutron scattering length densities (SLDs) of the SMA and DMPC using selective deuterium labeling such that the SLD of the nanodisc becomes homogeneous and its scattering can essentially be eliminated in solvents containing an appropriate amount of D2O. These finely tuned labeled polymer-based nanodiscs are expected to be useful to extract the size and molecular shape information of MPs using SANS-based contrast variation experiments, and they can be used with MPs of any molecular weight.
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Affiliation(s)
- Cheol Jeong
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States.,Department of Chemistry, The University of Tennessee, Knoxville, Tennessee 37996-1600, United States
| | - Ryan Franklin
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Karen J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| | - Kenno Vanommeslaeghe
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling─FABI, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
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12
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Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. NANOMATERIALS 2022; 12:nano12030361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
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Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (P.S.O.); (K.V.S.)
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Correspondence: (P.S.O.); (K.V.S.)
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13
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Caparotta M, Puiatti M, Masone D. Artificial stabilization of the fusion pore by intra-organelle styrene-maleic acid copolymers. SOFT MATTER 2021; 17:8314-8321. [PMID: 34550159 DOI: 10.1039/d1sm00978h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Styrene-maleic acid copolymers have become an advantageous detergent-free alternative for membrane protein isolation. Since their discovery, experimental membrane protein extraction and purification by keeping intact their lipid environment has become significantly easier. With the aim of identifying new applications of these interesting copolymers, their molecular binding and functioning mechanisms have recently become intense objects of study. In this work, we describe the use of styrene-maleic acid copolymers as an artificial tool to stabilize the fusion pore. We show that when these copolymers circumscribe the water channel that defines the fusion pore, they keep it from shrinking and closing. We describe how only intra-organelle copolymers have stabilizing capabilities while extra-organelle ones have negligible or even contrary effects on the fusion pore life-time.
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Affiliation(s)
- Marcelo Caparotta
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
| | - Marcelo Puiatti
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), 5016, Córdoba, Argentina
| | - Diego Masone
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina.
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14
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Farrelly MD, Martin LL, Thang SH. Polymer Nanodiscs and Their Bioanalytical Potential. Chemistry 2021; 27:12922-12939. [PMID: 34180107 DOI: 10.1002/chem.202101572] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/21/2022]
Abstract
Membrane proteins (MPs) play a pivotal role in cellular function and are therefore predominant pharmaceutical targets. Although detailed understanding of MP structure and mechanistic activity is invaluable for rational drug design, challenges are associated with the purification and study of MPs. This review delves into the historical developments that became the prelude to currently available membrane mimetic technologies before shining a spotlight on polymer nanodiscs. These are soluble nanosized particles capable of encompassing MPs embedded in a phospholipid ring. The expanding range of reported amphipathic polymer nanodisc materials is presented and discussed in terms of their tolerance to different solution conditions and their nanodisc properties. Finally, the analytical scope of polymer nanodiscs is considered in both the demonstration of basic nanodisc parameters as well as in the elucidation of structures, lipid-protein interactions, and the functional mechanisms of reconstituted membrane proteins. The final emphasis is given to the unique benefits and applications demonstrated for native nanodiscs accessed through a detergent free process.
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Affiliation(s)
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
| | - San H Thang
- School of Chemistry, Monash University, Clayton, 3800, Vic, Australia
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15
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Esmaili M, Eldeeb MA, Moosavi-Movahedi AA. Current Developments in Native Nanometric Discoidal Membrane Bilayer Formed by Amphipathic Polymers. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1771. [PMID: 34361157 PMCID: PMC8308186 DOI: 10.3390/nano11071771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Unlike cytosolic proteins, membrane proteins (MPs) are embedded within the plasma membrane and the lipid bilayer of intracellular organelles. MPs serve in various cellular processes and account for over 65% of the current drug targets. The development of membrane mimetic systems such as bicelles, short synthetic polymers or amphipols, and membrane scaffold proteins (MSP)-based nanodiscs has facilitated the accommodation of synthetic lipids to stabilize MPs, yet the preparation of these membrane mimetics remains detergent-dependent. Bio-inspired synthetic polymers present an invaluable tool for excision and liberation of superstructures of MPs and their surrounding annular lipid bilayer in the nanometric discoidal assemblies. In this article, we discuss the significance of self-assembling process in design of biomimetic systems, review development of multiple series of amphipathic polymers and the significance of these polymeric "belts" in biomedical research in particular in unraveling the structures, dynamics and functions of several high-value membrane protein targets.
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Affiliation(s)
- Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mohamed A. Eldeeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Chemistry, Faculty of Science, Cairo University, Cairo 12613, Egypt
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16
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Bjørnestad V, Orwick-Rydmark M, Lund R. Understanding the Structural Pathways for Lipid Nanodisc Formation: How Styrene Maleic Acid Copolymers Induce Membrane Fracture and Disc Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6178-6188. [PMID: 33979520 PMCID: PMC8280715 DOI: 10.1021/acs.langmuir.1c00304] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Lipid nanodiscs formed by mixtures of styrene maleic acid (SMA) copolymers and lipid membranes are important tools for studying membrane proteins in many biotechnological applications. However, molecular interactions leading up to their formation are not well understood. Here, we elucidate the nanodisc formation pathways for SMA/lipid vesicle mixtures using small-angle X-ray scattering (SAXS) that allows detailed in situ nanostructural information. SMA copolymer that is initially aggregated in solution inserts its styrene units into the lipid bilayer hydrocarbon region, leading to fractures in the membrane. The initial copolymer-lipid interactions observed in the vesicles are also present in the formed discs, with excess copolymer distributed along the normal of the bilayer. The size and SMA distribution in the resulting discs strongly depend on the temperature, lipid/copolymer ratio, and lipid type. We find that the solubilization limit increases for membranes above the melting point, suggesting that defects in gel-like lipid membranes play a significant role in membrane fracturing and nanodisc formation. These findings provide unique insights into the formation of nanodiscs as well as into the microscopic mechanism of solubilization, which plays an important role in many applications and products ranging from household goods to biotechnology and medicine.
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Affiliation(s)
| | | | - Reidar Lund
- Department
of Chemistry, University of Oslo, Sem Sælandsvei 26, 0371 Oslo, Norway
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17
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Lipid Dynamics in Diisobutylene-Maleic Acid (DIBMA) Lipid Particles in Presence of Sensory Rhodopsin II. Int J Mol Sci 2021; 22:ijms22052548. [PMID: 33806280 PMCID: PMC7961963 DOI: 10.3390/ijms22052548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/01/2023] Open
Abstract
Amphiphilic diisobutylene/maleic acid (DIBMA) copolymers extract lipid-encased membrane proteins from lipid bilayers in a detergent-free manner, yielding nanosized, discoidal DIBMA lipid particles (DIBMALPs). Depending on the DIBMA/lipid ratio, the size of DIBMALPs can be broadly varied which makes them suitable for the incorporation of proteins of different sizes. Here, we examine the influence of the DIBMALP sizes and the presence of protein on the dynamics of encased lipids. As shown by a set of biophysical methods, the stability of DIBMALPs remains unaffected at different DIBMA/lipid ratios. Coarse-grained molecular dynamics simulations confirm the formation of viable DIBMALPs with an overall size of up to 35 nm. Electron paramagnetic resonance spectroscopy of nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels reveals that the dynamics of enclosed lipids are not altered by the DIBMALP size. The presence of the membrane protein sensory rhodopsin II from Natronomonas pharaonis (NpSRII) results in a slight increase in the lipid dynamics compared to empty DIBMALPs. The light-induced photocycle shows full functionality of DIBMALPs-embedded NpSRII and a significant effect of the protein-to-lipid ratio during preparation on the NpSRII dynamics. This study indicates a possible expansion of the applicability of the DIBMALP technology on studies of membrane protein–protein interaction and oligomerization in a constraining environment.
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18
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Sharma P, Plant M, Lam SK, Chen Q. Kinetic analysis of antibody binding to integral membrane proteins stabilized in SMALPs. BBA ADVANCES 2021; 1:100022. [PMID: 37082021 PMCID: PMC10074945 DOI: 10.1016/j.bbadva.2021.100022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The fundamental importance of membrane protein (MP) targets in central biological and cellular events has driven a marked increase in the use of membrane mimetics for exploring these proteins as therapeutic targets. The main challenge associated with biophysical analysis of membrane protein is the need for detergent extraction from the bilayer environment, which in many cases causes the proteins to become insoluble, unstable or display altered structure or activity. Recent technological advances have tried to limit the exposure of purified membrane protein to detergents. One such method involves the amphipathic co-polymer of styrene and maleic acid (SMA), which can release lipids and integral membrane proteins into water soluble native particles (or vesicles) termed SMALPs (Styrene Maleic Acid Lipid Particles). In this study, assay conditions that leverage SMA for membrane protein stabilization were developed to perform kinetic analysis of antibody binding to integral membrane protein and complexes in SMALPs in both purified and complex mixture settings using multiple biosensor platforms. To develop a robust and flexible platform using SMALPs technology, we optimized various SPR assay formats to analyze SMALPs produced with cell membrane pellets as well as whole cell lysates from the cell lines overexpressing membrane protein of interest. Here we emphasize the extraction of model membrane proteins of diverse architecture and function from native environments to encapsulate with SMALPs. Given the importance of selected membrane targets in central biological events and therapeutic relevance, MP-specific or tag-specific antibodies were used as a proof-of-principal to validate the SMALPs platform for ligand binding studies to support drug discovery or tool generation processes. MP-SMALPs that retain specific binding capability in multiple assay formats and biosensors, such as waveguide interferometry and surface plasmon resonance, would be a versatile platform for a wide range of downstream applications.
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Affiliation(s)
- Pooja Sharma
- Discovery Attribute Sciences, Amgen Research, Amgen Inc., Thousand Oaks, CA, 91320
- Corresponding author.
| | - Matthew Plant
- Discovery Attribute Sciences, Amgen Research, Amgen Inc., Cambridge, MA, 02141
| | - Sheung Kwan Lam
- Biologics, Amgen Research, Amgen Inc., South San Francisco, CA 94080
| | - Qing Chen
- Discovery Attribute Sciences, Amgen Research, Amgen Inc., Thousand Oaks, CA, 91320
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19
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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20
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The effect of hydrophobic alkyl sidechains on size and solution behaviors of nanodiscs formed by alternating styrene maleamic copolymer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183360. [DOI: 10.1016/j.bbamem.2020.183360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]
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21
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Cunningham RD, Kopf AH, Elenbaas BOW, Staal BB, Pfukwa R, Killian JA, Klumperman B. Iterative RAFT-Mediated Copolymerization of Styrene and Maleic Anhydride toward Sequence- and Length-Controlled Copolymers and Their Applications for Solubilizing Lipid Membranes. Biomacromolecules 2020; 21:3287-3300. [DOI: 10.1021/acs.biomac.0c00736] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Randy D. Cunningham
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Adrian H. Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Barend O. W. Elenbaas
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Bastiaan B.P. Staal
- BASF SE, RAA/AC, E210, Carl-Bosch-Strasse 38, Ludwigshafen am Rhein 67056, Germany
| | - Rueben Pfukwa
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - J. Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Bert Klumperman
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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22
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Phan MD, Korotych OI, Brady NG, Davis MM, Satija SK, Ankner JF, Bruce BD. X-ray and Neutron Reflectivity Studies of Styrene-Maleic Acid Copolymer Interactions with Galactolipid-Containing Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:3970-3980. [PMID: 32207953 DOI: 10.1021/acs.langmuir.9b03817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Styrene-maleic acid (SMA) copolymers have recently gained attention for their ability to facilitate the detergent-free solubilization of membrane protein complexes and their native boundary lipids into polymer-encapsulated, nanosized lipid particles, referred to as SMALPs. However, the interfacial interactions between SMA and lipids, which dictate the mechanism, efficiency, and selectivity of lipid and membrane protein extraction, are barely understood. Our recent finding has shown that SMA 1440, a chemical derivative of the SMA family with a functionalized butoxyethanol group, was most active in galactolipid-rich membranes, as opposed to phospholipid membranes. In the present work, we have performed X-ray reflectometry (XRR) and neutron reflectometry (NR) on the lipid monolayers at the liquid-air interface followed by the SMA copolymer adsorption. XRR and Langmuir Π-A isotherms captured the fluidifying effect of galactolipids, which allowed SMA copolymers to infiltrate easily into the lipid membranes. NR results revealed the detailed structural arrangement of SMA 1440 copolymers within the membranes and highlighted the partition of butoxyethanol group into the lipid tail region. This work allows us to propose a possible mechanism for the membrane solubilization by SMA.
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Affiliation(s)
- Minh D Phan
- Large-Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Olena I Korotych
- Department of Biochemistry, and Cellular, and Molecular Biology, University of Tennessee at Knoxville, Knoxville, Tennessee 37966, United States
| | - Nathan G Brady
- Department of Biochemistry, and Cellular, and Molecular Biology, University of Tennessee at Knoxville, Knoxville, Tennessee 37966, United States
| | - Madeline M Davis
- Department of Biochemistry, and Cellular, and Molecular Biology, University of Tennessee at Knoxville, Knoxville, Tennessee 37966, United States
| | - Sushil K Satija
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - John F Ankner
- Large-Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Barry D Bruce
- Department of Biochemistry, and Cellular, and Molecular Biology, University of Tennessee at Knoxville, Knoxville, Tennessee 37966, United States
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee 37966, United States
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23
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Azouz M, Gonin M, Fiedler S, Faherty J, Decossas M, Cullin C, Villette S, Lafleur M, D Alves I, Lecomte S, Ciaccafava A. Microfluidic diffusional sizing probes lipid nanodiscs formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183215. [PMID: 32061645 DOI: 10.1016/j.bbamem.2020.183215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/29/2022]
Abstract
The biophysical characterisation of membrane proteins and their interactions with lipids in native membrane habitat remains a major challenge. Indeed, traditional solubilisation procedures with detergents often causes the loss of native lipids surrounding membrane proteins, which ultimately impacts structural and functional properties. Recently, copolymer-based nanodiscs have emerged as a highly promising tool, thanks to their unique ability of solubilising membrane proteins directly from native membranes, in the shape of discoidal patches of lipid bilayers. While this methodology finally set us free from the use of detergents, some limitations are however associated with the use of such copolymers. Among them, one can cite the tedious control of the nanodiscs size, their instability in basic pH and in the presence of divalent cations. In this respect, many variants of the widely used Styrene Maleic Acid (SMA) copolymer have been developed to specifically address those limitations. With the multiplication of new SMA copolymer variants and the growing interest in copolymer-based nanodiscs for the characterisation of membrane proteins, there is a need to better understand and control their formation. Among the techniques used to characterise the solubilisation of lipid bilayer by amphipathic molecules, cryo-TEM, 31P NMR, DLS, ITC and fluorescence spectroscopy are the most widely used, with a consensus made in the sense that a combination of these techniques is required. In this work, we propose to evaluate the capacity of Microfluidic Diffusional Sizing (MDS) as a new method to follow copolymer nanodiscs formation. Originally designed to determine protein size through laminar flow diffusion, we present a novel application along with a protocol development to observe nanodiscs formation by MDS. We show that MDS allows to precisely measure the size of nanodiscs, and to determine the copolymer/lipid ratio at the onset of solubilisation. Finally, we use MDS to characterise peptide/nanodisc interaction. The technique shows a promising ability to highlight the pivotal role of lipids in promoting interactions through a case study with an aggregating peptide. This confirmed the relevance of using the MDS and nanodiscs as biomimetic models for such investigations.
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Affiliation(s)
- Mehdi Azouz
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Mathilde Gonin
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Sebastian Fiedler
- Fluidic Analytics Ltd, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge CB1 8DH, United Kingdom
| | - Jonathan Faherty
- Fluidic Analytics Ltd, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge CB1 8DH, United Kingdom
| | - Marion Decossas
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Christophe Cullin
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Sandrine Villette
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Michel Lafleur
- Department of chemistry, Université de Montréal, 2900, Édouard-Montpetit blvd., Montréal, Québec, Canada
| | - Isabel D Alves
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Sophie Lecomte
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France.
| | - Alexandre Ciaccafava
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France.
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24
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Colbasevici A, Voskoboynikova N, Orekhov PS, Bozdaganyan ME, Karlova MG, Sokolova OS, Klare JP, Mulkidjanian AY, Shaitan KV, Steinhoff HJ. Lipid dynamics in nanoparticles formed by maleic acid-containing copolymers: EPR spectroscopy and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183207. [PMID: 31987867 DOI: 10.1016/j.bbamem.2020.183207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
Abstract
Amphiphilic maleic acid-containing copolymers account for a recent methodical breakthrough in the study of membrane proteins. Their application enables a detergent-free extraction of membrane proteins from lipid bilayers, yielding stable water-soluble, discoidal lipid bilayer particles with incorporated proteins, which are wrapped with copolymers. Although many studies confirm the potential of this approach for membrane protein research, the interactions between the maleic acid-containing copolymers and extracted lipids, as well as possible effects of the copolymers on lipid-embedded proteins deserve further scrutinization. Here, we combine electron paramagnetic resonance spectroscopy and coarse-grain molecular dynamics simulations to compare the distribution and dynamics of lipids in lipid particles of phospholipid bilayers encased either by an aliphatic diisobutylene/maleic acid copolymer (DIBMALPs) or by an aromatic styrene/maleic acid copolymer (SMALPs). Nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels experience restrictions of their reorientational motion depending on the type of encasing copolymer. The dynamics of the lipids was less constrained in DIBMALPs than in SMALPs with the affinity of spin labeled lipids to the polymeric rim being more pronounced in SMALPs.
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Affiliation(s)
| | | | - Philipp S Orekhov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Sechenov University, Moscow 119146, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marine E Bozdaganyan
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Maria G Karlova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga S Sokolova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Johann P Klare
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Konstantin V Shaitan
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
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25
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Overduin M, Esmaili M. Structures and Interactions of Transmembrane Targets in Native Nanodiscs. SLAS DISCOVERY 2019; 24:943-952. [PMID: 31242812 DOI: 10.1177/2472555219857691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transmembrane proteins function within a continuous layer of biologically relevant lipid molecules that stabilizes their structures and modulates their activities. Structures and interactions of biological membrane-protein complexes or "memteins" can now be elucidated using native nanodiscs made by poly(styrene co-maleic anhydride) derivatives. These linear polymers contain a series of hydrophobic and polar subunits that gently fragment membranes into water-soluble discs with diameters of 5-50 nm known as styrene maleic acid lipid particles (SMALPs). High-resolution structures of memteins that include endogenous lipid ligands and posttranslational modifications can be resolved without resorting to synthetic detergents or artificial lipids. The resulting ex situ structures better recapitulate the in vivo situation and can be visualized by methods including cryo-electron microscopy (cryoEM), electron paramagnetic resonance (EPR), mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, small angle x-ray scattering (SAXS), and x-ray diffraction (XRD). Recent progress including 3D structures of biological bilayers illustrates how polymers and native nanodiscs expose previously inaccessible membrane assemblies at atomic resolution and suggest ways in which the SMALP system could be exploited for drug discovery.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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26
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Bada Juarez JF, Harper AJ, Judge PJ, Tonge SR, Watts A. From polymer chemistry to structural biology: The development of SMA and related amphipathic polymers for membrane protein extraction and solubilisation. Chem Phys Lipids 2019; 221:167-175. [PMID: 30940445 DOI: 10.1016/j.chemphyslip.2019.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 12/13/2022]
Abstract
Nanoparticles assembled with poly(styrene-maleic acid) copolymers, identified in the literature as Lipodisq, SMALPs or Native Nanodisc, are routinely used as membrane mimetics to stabilise protein structures in their native conformation. To date, transmembrane proteins of varying complexity (up to 8 beta strands or 48 alpha helices) and of a range of molecular weights (from 27 kDa up to 500 kDa) have been incorporated into this particle system for structural and functional studies. SMA and related amphipathic polymers have become versatile components of the biochemist's tool kit for the stabilisation, extraction and structural characterization of membrane proteins by techniques including cryo-EM and X-ray crystallography. Lipodisq formation does not require the use of conventional detergents and thus avoids their associated detrimental consequences. Here the development of this technology, from its fundamental concept and design to the diverse range of experimental methodologies to which it can now be applied, will be reviewed.
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Affiliation(s)
| | - Andrew J Harper
- Malvern Cosmeceutics Ltd, Malvern Hills Science Park, Geraldine Road, Malvern, WR14 3SZ, UK
| | - Peter J Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Stephen R Tonge
- Malvern Cosmeceutics Ltd, Malvern Hills Science Park, Geraldine Road, Malvern, WR14 3SZ, UK
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK.
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Native Nanodiscs and the Convergence of Lipidomics, Metabolomics, Interactomics and Proteomics. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9061230] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The omics disciplines remain largely distinct sciences due to the necessity of separating molecular classes for different assays. For example, water-soluble and lipid bilayer-bound proteins and metabolites are usually studied separately. Nonetheless, it is at the interface between these sciences where biology happens. That is, lipid-interacting proteins typically recognize and transduce signals and regulate the flow of metabolites in the cell. Technologies are emerging to converge the omics. It is now possible to separate intact membrane:protein assemblies (memteins) directly from intact cells or cell membranes. Such complexes mediate complete metabolon, receptor, channel, and transporter functions. The use of poly(styrene-co-maleic acid) (SMA) copolymers has allowed their separation in a single step without any exposure to synthetic detergents or artificial lipids. This is a critical development as these agents typically strip away biological lipids, signals, and metabolites from their physiologically-relevant positions on proteins. The resulting SMA lipid particles (SMALPs) represent native nanodiscs that are suitable for elucidation of structures and interactions that occur in vivo. Compatible tools for resolving the contained memteins include X-ray diffraction (XRD), cryo-electron microscopy (cryoEM), mass spectrometry (MS), and nuclear magnetic resonance (NMR) spectroscopy. Recent progress shows that memteins are more representative than naked membrane proteins devoid of natural lipid and is driving the development of next generation polymers.
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