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Levesque I, Juliano BR, Parson KF, Ruotolo BT. A Critical Evaluation of Detergent Exchange Methodologies for Membrane Protein Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2662-2671. [PMID: 37956121 DOI: 10.1021/jasms.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Membrane proteins (MPs) play many critical roles in cellular physiology and constitute the majority of current pharmaceutical targets. However, MPs are comparatively understudied relative to soluble proteins due to the challenges associated with their solubilization in membrane mimetics. Native mass spectrometry (nMS) has emerged as a useful technique to probe the structures of MPs. Typically, nMS studies using MPs have employed detergent micelles to solubilize the MP. Oftentimes, the detergent micelle that the MP was purified in will be exchanged into another detergent prior to analysis by nMS. While methodologies for performing detergent exchange have been extensively described in prior reports, the effectiveness of these protocols remains understudied. Here, we present a critical analysis of detergent exchange efficacy using several model transmembrane proteins and a variety of commonly used detergents, evaluating the completeness of the exchange using a battery of existing protocols. Our data include results for octyl glucoside (OG), octaethylene glycol monododecyl ether (C12E8), and tetraethylene glycol monooctyl ether (C8E4), and these data demonstrate that existing protocols are insufficient and yield incomplete exchange for the proteins under the conditions probed here. In some cases, our data indicate that up to 99% of the measured detergent corresponds to the original pre-exchange detergent rather than the desired post-exchange detergent. We conclude by discussing the need for new detergent exchange methodologies alongside improved exchange yield expectations for studying the potential influence of detergents on MP structures.
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Affiliation(s)
- Iliana Levesque
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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2
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Van Doren SR, Scott BS, Koppisetti RK. SARS-CoV-2 fusion peptide sculpting of a membrane with insertion of charged and polar groups. Structure 2023; 31:1184-1199.e3. [PMID: 37625399 PMCID: PMC10592393 DOI: 10.1016/j.str.2023.07.015] [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: 12/14/2022] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike is essential for infection. How this charged and hydrophobic domain occupies and affects membranes needs clarification. Its depth in zwitterionic, bilayered micelles at pH 5 (resembling late endosomes) was measured by paramagnetic NMR relaxation enhancements used to bias molecular dynamics simulations. Asp830 inserted deeply, along with Lys825 or Lys835. Protonation of Asp830 appeared to enhance agreement of simulated and NMR-measured depths. While the fusion peptide occupied a leaflet of the DMPC bilayer, the opposite leaflet invaginated with influx of water and choline head groups in around Asp830 and bilayer-inserted polar side chains. NMR-detected hydrogen exchange found corroborating hydration of the backbone of Thr827-Phe833 inserted deeply in bicelles. Pinching of the membrane at the inserted charge and the intramembrane hydration of polar groups agree with theory. Formation of corridors of hydrated, inward-turned head groups was accompanied by flip-flop of head groups. Potential roles of the defects are discussed.
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Affiliation(s)
- Steven R Van Doren
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA.
| | - Benjamin S Scott
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Rama K Koppisetti
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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3
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Scheyer MW, Campbell C, William PL, Hussain M, Begum A, Fonseca SE, Asare IK, Dabney P, Dabney-Smith C, Lorigan GA, Sahu ID. Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins. Biophys Chem 2023; 301:107080. [PMID: 37531799 DOI: 10.1016/j.bpc.2023.107080] [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: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
One of the major challenges in solubilization of membrane proteins is to find the optimal physiological environment for their biophysical studies. EPR spectroscopy is a powerful biophysical technique for studying the structural and dynamic properties of macromolecules. However, the challenges in the membrane protein sample preparation and flexible motion of the spin label limit the utilization of EPR spectroscopy to a majority of membrane protein systems in a physiological membrane-bound state. Recently, lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have emerged as a membrane mimetic system for investigating the structural studies of membrane proteins. However, its detail characterization for membrane protein studies is still poorly understood. Recently, we characterized the potassium channel membrane protein KCNQ1 voltage sensing domain (KCNQ1-VSD) and KCNE1 reconstituted into lipodisq nanoparticles using EPR spectroscopy. In this study, the potassium channel accessory protein KCNE3 containing flexible N- and C-termini was encapsulated into proteoliposomes and lipodisq nanoparticles and characterized for studying its structural and dynamic properties using nitroxide based site-directed spin labeling EPR spectroscopy. CW-EPR lineshape analysis data indicated an increase in spectral line broadenings with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated an enhanced quality of distance measurements with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles, when compared to proteoliposomes. These results agree with the solution NMR structural structure of the KCNE3 and EPR studies of other membrane proteins in lipodisq nanoparticles. This study along with our earlier studies will provide the reference characterization data that will provide benefit to the membrane protein researchers for studying structural dynamics of challenging membrane proteins.
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Affiliation(s)
- Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Patrick L William
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mustakim Hussain
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Afsana Begum
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Peyton Dabney
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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4
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Juliano BR, Keating JW, Ruotolo BT. Infrared Photoactivation Enables Improved Native Top-Down Mass Spectrometry of Transmembrane Proteins. Anal Chem 2023; 95:13361-13367. [PMID: 37610409 PMCID: PMC11081007 DOI: 10.1021/acs.analchem.3c02788] [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: 08/24/2023]
Abstract
Membrane proteins are often challenging targets for native top-down mass spectrometry experimentation. The requisite use of membrane mimetics to solubilize such proteins necessitates the application of supplementary activation methods to liberate protein ions prior to sequencing, which typically limits the sequence coverage achieved. Recently, infrared photoactivation has emerged as an alternative to collisional activation for the liberation of membrane proteins from surfactant micelles. However, much remains unknown regarding the mechanism by which IR activation liberates membrane protein ions from such micelles, the extent to which such methods can improve membrane protein sequence coverage, and the degree to which such approaches can be extended to support native proteomics. Here, we describe experiments designed to evaluate and probe infrared photoactivation for membrane protein sequencing, proteoform identification, and native proteomics applications. Our data reveal that infrared photoactivation can dissociate micelles composed of a variety of detergent classes, without the need for a strong IR chromophore by leveraging the relatively weak association energies of such detergent clusters in the gas phase. Additionally, our data illustrate how IR photoactivation can be extended to include membrane mimetics beyond micelles and liberate proteins from nanodiscs, liposomes, and bicelles. Finally, our data quantify the improvements in membrane protein sequence coverage produced through the use of IR photoactivation, which typically leads to membrane protein sequence coverage values ranging from 40 to 60%.
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Affiliation(s)
- Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph W Keating
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Koppisetti RK, Fulcher YG, Van Doren SR. Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles. J Am Chem Soc 2021; 143:13205-13211. [PMID: 34375093 PMCID: PMC8370118 DOI: 10.1021/jacs.1c05435] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/28/2022]
Abstract
The receptor binding and proteolysis of Spike of SARS-CoV-2 release its S2 subunit to rearrange and catalyze viral-cell fusion. This deploys the fusion peptide for insertion into the cell membranes targeted. We show that this fusion peptide transforms from intrinsic disorder in solution into a wedge-shaped structure inserted in bilayered micelles, according to chemical shifts, 15N NMR relaxation, and NOEs. The globular fold of three helices contrasts the open, extended forms of this region observed in the electron density of compact prefusion states. In the hydrophobic, narrow end of the wedge, helices 1 and 2 contact the fatty acyl chains of phospholipids, according to NOEs and proximity to a nitroxide spin label deep in the membrane mimic. The polar end of the wedge may engage and displace lipid head groups and bind Ca2+ ions for membrane fusion. Polar helix 3 protrudes from the bilayer where it might be accessible to antibodies.
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Affiliation(s)
| | - Yan G. Fulcher
- Dept. of Biochemistry, University of Missouri, Columbia, MO 65211 USA
| | - Steven R. Van Doren
- Dept. of Biochemistry, University of Missouri, Columbia, MO 65211 USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211 USA
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6
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Nakano M, Hanashima S, Hara T, Kabayama K, Asahina Y, Hojo H, Komura N, Ando H, Nyholm TKM, Slotte JP, Murata M. FRET detects lateral interaction between transmembrane domain of EGF receptor and ganglioside GM3 in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183623. [PMID: 33933428 DOI: 10.1016/j.bbamem.2021.183623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 12/16/2022]
Abstract
Ganglioside GM3 in the plasma membranes suppresses cell growth by preventing the autophosphorylation of the epidermal growth factor receptor (EGFR). Biological studies have suggested that GM3 interacts with the transmembrane segment of EGFR. Further biophysical experiments are particularly important for quantitative evaluation of the peptide-glycolipid interplay in bilayer membranes using a simple reconstituted system. To examine these interactions in this way, we synthesized the transmembrane segment of EGFR bearing a nitrobenzoxadiazole fluorophore (NBD-TM) at the N-terminus. The affinity between EGFR and GM3 was evaluated based on Förster resonance energy transfer (FRET) between NBD-TM and ATTO594-labeled GM3 in bilayers where their non-specific interaction due to lateral proximity was subtracted by using NBD-labeled phospholipid. This method for selectively detecting the specific lipid-peptide interactions in model lipid bilayers disclosed that the lateral interaction between GM3 and the transmembrane segment of EGFR plays a certain role in disturbing the formation of active EGFR dimers.
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Affiliation(s)
- Mikito Nakano
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Toshiaki Hara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Kazuya Kabayama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuya Asahina
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Naoko Komura
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Thomas K M Nyholm
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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7
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Kim J, Mandal R, Hilty C. Characterization of Membrane Protein‐Lipid Interactions in Unfolded OmpX with Enhanced Time Resolution by Hyperpolarized NMR. Chembiochem 2020; 21:2861-2867. [DOI: 10.1002/cbic.202000271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Jihyun Kim
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Ratnamala Mandal
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Christian Hilty
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
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8
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Sahu ID, Dixit G, Reynolds WD, Kaplevatsky R, Harding BD, Jaycox CK, McCarrick RM, Lorigan GA. Characterization of the Human KCNQ1 Voltage Sensing Domain (VSD) in Lipodisq Nanoparticles for Electron Paramagnetic Resonance (EPR) Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2020; 124:2331-2342. [PMID: 32130007 DOI: 10.1021/acs.jpcb.9b11506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane proteins are responsible for conducting essential biological functions that are necessary for the survival of living organisms. In spite of their physiological importance, limited structural information is currently available as a result of challenges in applying biophysical techniques for studying these protein systems. Electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study the structural and dynamic properties of membrane proteins. However, the application of EPR spectroscopy to membrane proteins in a native membrane-bound state is extremely challenging due to the complexity observed in inhomogeneity sample preparation and the dynamic motion of the spin label. Detergent micelles are very popular membrane mimetics for membrane proteins due to their smaller size and homogeneity, providing high-resolution structure analysis by solution NMR spectroscopy. However, it is important to test whether the protein structure in a micelle environment is the same as that of its membrane-bound state. Lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have been introduced as a potentially good membrane-mimetic system for structural studies of membrane proteins. Recently, we reported on the EPR characterization of the KCNE1 membrane protein having a single transmembrane incorporated into lipodisq nanoparticles. In this work, lipodisq nanoparticles were used as a membrane mimic system for probing the structural and dynamic properties of the more complicated membrane protein system human KCNQ1 voltage sensing domain (Q1-VSD) having four transmembrane helices using site-directed spin-labeling EPR spectroscopy. Characterization of spin-labeled Q1-VSD incorporated into lipodisq nanoparticles was carried out using CW-EPR spectral line shape analysis and pulsed EPR double-electron electron resonance (DEER) measurements. The CW-EPR spectra indicate an increase in spectral line broadening with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated a superior quality of distance measurement with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles when compared to proteoliposomes. These results are consistent with the solution NMR structural studies on the Q1-VSD. This study will be beneficial for researchers working on investigating the structural and dynamic properties of more complicated membrane protein systems using lipodisq nanoparticles.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
| | - Gunjan Dixit
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Warren D Reynolds
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ryan Kaplevatsky
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Colleen K Jaycox
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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9
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F Dudás E, Wacha A, Bóta A, Bodor A. Peptide-bicelle interaction: Following variations in size and morphology by a combined NMR-SAXS approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183095. [PMID: 31672542 DOI: 10.1016/j.bbamem.2019.183095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
Abstract
Changes in membrane properties occurring upon protein interaction are key questions in understanding membrane protein function. To report on the occurring size and shape variation we present here a combined NMR-SAXS method performed under physiological conditions using the same samples, enabling determination of a global parameter, the hydration radius (rH) and estimating the bicelle shape. We use zwitterionic (DMPC/DHPC) and negatively charged (DMPC/DHPC/DMPG) bicelles and investigate the interaction with model transmembrane and surface active peptides (KALP23 and melittin). 1H NMR measurements based mostly on the translational diffusion coefficient D determination are used to characterize cmc values of DHPC micelles under the investigated conditions, to describe DHPC distribution with exact determination of the q (long chain/short chain) lipid ratio, to estimate aggregation numbers and effective rH values. The scattering curve is used to fit a lenticular core-shell model enabling us to describe the bicelle shape in terms of ellipsoidal axis length parameters. For all studied systems formation of oblate ellipsoids is found. Even though the rG/rH ratio would be an elegant way to characterize shape variations, we show that changes occurring upon peptide-bicelle interaction in the "effective" size and in the measure on the anisometry - morphology - of the objects can be described by using rH and the simplistic ellipsoidal core-shell model. While the influence of the transmembrane KALP peptide is significant, effects upon addition of surface active melittin peptide seem negligible. This synergy of techniques under controlled conditions can provide information about bicellar shape modulation occurring during peptide-bicelle interactions.
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Affiliation(s)
- E F Dudás
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - A Wacha
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bóta
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary.
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10
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Bibow S. Opportunities and Challenges of Backbone, Sidechain, and RDC Experiments to Study Membrane Protein Dynamics in a Detergent-Free Lipid Environment Using Solution State NMR. Front Mol Biosci 2019; 6:103. [PMID: 31709261 PMCID: PMC6823230 DOI: 10.3389/fmolb.2019.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022] Open
Abstract
Whereas solution state NMR provided a wealth of information on the dynamics landscape of soluble proteins, only few studies have investigated membrane protein dynamics in a detergent-free lipid environment. Recent developments of smaller nanodiscs and other lipid-scaffolding polymers, such as styrene maleic acid (SMA), however, open new and promising avenues to explore the function-dynamics relationship of membrane proteins as well as between membrane proteins and their surrounding lipid environment. Favorably sized lipid-bilayer nanodiscs, established membrane protein reconstitution protocols and sophisticated solution NMR relaxation methods probing dynamics over a wide range of timescales will eventually reveal unprecedented lipid-membrane protein interdependencies that allow us to explain things we have not been able to explain so far. In particular, methyl group dynamics resulting from CEST, CPMG, ZZ exchange, and RDC experiments are expected to provide new and surprising insights due to their proximity to lipids, their applicability in large 100+ kDa assemblies and their simple labeling due to the availability of commercial precursors. This review summarizes the recent developments of membrane protein dynamics with a special focus on membrane protein dynamics in lipid-bilayer nanodiscs. Opportunities and challenges of backbone, side chain and RDC dynamics applied to membrane proteins are discussed. Solution-state NMR and lipid nanodiscs bear great potential to change our molecular understanding of lipid-membrane protein interactions.
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Affiliation(s)
- Stefan Bibow
- Biozentrum, University of Basel, Basel, Switzerland
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11
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Ni Y, Zhang H, Chai C, Peng B, Zhao A, Zhang J, Li L, Zhang C, Ma B, Bai H, Lim K, Huang W. Mitochondria-Targeted Two-Photon Fluorescent Photosensitizers for Cancer Cell Apoptosis via Spatial Selectability. Adv Healthc Mater 2019; 8:e1900212. [PMID: 31081268 DOI: 10.1002/adhm.201900212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/18/2019] [Indexed: 12/14/2022]
Abstract
Organelle-targeted photosensitizers have been reported to be effective cell apoptosis agents. Mitochondria is recognized as an ideal target for cancer treatment due to its central role in oxidative metabolism and apoptosis. Meanwhile, two-photon (TP) fluorescence microscopy has become a powerful tool for fluorescence imaging in biological events based on its minimizing photodamage/photobleaching and intrinsic 3D resolution in deep tissues and in vivo. In this study, a series of novel mitochondrial-targeted TP fluorescent photosensitizers (TP-tracers) are designed, synthesized, and systematically investigated. These TP-tracers exhibit extraordinary anti-interference capability among different cations, anions, and amino acids as well as the insensitivity to the changes of pH and complex biological environments. TP-tracers are further used in fluorescence living cells, Drosophila brains, and zebrafish imaging with low cytotoxicity, excellent mitochondria-targeting, and TP properties. The results demonstrate efficient mitochondria-targeting cell selective apoptosis based on TP-activated cancer cells with highly single cell selectivity, and the pharmacokinetic study reveals that MitoY2 does not have accumulation in rats. It is believed that these molecules hold great potential in TP-related smart phototherapy.
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Affiliation(s)
- Yun Ni
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) Nanjing 210009 P. R. China
| | - Hang Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) Nanjing 210009 P. R. China
| | - Chou Chai
- National Neuroscience Institute Singapore 308433 Singapore
| | - Bo Peng
- Shaanxi Institute of Flexible Electronics (SIFE)Northwestern Polytechnical University (NPU) Xi'an 710072 P. R. China
| | - Ang Zhao
- School of Pharmaceutical SciencesNanjing Tech University Nanjing 210023 P. R. China
| | - Jie Zhang
- School of Pharmaceutical SciencesNanjing Tech University Nanjing 210023 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) Nanjing 210009 P. R. China
| | - Chengwu Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) Nanjing 210009 P. R. China
| | - Bo Ma
- School of Pharmaceutical SciencesNanjing Tech University Nanjing 210023 P. R. China
| | - Hua Bai
- Shaanxi Institute of Flexible Electronics (SIFE)Northwestern Polytechnical University (NPU) Xi'an 710072 P. R. China
| | - Kah‐Leong Lim
- National Neuroscience Institute Singapore 308433 Singapore
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) Nanjing 210009 P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE)Northwestern Polytechnical University (NPU) Xi'an 710072 P. R. China
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12
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Huang H, Ge B, Zhang S, Li J, Sun C, Yue T, Huang F. Using Fluorescence Quenching Titration to Determine the Orientation of a Model Transmembrane Protein in Mimic Membranes. MATERIALS 2019; 12:ma12030349. [PMID: 30678051 PMCID: PMC6384929 DOI: 10.3390/ma12030349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 11/21/2022]
Abstract
After synthesis of transmembrane proteins (TMPs), they are transferred and inserted into plasma membranes to play biological functions. Crucially, orientation of TMPs in membranes determines whether they have biological activities. In cellular environments, a number of cofactors, such as translocon, can assist TMPs to be inserted into membranes in defined orientations. During in vitro reconstitution of TMPs with mimic membranes, both insertion and orientation of TMPs are primarily determined by interactions with the membrane. Yet the knowledge is limited, hindering the in vitro applications of TMPs. Here, we take Bacteriorhodopsin (bR) as a model TMP, using fluorescence quenching titration experiment to identify orientation of bR in mimic membranes, examining effects of a number of factors, including lipid composition, pH value, ionic strength and membrane curvature. The most effective determinant is the lipid type, which modulates insertion and orientation of bR in membranes by changing the membrane surface charge and the membrane fluidity. Both the pH value and the ionic strength play secondary roles by tuning the nature of the electrostatic interaction. The membrane curvature was found to have a minor effect on orientation of bR in membranes. By comparing orientations of bR in folded and unfolded states, no obvious change was observed, informing that nascent proteins could be inserted into membranes in defined orientations before folding into the native state inside the membrane.
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Affiliation(s)
- Haihong Huang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Baosheng Ge
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Shuai Zhang
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Jiqiang Li
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Chenghao Sun
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
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13
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Harding BD, Dixit G, Burridge KM, Sahu ID, Dabney-Smith C, Edelmann RE, Konkolewicz D, Lorigan GA. Characterizing the structure of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using RAFT polymerization for membrane protein spectroscopic studies. Chem Phys Lipids 2018; 218:65-72. [PMID: 30528635 DOI: 10.1016/j.chemphyslip.2018.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/25/2022]
Abstract
Membrane proteins play an important role in maintaining the structure and physiology of an organism. Despite their significance, spectroscopic studies involving membrane proteins remain challenging due to the difficulties in mimicking their native lipid bilayer environment. Membrane mimetic systems such as detergent micelles, liposomes, bicelles, nanodiscs, lipodisqs have improved the solubility and folding properties of the membrane proteins for structural studies, however, each mimetic system suffers from its own limitations. In this study, using three different lipid environments, vesicles were titrated with styrene-maleic acid (StMA) copolymer leading to a homogeneous SMALP system (∼10 nm) at a weight ratio of 1:1.5 (vesicle: StMA solution). A combination of Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM) was used to characterize these SMALPs. We used a controlled synthesis mechanism to synthesize StMA based block copolymers called reversible addition-fragmentation chain transfer polymerization (RAFT) SMALPs. Incorporation of the Voltage Sensor Domain of KCNQ1 (Q1-VSD) into RAFT SMALPs indicates that this is a promising application of this system to study membrane proteins using different biophysical techniques. V165C in Q1-VSD corresponding to the hydrophobic region was incorporated into the SMALP system. Continuous Wave-Electron Paramagnetic Resonance (CW-EPR) line shape analysis showed line shape broadening, exposing a lower rigid component and a faster component of the spin label.
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Affiliation(s)
- Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Gunjan Dixit
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Kevin M Burridge
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Richard E Edelmann
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States.
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States.
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14
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Bragin PE, Kuznetsov AS, Bocharova OV, Volynsky PE, Arseniev AS, Efremov RG, Mineev KS. Probing the effect of membrane contents on transmembrane protein-protein interaction using solution NMR and computer simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2486-2498. [PMID: 30279150 DOI: 10.1016/j.bbamem.2018.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/03/2018] [Accepted: 09/17/2018] [Indexed: 12/18/2022]
Abstract
The interaction between the secondary structure elements is the key process, determining the spatial structure and activity of a membrane protein. Transmembrane (TM) helix-helix interaction is known to be especially important for the function of so-called type I or bitopic membrane proteins. In the present work, we present the approach to study the helix-helix interaction in the TM domains of membrane proteins in various lipid environment using solution NMR spectroscopy and phospholipid bicelles. The technique is based on the ability of bicelles to form particles with the size, depending on the lipid/detergent ratio. To implement the approach, we report the experimental parameters of "ideal bicelle" models for four kinds of zwitterionic phospholipids, which can be also used in other structural studies. We show that size of bicelles and type of the rim-forming detergent do not affect substantially the spatial structure and stability of the model TM dimer. On the other hand, the effect of bilayer thickness on the free energy of the dimer is dramatic, while the structure of the protein is unchanged in various lipids with fatty chains having a length from 12 to 18 carbon atoms. The obtained data is analyzed using the computer simulations to find the physical origin of the observed effects.
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Affiliation(s)
- P E Bragin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow 119991, Russian Federation
| | - A S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation; National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| | - O V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation
| | - P E Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation
| | - R G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation; National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudnyi, Russian Federation.
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15
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Bibow S, Hiller S. A guide to quantifying membrane protein dynamics in lipids and other native-like environments by solution-state NMR spectroscopy. FEBS J 2018; 286:1610-1623. [PMID: 30133960 DOI: 10.1111/febs.14639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/04/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023]
Abstract
Recent biochemical and technical developments permit residue-specific solution NMR measurements of membrane protein (MP) dynamics in lipidic and chaperone-bound environments. This is possible by combinations of improved sample preparations with suitable NMR relaxation experiments to correlate protein function to backbone dynamics on timescales from picoseconds to seconds, even for large MP-lipid assemblies above 100 kDa in molecular mass. Here, we introduce the basic concepts of different NMR relaxation experiments, individually sensitive to specific timescales. We discuss the general limitations of detergent environments and highlight the importance for native-like environments when studying MPs. We then review three practical studies of fast- and slow-timescale MP dynamics in lipid environments, as well as in a natively unfolded, chaperone-bound state. These examples illustrate the new avenues solution NMR spectroscopy is taking to investigate MP dynamics in native-like environments with atomic resolution.
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16
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Sarker M, Speckert M, Rainey JK. Bicelle composition-dependent modulation of phospholipid dynamics by apelin peptides 1. Biochem Cell Biol 2018; 97:325-332. [PMID: 30092142 DOI: 10.1139/bcb-2018-0172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Apelin peptides are cognate ligands for the apelin receptor, a G-protein-coupled receptor (GPCR). The apelinergic system plays critical roles in wide-ranging physiological activities including function and development of the central nervous and cardiovascular systems. Apelin is found in 13-55 residue isoforms in vivo, all of which share the C-terminal portion of the preproapelin precursor. Characterization of high-resolution structures and detergent micelle interactions of apelin-17 led to a two-step membrane-catalyzed binding and GPCR activation mechanism hypothesis recapitulated in longer isoforms. Here, we examine interactions of the apelin-13 and -17 isoforms with isotropic zwitterionic and mixed zwitterionic-anionic lipid bicelles to test for hallmarks of membrane catalysis in a more physiological membrane-mimetic environment than a micelle. Specifically, 1H and 31P relaxation and diffusion solution-state NMR techniques demonstrate that both apelin isoforms interact with both types of isotropic bicelles. Bicelle hydrodynamics were observed to be differentially modulated by apelin peptides, although these effects were minimal. Phospholipid headgroup 31P spin relaxation behaviour was, conversely, clearly perturbed. Perturbation of this nature was also observed in magnetically aligned bicelles by 31P solid-state NMR spectroscopy and spin relaxation experiments. This behaviour is consistent with an apelin-bicelle binding process allowing significant peptide mobility, facilitating membrane-catalyzed GPCR encounter.
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Affiliation(s)
- Muzaddid Sarker
- a Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Matt Speckert
- a Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jan K Rainey
- a Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.,b Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
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17
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Hameed S, Bhattarai P, Dai Z. Cerasomes and Bicelles: Hybrid Bilayered Nanostructures With Silica-Like Surface in Cancer Theranostics. Front Chem 2018; 6:127. [PMID: 29721494 PMCID: PMC5915561 DOI: 10.3389/fchem.2018.00127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/03/2018] [Indexed: 01/10/2023] Open
Abstract
Over years, theranostic nanoplatforms have provided a new avenue for the diagnosis and treatment of various cancer types. To this end, a myriad of nanocarriers such as polymeric micelles, liposomes, and inorganic nanoparticles (NPs) with distinct physiochemical and biological properties are routinely investigated for preclinical and clinical studies. So far, liposomes have received great attention for various biomedical applications, however, it still suffers from insufficient morphological stability. On the other hand, inorganic NPs depicting excellent therapeutic ability have failed to address biocompatibility issues. This has raised a serious concern about the clinical approval of multifunctional organic or inorganic-based theranostic agents. Recently, partially silica coated nanohybrids such as cerasomes and bicelles demonstrating both diagnostic and therapeutic ability in a single system, have drawn profound attention as a fascinating novel drug delivery system. Compared with traditional liposomal or inorganic-based nanoformulations, this new and highly stable nanocarriers integrates the functional attributes of biomimetic liposomes and silica NPs, therefore, synergize strengths and functions, or even surpass weaknesses of individual components. This review at its best enlightens the emerging concept of such partially silica coated nanohybrids, fabrication strategies, and theranostic opportunities to combat cancer and related diseases.
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Affiliation(s)
- Sadaf Hameed
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Pravin Bhattarai
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Zhifei Dai
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
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18
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Kot EF, Goncharuk SA, Arseniev AS, Mineev KS. Phase Transitions in Small Isotropic Bicelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:3426-3437. [PMID: 29486112 DOI: 10.1021/acs.langmuir.7b03610] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Isotropic phospholipid bicelles are one of the most prospective membrane mimetics for the structural studies of membrane proteins in solution. Recent works provided an almost full set of data regarding the properties of isotropic bicelles; however, one major aspect of their behavior is still under consideration: the possible mixing between the lipid and detergent in the bilayer area. This problem may be resolved by studying the lipid phase transitions in bicelle particles. In the present work, we investigate two effects: phase transitions of bilayer lipids and temperature-induced growth of isotropic bicelles using the NMR spectroscopy. We propose an approach to study the phase transitions in isotropic bicelles based on the properties of 31P NMR spectra of bilayer-forming lipids. We show that phase transitions in small bicelles are "fractional", particles with the liquid-crystalline and gel bilayers coexist in solution at certain temperatures. We study the effects of lipid fatty chain type and demonstrate that the behavior of various lipids in bilayers is reproduced in the isotropic bicelles. We show that the temperature-induced growth of isotropic bicelles is not related directly to the phase transition but is the result of the reversible fusion of bicelle particles. In accordance with our data, rim detergents also have an impact on phase transitions: detergents that resist the temperature-induced growth provide the narrowest and most expressed transitions at higher temperatures. We demonstrate clearly that phase transitions take place even in the smallest bicelles that are applicable for structural studies of membrane proteins by solution NMR spectroscopy. This last finding, together with other data draws a thick line under the long-lasting argument about the relevance of small isotropic bicelles. We show with certainty that the small bicelles can reproduce the most fundamental property of lipid membranes: the ability to undergo phase transition.
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Affiliation(s)
- Erik F Kot
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10 , Moscow 117997 , Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9 , 141700 Dolgoprudnyi , Russian Federation
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10 , Moscow 117997 , Russian Federation
- Lomonosov Moscow State University , Leninskiye Gory, 1 , Moscow 119991 , Russian Federation
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10 , Moscow 117997 , Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9 , 141700 Dolgoprudnyi , Russian Federation
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10 , Moscow 117997 , Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9 , 141700 Dolgoprudnyi , Russian Federation
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19
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Sahu ID, Zhang R, Dunagan MM, Craig AF, Lorigan GA. Characterization of KCNE1 inside Lipodisq Nanoparticles for EPR Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2017; 121:5312-5321. [DOI: 10.1021/acs.jpcb.7b01705] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Megan M. Dunagan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Andrew F. Craig
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A. Lorigan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
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20
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Liebau J, Ye W, Mäler L. Characterization of fast-tumbling isotropic bicelles by PFG diffusion NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:395-404. [PMID: 26662467 DOI: 10.1002/mrc.4399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
Small isotropic bicelles are versatile membrane mimetics, which, in contrast to micelles, provide a lipid bilayer and are at the same time suitable for solution-state NMR studies. The lipid composition of the bilayer is flexible allowing for incorporation of various head groups and acyl chain types. In bicelles, lipids are solubilized by detergents, which are localized in the rim of the disk-shaped lipid bilayer. Bicelles have been characterized by a broad array of biophysical methods, pulsed-field gradient NMR (PFG NMR) being one of them. PFG NMR can readily be used to measure diffusion coefficients of macromolecules. It is thus employed to characterize bicelle size and morphology. Even more importantly, PFG NMR can be used to study the degree of protein association to membranes. Here, we present the advances that have been made in producing small, fast-tumbling isotropic bicelles from a variety of lipids and detergents, together with insights on the morphology of such mixtures gained from PFG NMR. Furthermore, we review approaches to study protein-membrane interaction by PFG NMR. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Weihua Ye
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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21
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Frey L, Lakomek NA, Riek R, Bibow S. Micelles, Bicelles, and Nanodiscs: Comparing the Impact of Membrane Mimetics on Membrane Protein Backbone Dynamics. Angew Chem Int Ed Engl 2016; 56:380-383. [PMID: 27882643 PMCID: PMC6680326 DOI: 10.1002/anie.201608246] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/29/2016] [Indexed: 11/10/2022]
Abstract
Detergents are often used to investigate the structure and dynamics of membrane proteins. Whereas the structural integrity seems to be preserved in detergents for many membrane proteins, their functional activity is frequently compromised, but can be restored in a lipid environment. Herein we show with per‐residue resolution that while OmpX forms a stable β‐barrel in DPC detergent micelles, DHPC/DMPC bicelles, and DMPC nanodiscs, the pico‐ to nanosecond and micro‐ to millisecond motions differ substantially between the detergent and lipid environment. In particular for the β‐strands, there is pronounced dynamic variability in the lipid environment, which appears to be suppressed in micelles. This unexpected complex and membrane‐mimetic‐dependent dynamic behavior indicates that the frequent loss of membrane protein activity in detergents might be related to reduced internal dynamics and that membrane protein activity correlates with lipid flexibility.
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Affiliation(s)
- Lukas Frey
- Laboratory for Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Roland Riek
- Laboratory for Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Stefan Bibow
- Laboratory for Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
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22
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Frey L, Lakomek N, Riek R, Bibow S. Mizellen, Bizellen und Nanoscheiben: Einfluss von membranimitierenden Umgebungen auf die Membranproteindynamik. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lukas Frey
- Laboratorium für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | | | - Roland Riek
- Laboratorium für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Stefan Bibow
- Laboratorium für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
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23
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Schmidt T, Situ AJ, Ulmer TS. Direct Evaluation of Protein-Lipid Contacts Reveals Protein Membrane Immersion and Isotropic Bicelle Structure. J Phys Chem Lett 2016; 7:4420-4426. [PMID: 27776216 PMCID: PMC11027914 DOI: 10.1021/acs.jpclett.6b02159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The solvation of membrane proteins by both lipids and water makes their membrane immersion difficult to predict and the choice of a membrane mimic challenging. To characterize protein-lipid contacts and bicelle membrane mimics, we examined protein-lipid cross-relaxation of integrin αIIb and β3(A711P) transmembrane helices in isotropic phospholipid bicelles (q = 0.5 and 0.7). Long-chain bicelle lipids dominated contacts with central helix segments, whereas both short- and long-chain lipids contacted the terminal turns of each helix in corroboration of the mixed bicelle model. The saturation transfer profiles from long-chain lipids directly established helix midpoints in the lipid bilayer. Lipid headgroups and water molecules engaged the side chains of buried serine and threonine in competition with intrahelical hydrogen bonding, illustrating that polar side chains seek the most favorable electrostatic contacts.
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Affiliation(s)
- Thomas Schmidt
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
- Present address: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan J. Situ
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Tobias S. Ulmer
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
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24
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Aβ42 assembles into specific β-barrel pore-forming oligomers in membrane-mimicking environments. Proc Natl Acad Sci U S A 2016; 113:10866-71. [PMID: 27621459 DOI: 10.1073/pnas.1605104113] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The formation of amyloid-β peptide (Aβ) oligomers at the cellular membrane is considered to be a crucial process underlying neurotoxicity in Alzheimer's disease (AD). Therefore, it is critical to characterize the oligomers that form within a membrane environment. To contribute to this characterization, we have applied strategies widely used to examine the structure of membrane proteins to study the two major Aβ variants, Aβ40 and Aβ42. Accordingly, various types of detergent micelles were extensively screened to identify one that preserved the properties of Aβ in lipid environments-namely the formation of oligomers that function as pores. Remarkably, under the optimized detergent micelle conditions, Aβ40 and Aβ42 showed different behavior. Aβ40 aggregated into amyloid fibrils, whereas Aβ42 assembled into oligomers that inserted into lipid bilayers as well-defined pores and adopted a specific structure with characteristics of a β-barrel arrangement that we named β-barrel pore-forming Aβ42 oligomers (βPFOsAβ42). Because Aβ42, relative to Aβ40, has a more prominent role in AD, the higher propensity of Aβ42 to form βPFOs constitutes an indication of their relevance in AD. Moreover, because βPFOsAβ42 adopt a specific structure, this property offers an unprecedented opportunity for testing a hypothesis regarding the involvement of βPFOs and, more generally, membrane-associated Aβ oligomers in AD.
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25
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Craig AF, Clark EE, Sahu ID, Zhang R, Frantz ND, Al-Abdul-Wahid MS, Dabney-Smith C, Konkolewicz D, Lorigan GA. Tuning the size of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using RAFT polymerization for biophysical studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2931-2939. [PMID: 27539205 DOI: 10.1016/j.bbamem.2016.08.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/15/2016] [Accepted: 08/07/2016] [Indexed: 11/29/2022]
Abstract
Characterization of membrane proteins is challenging due to the difficulty in mimicking the native lipid bilayer with properly folded and functional membrane proteins. Recently, styrene-maleic acid (StMA) copolymers have been shown to facilitate the formation of disc-like lipid bilayer mimetics that maintain the structural and dynamic integrity of membrane proteins. Here we report the controlled synthesis and characterization of StMA containing block copolymers. StMA polymers with different compositions and molecular weights were synthesized and characterized by size exclusion chromatography (SEC). These polymers act as macromolecular surfactants for 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol (POPG) lipids, forming disc like structures of the lipids with the polymer wrapping around the hydrophobic lipid edge. A combination of dynamic light scattering (DLS), solid-state nuclear magnetic resonance (SSNMR) spectroscopy, and transmission electron microscopy (TEM) was used to characterize the size of the nanoparticles created using these StMA polymers. At a weight ratio of 1.25:1 StMA to lipid, the nanoparticle size created is 28+1nm for a 2:1 ratio, 10+1nm for a 3:1 StMA ratio and 32+1nm for a 4:1 StMA ratio independent of the molecular weight of the polymer. Due to the polymer acting as a surfactant that forms disc like nanoparticles, we term these StMA based block copolymers "RAFT SMALPs". RAFT SMALPs show promise as a new membrane mimetic with different nanoscale sizes, which can be used for a wide variety of biophysical studies of membrane proteins.
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Affiliation(s)
- Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Emily E Clark
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Nick D Frantz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - M Sameer Al-Abdul-Wahid
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States.
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Mineev KS, Nadezhdin KD, Goncharuk SA, Arseniev AS. Characterization of Small Isotropic Bicelles with Various Compositions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6624-6637. [PMID: 27285636 DOI: 10.1021/acs.langmuir.6b00867] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structural studies of membrane proteins are of great importance and interest, with solution and solid state NMR spectroscopy being very promising tools for that task. However, such investigations are hindered by a number of obstacles, and in the first place by the fact that membrane proteins need an adequate environment that models the cell membrane. One of the most widely used and prospective membrane mimetics is isotropic bicelles. While large anisotropic bicelles are well-studied, the field of small bicelles contains a lot of "white spots". The present work reports the radii of particles and concentration of the detergents in the monomeric state in solutions of isotropic bicelles, formed by 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO), and sodium cholate, as a function of lipid/detergent ratio and temperature. These parameters were measured using (1)H NMR diffusion spectroscopy for the bicelles composed of lipids with saturated fatty chains of different length and lipids, containing unsaturated fatty acid residue. The influence of a model transmembrane protein (membrane domain of rat TrkA) on the properties of bicelles and the effect of the bicelle size and composition on the properties of the transmembrane protein were investigated with heteronuclear NMR and nuclear Overhauser effect spectroscopy. We show that isotropic bicelles that are applicable for solution NMR spectroscopy behave as predicted by the theoretical models and are likely to be bicelles rather than mixed micelles. Using the obtained data, we propose a simple approach to control the size of bicelles at low concentrations. On the basis of our results, we compared different rim-forming agents and selected CHAPS as a detergent of choice for structural studies in bicelles, if the deuteration of the detergent is not required.
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Affiliation(s)
- K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - K D Nadezhdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141700, Dolgoprudnyi, Russian Federation
| | - S A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Lomonosov Moscow State University , Leninskiye Gory, 1, Moscow, 119991, Russian Federation
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141700, Dolgoprudnyi, Russian Federation
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27
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Bocharov EV, Lesovoy DM, Pavlov KV, Pustovalova YE, Bocharova OV, Arseniev AS. Alternative packing of EGFR transmembrane domain suggests that protein-lipid interactions underlie signal conduction across membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1254-61. [PMID: 26903218 DOI: 10.1016/j.bbamem.2016.02.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 10/22/2022]
Abstract
The human epidermal growth factor receptor (EGFR) of HER/ErbB receptor tyrosine kinase family mediates a broad spectrum of cellular responses transducing biochemical signals via lateral dimerization in plasma membrane, while inactive receptors can exist in both monomeric and dimeric forms. Recently, the dimeric conformation of the helical single-span transmembrane domains of HER/ErbB employing the relatively polar N-terminal motifs in a fashion permitting proper kinase activation was experimentally determined. Here we describe the EGFR transmembrane domain dimerization via an alternative weakly polar C-terminal motif A(661)xxxG(665) presumably corresponding to the inactive receptor state. During association, the EGFR transmembrane helices undergo a structural adjustment with adaptation of inter-molecular polar and hydrophobic interactions depending upon the surrounding membrane properties that directly affect the transmembrane helix packing. This might imply that signal transduction through membrane and allosteric regulation are inclusively mediated by coupled protein-protein and protein-lipid interactions, elucidating paradoxically loose linkage between ligand binding and kinase activation.
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Affiliation(s)
- Eduard V Bocharov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation.
| | - Dmitry M Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Yulia E Pustovalova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Olga V Bocharova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Alexander S Arseniev
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
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28
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Mineev KS, Panova SV, Bocharova OV, Bocharov EV, Arseniev AS. The Membrane Mimetic Affects the Spatial Structure and Mobility of EGFR Transmembrane and Juxtamembrane Domains. Biochemistry 2015; 54:6295-8. [DOI: 10.1021/acs.biochem.5b00851] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Stanislava V. Panova
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Olga V. Bocharova
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences RAS, str.
Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
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29
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Zhang M, Huang R, Im SC, Waskell L, Ramamoorthy A. Effects of membrane mimetics on cytochrome P450-cytochrome b5 interactions characterized by NMR spectroscopy. J Biol Chem 2015; 290:12705-18. [PMID: 25795780 DOI: 10.1074/jbc.m114.597096] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Indexed: 01/08/2023] Open
Abstract
Mammalian cytochrome P450 (P450) is a membrane-bound monooxygenase whose catalytic activities require two electrons to be sequentially delivered from its redox partners: cytochrome b5 (cytb5) and cytochrome P450 reductase, both of which are membrane proteins. Although P450 functional activities are known to be affected by lipids, experimental evidence to reveal the effect of membrane on P450-cytb5 interactions is still lacking. Here, we present evidence for the influence of phospholipid bilayers on complex formation between rabbit P450 2B4 (CYP2B4) and rabbit cytb5 at the atomic level, utilizing NMR techniques. General line broadening and modest chemical shift perturbations of cytb5 resonances characterize CYP2B4-cytb5 interactions on the intermediate time scale. More significant intensity attenuation and a more specific protein-protein binding interface are observed in bicelles as compared with lipid-free solution, highlighting the importance of the lipid bilayer in stabilizing stronger and more specific interactions between CYP2B4 and cytb5, which may lead to a more efficient electron transfer. Similar results observed for the interactions between CYP2B4 lacking the transmembrane domain (tr-CYP2B4) and cytb5 imply interactions between tr-CYP2B4 and the membrane surface, which might assist in CYP2B4-cytb5 complex formation by orienting tr-CYP2B4 for efficient contact with cytb5. Furthermore, the observation of weak and nonspecific interactions between CYP2B4 and cytb5 in micelles suggests that lipid bilayer structures and low curvature membrane surface are preferable for CYP2B4-cytb5 complex formation. Results presented in this study provide structural insights into the mechanism behind the important role that the lipid bilayer plays in the interactions between P450s and their redox partners.
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Affiliation(s)
- Meng Zhang
- From the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
| | - Rui Huang
- From the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
| | - Sang-Choul Im
- the Department of Anesthesiology, University of Michigan and Veterans Affairs Medical Center, Ann Arbor, Michigan 48105
| | - Lucy Waskell
- the Department of Anesthesiology, University of Michigan and Veterans Affairs Medical Center, Ann Arbor, Michigan 48105
| | - Ayyalusamy Ramamoorthy
- From the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055 and
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30
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Eichmann C, Orts J, Tzitzilonis C, Vögeli B, Smrt S, Lorieau J, Riek R. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes. J Phys Chem B 2014; 118:14288-301. [PMID: 25419869 DOI: 10.1021/jp509137q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.
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Affiliation(s)
- Cédric Eichmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , CH-8093 Zürich, Switzerland
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31
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Eichmann C, Tzitzilonis C, Bordignon E, Maslennikov I, Choe S, Riek R. Solution NMR structure and functional analysis of the integral membrane protein YgaP from Escherichia coli. J Biol Chem 2014; 289:23482-503. [PMID: 24958726 DOI: 10.1074/jbc.m114.571935] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The solution NMR structure of the α-helical integral membrane protein YgaP from Escherichia coli in mixed 1,2-diheptanoyl-sn-glycerol-3-phosphocholine/1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) micelles is presented. In these micelles, YgaP forms a homodimer with the two transmembrane helices being the dimer interface, whereas the N-terminal cytoplasmic domain includes a rhodanese-fold in accordance to its sequence homology to the rhodanese family of sulfurtransferases. The enzymatic sulfur transfer activity of full-length YgaP as well as of the N-terminal rhodanese domain only was investigated performing a series of titrations with sodium thiosulfate and potassium cyanide monitored by NMR and EPR. The data indicate the thiosulfate concentration-dependent addition of several sulfur atoms to the catalytic Cys-63, which process can be reversed by the addition of potassium cyanide. The catalytic reaction induces thereby conformational changes within the rhodanese domain, as well as on the transmembrane α-helices of YgaP. These results provide insights into a potential mechanism of YgaP during the catalytic thiosulfate activity in vivo.
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Affiliation(s)
- Cédric Eichmann
- From the Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland and
| | - Christos Tzitzilonis
- From the Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland and the Structural Biology Laboratory, The Salk Institute, La Jolla, California 92037
| | - Enrica Bordignon
- From the Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland and
| | | | - Senyon Choe
- the Structural Biology Laboratory, The Salk Institute, La Jolla, California 92037
| | - Roland Riek
- From the Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland and the Structural Biology Laboratory, The Salk Institute, La Jolla, California 92037
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32
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Characterizing the structure of lipodisq nanoparticles for membrane protein spectroscopic studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:329-33. [PMID: 24853657 DOI: 10.1016/j.bbamem.2014.05.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/28/2014] [Accepted: 05/04/2014] [Indexed: 11/21/2022]
Abstract
Membrane protein spectroscopic studies are challenging due to the difficulty introduced in preparing homogenous and functional hydrophobic proteins incorporated into a lipid bilayer system. Traditional membrane mimics such as micelles or liposomes have proved to be powerful in solubilizing membrane proteins for biophysical studies, however, several drawbacks have limited their applications. Recently, a nanosized complex termed lipodisq nanoparticles was utilized as an alternative membrane mimic to overcome these caveats by providing a homogeneous lipid bilayer environment. Despite all the benefits that lipodisq nanoparticles could provide to enhance the biophysical studies of membrane proteins, structural characterization in different lipid compositions that closely mimic the native membrane environment is still lacking. In this study, the formation of lipodisq nanoparticles using different weight ratios of POPC/POPG lipids to SMA polymers was characterized via solid-state nuclear magnetic resonance (SSNMR) spectroscopy and dynamic light scattering (DLS). A critical weight ratio of (1/1.25) for the complete solubilization of POPC/POPG vesicles has been observed and POPC/POPG vesicles turned clear instantaneously upon the addition of the SMA polymer. The size of lipodisq nanoparticles formed from POPC/POPG lipids at this weight ratio of (1/1.25) was found to be about 30 nm in radius. We also showed that upon the complete solubilization of POPC/POPG vesicles by SMA polymers, the average size of the lipodisq nanoparticles is weight ratio dependent, when more SMA polymers were introduced, smaller lipodisq nanoparticles were obtained. The results of this study will be helpful for a variety of biophysical experiments when specific size of lipid disc is required. Further, this study will provide a proper path for researchers working on membrane proteins to obtain pertinent structure and dynamic information in a physiologically relevant membrane mimetic environment.
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33
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Bibow S, Carneiro MG, Sabo TM, Schwiegk C, Becker S, Riek R, Lee D. Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings. Protein Sci 2014; 23:851-6. [PMID: 24752984 DOI: 10.1002/pro.2482] [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] [Received: 04/08/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 11/11/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes. To understand membrane protein functionality, accurate structural information is required. Usually, structure determination and dynamics of membrane proteins are studied in micelles using either solution state NMR or X-ray crystallography. Even though invaluable information has been obtained by this approach, micelles are known to be far from ideal mimics of biological membranes often causing the loss or decrease of membrane protein activity. Recently, nanodiscs, which are composed of a lipid bilayer surrounded by apolipoproteins, have been introduced as a more physiological alternative than micelles for NMR investigations on membrane proteins. Here, we show that membrane protein bond orientations in nanodiscs can be obtained by measuring residual dipolar couplings (RDCs) with the outer membrane protein OmpX embedded in nanodiscs using Pf1 phage as an alignment medium. The presented collection of membrane protein RDCs in nanodiscs represents an important step toward more comprehensive structural and dynamical NMR-based investigations of membrane proteins in a natural bilayer environment.
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Affiliation(s)
- Stefan Bibow
- Laboratory for Physical Chemistry, ETH Zürich, CH-8093, Zürich, Switzerland
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34
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Vácha R, Frenkel D. Stability of bicelles: a simulation study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4229-4235. [PMID: 24670113 DOI: 10.1021/la4048159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Aqueous mixtures of long-tailed lipids (e.g., dimyristoylphosphatidylcholine - DMPC) and detergents can sometimes form membrane disks called bicelles. Bicelles have found applications as an embedding medium for membrane proteins in the context of NMR studies and protein crystallization. However, the parameters that determine the thermodynamic stability of bicelles are not well understood. Here we report a coarse-grained simulation study of the relationship between lipid-aggregate morphology and the composition and temperature of the surfactant mixture. In agreement with experiments, we find that bicellar mixtures are destabilized at higher temperatures and detergents are present at membrane edges as well as in flat membranes with a strong preference for the edges. In addition, our results suggest that the free-energy difference between bicelles and the perforated lamellar phase is typically very small for molecules without intrinsic curvature and charge. Cone shaped surfactant molecules tend to favor the formation of bicelles; however, none of the systems that we have studied provide unambiguous evidence for the existence of thermodynamically stable bicelles in mixtures of uncharged lipids with long and short tails. We speculate that small changes in the properties of the system (charge, dopants) may make bicelles thermodynamically stable.
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Affiliation(s)
- Robert Vácha
- National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University , Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
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35
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Planchard N, Point É, Dahmane T, Giusti F, Renault M, Le Bon C, Durand G, Milon A, Guittet É, Zoonens M, Popot JL, Catoire LJ. The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media. J Membr Biol 2014; 247:827-42. [PMID: 24676477 DOI: 10.1007/s00232-014-9654-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/07/2014] [Indexed: 01/24/2023]
Abstract
Solution-state nuclear magnetic resonance studies of membrane proteins are facilitated by the increased stability that trapping with amphipols confers to most of them as compared to detergent solutions. They have yielded information on the state of folding of the proteins, their areas of contact with the polymer, their dynamics, water accessibility, and the structure of protein-bound ligands. They benefit from the diversification of amphipol chemical structures and the availability of deuterated amphipols. The advantages and constraints of working with amphipols are discussed and compared to those associated with other non-conventional environments, such as bicelles and nanodiscs.
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Affiliation(s)
- Noelya Planchard
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique (FRC 550), UMR 7099, CNRS, Université Paris 7, 13 rue Pierre et Marie Curie, 75005, Paris, France
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36
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Liang B, Dawidowski D, Ellena JF, Tamm LK, Cafiso DS. The SNARE motif of synaptobrevin exhibits an aqueous-interfacial partitioning that is modulated by membrane curvature. Biochemistry 2014; 53:1485-94. [PMID: 24552121 PMCID: PMC3985803 DOI: 10.1021/bi401638u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The structure and interfacial association of the full-length vesicle SNARE, synaptobrevin, were compared in four different lipid environments using nuclear magnetic resonance and electron paramagnetic resonance spectroscopy. In micelles, segments of the SNARE motif are helical and associated with the interface. However, the fraction of helix and interfacial association decreases as synaptobrevin is moved from micelle to bicelle to bilayer environments, indicating that the tendency toward interfacial association is sensitive to membrane curvature. In bilayers, the SNARE motif of synaptobrevin transiently associates with the lipid interface, and regions that are helical in micelles are in conformational and environmental exchange in bicelles and bilayers. This work demonstrates that the SNARE motif of synaptobrevin has a significant propensity to form a helix and exchange with the membrane interface prior to SNARE assembly. This transient interfacial association and its sensitivity to membrane curvature are likely to play a role in SNARE recognition events that regulate membrane fusion.
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Affiliation(s)
- Binyong Liang
- Biomolecular Magnetic Resonance Research Core, University of Virginia , P.O. Box 800741, Charlottesville, Virginia 22908, United States
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37
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Lu GJ, Opella SJ. Resonance assignments of a membrane protein in phospholipid bilayers by combining multiple strategies of oriented sample solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2014; 58:69-81. [PMID: 24356892 PMCID: PMC3928288 DOI: 10.1007/s10858-013-9806-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 12/12/2013] [Indexed: 06/01/2023]
Abstract
Oriented sample solid-state NMR spectroscopy can be used to determine the three-dimensional structures of membrane proteins in magnetically or mechanically aligned lipid bilayers. The bottleneck for applying this technique to larger and more challenging proteins is making resonance assignments, which is conventionally accomplished through the preparation of multiple selectively isotopically labeled samples and performing an analysis of residues in regular secondary structure based on Polarity Index Slant Angle (PISA) Wheels and Dipolar Waves. Here we report the complete resonance assignment of the full-length mercury transporter, MerF, an 81-residue protein, which is challenging because of overlapping PISA Wheel patterns from its two trans-membrane helices, by using a combination of solid-state NMR techniques that improve the spectral resolution and provide correlations between residues and resonances. These techniques include experiments that take advantage of the improved resolution of the MSHOT4-Pi4/Pi pulse sequence; the transfer of resonance assignments through frequency alignment of heteronuclear dipolar couplings, or through dipolar coupling correlated isotropic chemical shift analysis; (15)N/(15)N dilute spin exchange experiments; and the use of the proton-evolved local field experiment with isotropic shift analysis to assign the irregular terminal and loop regions of the protein, which is the major "blind spot" of the PISA Wheel/Dipolar Wave method.
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38
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Khatun UL, Mukhopadhyay C. Interaction of bee venom toxin melittin with ganglioside GM1 bicelle. Biophys Chem 2013; 180-181:66-75. [DOI: 10.1016/j.bpc.2013.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 12/11/2022]
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39
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Mineev KS, Lyukmanova EN, Krabben L, Serebryakova MV, Shulepko MA, Arseniev AS, Kordyukova LV, Veit M. Structural investigation of influenza virus hemagglutinin membrane-anchoring peptide. Protein Eng Des Sel 2013; 26:547-52. [PMID: 23873663 DOI: 10.1093/protein/gzt034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hemagglutinin (HA), the trimeric spike of influenza virus, catalyzes fusion of viral and cellular membranes. We have synthesized the anchoring peptide including the linker, transmembrane region and cytoplasmic tail (HA-TMR-CT) in a cell-free system. Furthermore, to mimic the palmitoylation of three conserved cysteines within the CT, we chemically alkylated HA-TMR-CT using hexadecyl-methanethiosulfonate. While the nuclear magnetic resonance spectroscopy showed pure and refolded peptides, the formation of multiple oligomers of higher order impeded further structural analysis. Circular dichroism spectroscopy of both alkylated and non-alkylated HA-TMR-CT revealed an α-helical secondary structure. No major impact of the fatty acids on the secondary structure was detected.
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Affiliation(s)
- Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, 117997 Moscow, Russia
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40
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Gangliosides containing different numbers of sialic acids affect the morphology and structural organization of isotropic phospholipid bicelles. Chem Phys Lipids 2013; 170-171:8-18. [DOI: 10.1016/j.chemphyslip.2013.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 11/22/2022]
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Neale C, Ghanei H, Holyoake J, Bishop RE, Privé GG, Pomès R. Detergent-mediated protein aggregation. Chem Phys Lipids 2013; 169:72-84. [PMID: 23466535 PMCID: PMC5007131 DOI: 10.1016/j.chemphyslip.2013.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation.
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Affiliation(s)
- Chris Neale
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Hamed Ghanei
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - John Holyoake
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Russell E. Bishop
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Gilbert G. Privé
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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42
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Dürr UH, Soong R, Ramamoorthy A. When detergent meets bilayer: birth and coming of age of lipid bicelles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:1-22. [PMID: 23465641 PMCID: PMC3741677 DOI: 10.1016/j.pnmrs.2013.01.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/30/2012] [Indexed: 05/12/2023]
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Yamaguchi T, Uno T, Uekusa Y, Yagi-Utsumi M, Kato K. Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins. Chem Commun (Camb) 2013; 49:1235-7. [DOI: 10.1039/c2cc38016a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Dürr UN, Gildenberg M, Ramamoorthy A. The magic of bicelles lights up membrane protein structure. Chem Rev 2012; 112:6054-74. [PMID: 22920148 PMCID: PMC3497859 DOI: 10.1021/cr300061w] [Citation(s) in RCA: 266] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Indexed: 12/12/2022]
Affiliation(s)
| | - Melissa Gildenberg
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
| | - Ayyalusamy Ramamoorthy
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
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45
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Khatun UL, Goswami SK, Mukhopadhyay C. Modulation of the neurotensin solution structure in the presence of ganglioside GM1 bicelle. Biophys Chem 2012; 168-169:48-59. [DOI: 10.1016/j.bpc.2012.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 06/25/2012] [Accepted: 06/26/2012] [Indexed: 01/16/2023]
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Brindley AJ, Martin RW. Effect of divalent cations on DMPC/DHPC bicelle formation and alignment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:7788-7796. [PMID: 22548306 DOI: 10.1021/la300885u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Many important classes of biomolecules require divalent cations for optimal activity, making these ions essential for biologically relevant structural studies. Bicelle mixtures composed of short-chain and long-chain lipids are often used in solution- and solid-state NMR structure determination; however, the phase diagrams of these useful orienting media and membrane mimetics are sensitive to other solution components. Therefore, we have investigated the effect of varying concentrations of four divalent cations, Ca(2+), Mg(2+), Zn(2+), and Cd(2+), on cholesterol sulfate-stabilized DMPC/DHPC bicelles. We found that low concentrations of all the divalent ions are tolerated with minimal perturbation. At higher concentrations Zn(2+) and Cd(2+) disrupt the magnetically aligned phase while Ca(2+) and Mg(2+) produce more strongly oriented phases. This result indicates that divalent cations are not only required to maintain the biological activity of proteins and nucleic acids; they may also be used to manipulate the behavior of the magnetically aligned phase.
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Affiliation(s)
- Amanda J Brindley
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, USA
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47
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Bechinger B, Salnikov ES. The membrane interactions of antimicrobial peptides revealed by solid-state NMR spectroscopy. Chem Phys Lipids 2012; 165:282-301. [DOI: 10.1016/j.chemphyslip.2012.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/25/2012] [Accepted: 01/27/2012] [Indexed: 01/29/2023]
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48
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Bazzacco P, Billon-Denis E, Sharma KS, Catoire LJ, Mary S, Le Bon C, Point E, Banères JL, Durand G, Zito F, Pucci B, Popot JL. Nonionic Homopolymeric Amphipols: Application to Membrane Protein Folding, Cell-Free Synthesis, and Solution Nuclear Magnetic Resonance. Biochemistry 2012; 51:1416-30. [DOI: 10.1021/bi201862v] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Paola Bazzacco
- Unité Mixte de Recherche
7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique,
13 rue Pierre-et-Marie Curie, F-75005 Paris, France
| | - Emmanuelle Billon-Denis
- Unité Mixte de Recherche
7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique,
13 rue Pierre-et-Marie Curie, F-75005 Paris, France
| | - K. Shivaji Sharma
- Université d′Avignon et des Pays de Vaucluse, Equipe Chimie
Bioorganique et Systèmes Amphiphiles, 33 rue Louis Pasteur,
F-84000 Avignon, France
| | - Laurent J. Catoire
- Unité Mixte de Recherche
7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique,
13 rue Pierre-et-Marie Curie, F-75005 Paris, France
| | - Sophie Mary
- Unité Mixte de Recherche 5247, Centre National de la Recherche Scientifique and Universités de Montpellier 1 & 2, Faculté de Pharmacie, Institut des Biomolécules Max Mousseron, 15 avenue Charles Flahault, F-34093 Montpellier Cedex 05, France
| | - Christel Le Bon
- Unité Mixte de Recherche
7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique,
13 rue Pierre-et-Marie Curie, F-75005 Paris, France
| | - Elodie Point
- Unité Mixte de Recherche
7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique,
13 rue Pierre-et-Marie Curie, F-75005 Paris, France
| | - Jean-Louis Banères
- Unité Mixte de Recherche 5247, Centre National de la Recherche Scientifique and Universités de Montpellier 1 & 2, Faculté de Pharmacie, Institut des Biomolécules Max Mousseron, 15 avenue Charles Flahault, F-34093 Montpellier Cedex 05, France
| | - Grégory Durand
- Université d′Avignon et des Pays de Vaucluse, Equipe Chimie
Bioorganique et Systèmes Amphiphiles, 33 rue Louis Pasteur,
F-84000 Avignon, France
- Unité Mixte de Recherche 5247, Centre National de la Recherche Scientifique and Universités de Montpellier 1 & 2, Faculté de Pharmacie, Institut des Biomolécules Max Mousseron, 15 avenue Charles Flahault, F-34093 Montpellier Cedex 05, France
| | - Francesca Zito
- Unité Mixte de Recherche
7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique,
13 rue Pierre-et-Marie Curie, F-75005 Paris, France
| | - Bernard Pucci
- Université d′Avignon et des Pays de Vaucluse, Equipe Chimie
Bioorganique et Systèmes Amphiphiles, 33 rue Louis Pasteur,
F-84000 Avignon, France
- Unité Mixte de Recherche 5247, Centre National de la Recherche Scientifique and Universités de Montpellier 1 & 2, Faculté de Pharmacie, Institut des Biomolécules Max Mousseron, 15 avenue Charles Flahault, F-34093 Montpellier Cedex 05, France
| | - Jean-Luc Popot
- Unité Mixte de Recherche
7099, Centre National de la Recherche Scientifique and Université Paris 7, Institut de Biologie Physico-Chimique,
13 rue Pierre-et-Marie Curie, F-75005 Paris, France
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Lu Z, Van Horn WD, Chen J, Mathew S, Zent R, Sanders CR. Bicelles at low concentrations. Mol Pharm 2012; 9:752-61. [PMID: 22221179 DOI: 10.1021/mp2004687] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bilayered detergent-lipid assemblies known as bicelles have been widely used as model membranes in structural biological studies and are being explored for wider applications, including pharmaceutical use. Most studies to date have involved the use of concentrated bicelle mixtures, such that little is known about the capacity of bicellar mixtures to be diluted without unwanted transitions to nonisotropic phases. Here, different detergent/lipid mixtures have been explored, leading to the identification of two different families of bicelles for which it is possible to lower the total amphiphile (detergent + lipid) concentration to <1% (w/v) while retaining isotropic assemblies. These include a novel family of bicelles based on mixtures of 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and the lipid dimyristoylphosphatidylcholine (DMPC). Bicelles formed by these mixtures can be diluted to <0.5% and also have attractive biochemical properties. However, a caveat of our results is that the diffusion coefficients measured for the lipid component of the different bicelles tested were seen to be dependent on sample history, even though all samples were optically transparent. This suggests that the phase behavior of bicelles at low lipid-to-detergent ratios may be more complex than previously appreciated.
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Affiliation(s)
- Zhenwei Lu
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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50
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Son WS, Park SH, Nothnagel HJ, Lu GJ, Wang Y, Zhang H, Cook GA, Howell SC, Opella SJ. 'q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:111-8. [PMID: 22079194 PMCID: PMC3257358 DOI: 10.1016/j.jmr.2011.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/07/2011] [Accepted: 10/18/2011] [Indexed: 05/13/2023]
Abstract
'q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly (15)N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios (q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers (q>2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (∼10(5)Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features of the secondary structure and basic topology of the protein. Even in the absence of assignments, this information can be used to help establish optimal experimental conditions.
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