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Favell JW, Bui DT, Li J, Han L, Kitova EN, Schmidt EN, Brassard R, Kitov PI, St-Pierre Y, Mahal LK, Lemieux MJ, Macauley MS, Klassen JS. Elusive Protein-Glycosphingolipid Interactions Revealed by Membrane Anchor-Assisted Native Mass Spectrometry. J Am Chem Soc 2024; 146:21700-21709. [PMID: 39052014 DOI: 10.1021/jacs.4c05805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Interactions between glycan-binding proteins (GBPs) and glycosphingolipids (GSLs) present in cell membranes are implicated in a wide range of biological processes. However, studying GSL binding is hindered by the paucity of purified GSLs and the weak affinities typical of monovalent GBP-GSL interactions. Native mass spectrometry (nMS) performed using soluble model membranes is a promising approach for the discovery of GBP ligands, but the detection of weak interactions remains challenging. The present work introduces MEmbrane ANchor-assisted nMS (MEAN-nMS) for the detection of low-affinity GBP-GSL complexes. The assay utilizes a membrane anchor, produced by covalent cross-linking of the GBP and a lipid in the membrane, to localize the GBP on the surface and promote GSL binding. Ligands are identified by nMS detection of intact GBP-GSL complexes (MEAN-nMS) or using a catch-and-release (CaR) strategy, wherein GSLs are released from GBP-GSL complexes upon collisional activation and detected (MEAN-CaR-nMS). To establish reliability, a library of purified gangliosides incorporated into nanodiscs was screened against human immune lectins, and the results compared with affinities of the corresponding ganglioside oligosaccharides. Without a membrane anchor, nMS analysis yielded predominantly false negatives. In contrast, all ligands were identified by MEAN-(CaR)-nMS, with no false positives. To highlight the potential of MEAN-CaR-nMS for ligand discovery, a natural library of GSLs was incorporated into nanodiscs and screened against human and viral proteins to uncover elusive ligands. Finally, nMS-based detection of GSL ligands directly from cells is demonstrated. This breakthrough paves the way for shotgun glycomics screening using intact cells.
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Affiliation(s)
- James W Favell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jianing Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ling Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Edward N Schmidt
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Raelynn Brassard
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Pavel I Kitov
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yves St-Pierre
- INRS-Institut Armand-Frappier, Laval, Québec H7V 1B7, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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2
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Wang B, Tieleman DP. The structure, self-assembly and dynamics of lipid nanodiscs revealed by computational approaches. Biophys Chem 2024; 309:107231. [PMID: 38569455 DOI: 10.1016/j.bpc.2024.107231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
Nanodisc technology is increasingly being used in structural, biochemical and biophysical studies of membrane proteins. The computational approaches have revealed many important features of nanodisc assembly, structures and dynamics. Therefore, we reviewed the application of computational approaches, especially molecular modeling and molecular dyncamics (MD) simulations, to characterize nanodiscs, including the structural models, assembly and disassembly, protocols for modeling, structural properties and dynamics, and protein-lipid interactions in nanodiscs. More amazing computational studies about nanodiscs are looked forward to in the future.
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Affiliation(s)
- Beibei Wang
- Centre for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China.
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary T2N 1N4, Canada.
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3
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Correa Y, Ravel M, Imbert M, Waldie S, Clifton L, Terry A, Roosen‐Runge F, Lagerstedt JO, Moir M, Darwish T, Cárdenas M, Del Giudice R. Lipid exchange of apolipoprotein A-I amyloidogenic variants in reconstituted high-density lipoprotein with artificial membranes. Protein Sci 2024; 33:e4987. [PMID: 38607188 PMCID: PMC11010956 DOI: 10.1002/pro.4987] [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: 11/06/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
High-density lipoproteins (HDLs) are responsible for removing cholesterol from arterial walls, through a process known as reverse cholesterol transport. The main protein in HDL, apolipoprotein A-I (ApoA-I), is essential to this process, and changes in its sequence significantly alter HDL structure and functions. ApoA-I amyloidogenic variants, associated with a particular hereditary degenerative disease, are particularly effective at facilitating cholesterol removal, thus protecting carriers from cardiovascular disease. Thus, it is conceivable that reconstituted HDL (rHDL) formulations containing ApoA-I proteins with functional/structural features similar to those of amyloidogenic variants hold potential as a promising therapeutic approach. Here we explored the effect of protein cargo and lipid composition on the function of rHDL containing one of the ApoA-I amyloidogenic variants G26R or L174S by Fourier transformed infrared spectroscopy and neutron reflectometry. Moreover, small-angle x-ray scattering uncovered the structural and functional differences between rHDL particles, which could help to comprehend higher cholesterol efflux activity and apparent lower phospholipid (PL) affinity. Our findings indicate distinct trends in lipid exchange (removal vs. deposition) capacities of various rHDL particles, with the rHDL containing the ApoA-I amyloidogenic variants showing a markedly lower ability to remove lipids from artificial membranes compared to the rHDL containing the native protein. This effect strongly depends on the level of PL unsaturation and on the particles' ultrastructure. The study highlights the importance of the protein cargo, along with lipid composition, in shaping rHDL structure, contributing to our understanding of lipid-protein interactions and their behavior.
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Affiliation(s)
- Yubexi Correa
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Mathilde Ravel
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Marie Imbert
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Sarah Waldie
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Luke Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities CouncilRutherford Appleton Laboratory, Harwell Science and Innovation CampusDidcotUK
| | - Ann Terry
- MAX IV LaboratoryCoSAXS Beamline, Lund UniversityLundSweden
| | - Felix Roosen‐Runge
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Jens O. Lagerstedt
- Islet Cell Exocytosis, Department of Clinical Sciences in Malmö, Lund University Diabetes CentreLund UniversityMalmöSweden
- Rare Endocrine Disorders, Research and Early DevelopmentNovo NordiskCopenhagenDenmark
| | - Michael Moir
- National Deuteration FacilityAustralian Nuclear Science and Technology Organization (ANSTO)Lucas HeightsNew South WalesAustralia
| | - Tamim Darwish
- National Deuteration FacilityAustralian Nuclear Science and Technology Organization (ANSTO)Lucas HeightsNew South WalesAustralia
- Faculty of Science and TechnologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Marité Cárdenas
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
- Biofisika Institute (University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC))LeioaSpain
| | - Rita Del Giudice
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
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4
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Caron NS, Aly AEE, Findlay Black H, Martin DDO, Schmidt ME, Ko S, Anderson C, Harvey EM, Casal LL, Anderson LM, Rahavi SMR, Reid GSD, Oda MN, Stanimirovic D, Abulrob A, McBride JL, Leavitt BR, Hayden MR. Systemic delivery of mutant huntingtin lowering antisense oligonucleotides to the brain using apolipoprotein A-I nanodisks for Huntington disease. J Control Release 2024; 367:27-44. [PMID: 38215984 DOI: 10.1016/j.jconrel.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/09/2023] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Efficient delivery of therapeutics to the central nervous system (CNS) remains a major challenge for the treatment of neurological diseases. Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by a CAG trinucleotide expansion mutation in the HTT gene which codes for a toxic mutant huntingtin (mHTT) protein. Pharmacological reduction of mHTT in the CNS using antisense oligonucleotides (ASO) ameliorates HD-like phenotypes in rodent models of HD, with such therapies being investigated in clinical trials for HD. In this study, we report the optimization of apolipoprotein A-I nanodisks (apoA-I NDs) as vehicles for delivery of a HTT-targeted ASO (HTT ASO) to the brain and peripheral organs for HD. We demonstrate that apoA-I wild type (WT) and the apoA-I K133C mutant incubated with a synthetic lipid, 1,2-dimyristoyl-sn-glycero-3-phosphocholine, can self-assemble into monodisperse discoidal particles with diameters <20 nm that transmigrate across an in vitro blood-brain barrier model of HD. We demonstrate that apoA-I NDs are well tolerated in vivo, and that apoA-I K133C NDs show enhanced distribution to the CNS and peripheral organs compared to apoA-I WT NDs following systemic administration. ApoA-I K133C conjugated with HTT ASO forms NDs (HTT ASO NDs) that induce significant mHTT lowering in the liver, skeletal muscle and heart as well as in the brain when delivered intravenously in the BACHD mouse model of HD. Furthermore, HTT ASO NDs increase the magnitude of mHTT lowering in the striatum and cortex compared to HTT ASO alone following intracerebroventricular administration. These findings demonstrate the potential utility of apoA-I NDs as biocompatible vehicles for enhancing delivery of mutant HTT lowering ASOs to the CNS and peripheral organs for HD.
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Affiliation(s)
- Nicholas S Caron
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amirah E-E Aly
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hailey Findlay Black
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dale D O Martin
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biology, University of Waterloo, Ontario, Canada
| | - Mandi E Schmidt
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Neuroscience, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seunghyun Ko
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Christine Anderson
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Emily M Harvey
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Lorenzo L Casal
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Lisa M Anderson
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Seyed M R Rahavi
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregor S D Reid
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Danica Stanimirovic
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Abedelnasser Abulrob
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jodi L McBride
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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5
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Allen P, Smith AC, Benedicto V, Abdulhasan A, Narayanaswami V, Tapavicza E. Molecular dynamics simulation of apolipoprotein E3 lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184230. [PMID: 37704040 PMCID: PMC11318356 DOI: 10.1016/j.bbamem.2023.184230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
Nanodiscs are binary discoidal complexes of a phospholipid bilayer circumscribed by belt-like helical scaffold proteins. Using coarse-grained and all-atom molecular dynamics simulations, we explore the stability, size, and structure of nanodiscs formed between the N-terminal domain of apolipoprotein E3 (apoE3-NT) and variable number of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) molecules. We study both parallel and antiparallel double-belt configurations, consisting of four proteins per nanodisc. Our simulations predict nanodiscs containing between 240 and 420 DMPC molecules to be stable. The antiparallel configurations exhibit an average of 1.6 times more amino acid interactions between protein chains and 2 times more ionic contacts, compared to the parallel configuration. With one exception, DMPC order parameters are consistently larger in the antiparallel configuration than in the parallel one. In most cases, the root mean square deviation of the positions of the protein backbone atoms is smaller in the antiparallel configuration. We further report nanodisc size, thickness, radius of gyration, and solvent accessible surface area. Combining all investigated parameters, we hypothesize the antiparallel protein configuration leading to more stable and more rigid nanodiscs than the parallel one.
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Affiliation(s)
- Patrick Allen
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, 90840, CA, USA
| | - Adam C Smith
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, 90840, CA, USA
| | - Vernon Benedicto
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, 90840, CA, USA
| | - Abbas Abdulhasan
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, 90840, CA, USA
| | - Vasanthy Narayanaswami
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, 90840, CA, USA
| | - Enrico Tapavicza
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, 90840, CA, USA.
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6
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Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
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7
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You X, Thakur N, Ray AP, Eddy MT, Baiz CR. A comparative study of interfacial environments in lipid nanodiscs and vesicles. BIOPHYSICAL REPORTS 2022; 2. [PMID: 36176716 PMCID: PMC9518727 DOI: 10.1016/j.bpr.2022.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane protein conformations and dynamics are driven by the protein-lipid interactions occurring within the local environment of the membrane. These environments remain challenging to accurately capture in structural and biophysical experiments using bilayers. Consequently, there is an increasing need for realistic cell-membrane mimetics for in vitro studies. Lipid nanodiscs provide certain advantages over vesicles for membrane protein studies. Nanodiscs are increasingly used for structural and spectroscopic characterization of membrane proteins. Despite the common use of nanodiscs, the interfacial environments of lipids confined to a ~10-nm diameter area have remained relatively underexplored. Here, we use ultrafast two-dimensional infrared spectroscopy and temperature-dependent infrared absorption measurements of the ester carbonyls to compare the interfacial hydrogen bond structure and dynamics in lipid nanodiscs of varying lipid compositions and sizes with ~100-nm vesicles. We examine the effects of lipid composition and nanodisc size. We found that nanodiscs and vesicles share largely similar lipid-water H-bond environments and interfacial dynamics. Differences in measured enthalpies of H-bonding suggest that H-bond dynamics in nanodiscs are modulated by the interaction between the annular lipids and the scaffold protein.
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Sharma R, Dong Y, Hu Y, Ma VPY, Salaita K. Gene Regulation Using Nanodiscs Modified with HIF-1-α Antisense Oligonucleotides. Bioconjug Chem 2022; 33:279-293. [PMID: 35080855 PMCID: PMC9884500 DOI: 10.1021/acs.bioconjchem.1c00505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Delivery of nucleic acids can be hindered by multiple factors including nuclease susceptibility, endosome trapping, and clearance. Multiple nanotechnology scaffolds have offered promising solutions, and among these, lipid-based systems are advantageous because of their high biocompatibility and low toxicity. However, many lipid nanoparticle systems still have issues regarding stability, rapid clearance, and cargo leakage. Herein, we demonstrate the use of a synthetic nanodisc (ND) scaffold functionalized with an anti-HIF-1-α antisense oligonucleotide (ASO) to reduce HIF-1-α mRNA transcript levels. We prepared ND conjugates by using a mixture of phosphoglycerolipids with phosphocholine and phosphothioethanol headgroups that self-assemble into a ∼13 × 5 nm discoidal structure upon addition of a 22-amino-acid ApoA1 mimetic peptide. Optimized reaction conditions yield 15 copies of the anti-HIF-1-α ASO DNA covalently conjugated to the thiolated phospholipids using maleimide-thiol chemistry. We show that DNA-ND conjugates are active, nuclease resistant, and rapidly internalized into cells to regulate HIF-1-α mRNA levels without the use of transfection agents. DNA-ND uptake is partially mediated through Scavenger Receptor B1 and the ND conjugates show enhanced knockdown of HIF-1-α compared to that of the soluble ASOs in multiple cell lines. Our results demonstrate that covalently functionalized NDs may offer an improved platform for ASO therapeutics.
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9
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Jeong C, Franklin R, Edler KJ, Vanommeslaeghe K, Krueger S, Curtis JE. Styrene-Maleic Acid Copolymer Nanodiscs to Determine the Shape of Membrane Proteins. J Phys Chem B 2022; 126:1034-1044. [PMID: 35089036 DOI: 10.1021/acs.jpcb.1c05050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipid nanodiscs can be used to solubilize functional membrane proteins (MPs) in nativelike environments. Thus, they are promising reagents that have been proven useful to characterize MPs. Both protein and non-protein molecular belts have shown promise to maintain the structural integrity of MPs in lipid nanodiscs. Small-angle neutron scattering (SANS) can be used to determine low-resolution structures of proteins in solution, which can be enhanced through the use of contrast variation methods. We present theoretical contrast variation SANS results for protein and styrene-maleic acid copolymer (SMA) belt 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) nanodiscs with and without additional bound or transmembrane proteins. The predicted scattering properties are derived from atomistic molecular dynamics simulations to account for conformational fluctuations, and we determine deuterium-labeling conditions such that SANS intensity profiles only include contributions from the scattering of the MP of interest. We propose strategies to tune the neutron scattering length densities (SLDs) of the SMA and DMPC using selective deuterium labeling such that the SLD of the nanodisc becomes homogeneous and its scattering can essentially be eliminated in solvents containing an appropriate amount of D2O. These finely tuned labeled polymer-based nanodiscs are expected to be useful to extract the size and molecular shape information of MPs using SANS-based contrast variation experiments, and they can be used with MPs of any molecular weight.
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Affiliation(s)
- Cheol Jeong
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States.,Department of Chemistry, The University of Tennessee, Knoxville, Tennessee 37996-1600, United States
| | - Ryan Franklin
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Karen J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| | - Kenno Vanommeslaeghe
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling─FABI, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
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10
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Heinrich F, Van QN, Jean-Francois F, Stephen AG, Lösche M. Membrane-bound KRAS approximates an entropic ensemble of configurations. Biophys J 2021; 120:4055-4066. [PMID: 34384763 PMCID: PMC8510975 DOI: 10.1016/j.bpj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/08/2021] [Accepted: 08/04/2021] [Indexed: 11/27/2022] Open
Abstract
KRAS4B is a membrane-anchored signaling protein and a primary target in cancer research. Predictions from molecular dynamics simulations that have previously shaped our mechanistic understanding of KRAS signaling disagree with recent experimental results from neutron reflectometry, NMR, and thermodynamic binding studies. To gain insight into these discrepancies, we compare this body of biophysical data to back-calculated experimental results from a series of molecular simulations that implement different subsets of molecular interactions. Our results show that KRAS4B approximates an entropic ensemble of configurations at model membranes containing 30% phosphatidylserine lipids, which is not significantly shaped by interactions between the globular G-domain of KRAS4B and the lipid membrane. These findings revise our understanding of KRAS signaling and promote a model in which the protein samples the accessible conformational space in a near-uniform manner while being available to bind to effector proteins.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland.
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Frantz Jean-Francois
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
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11
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Kjølbye LR, De Maria L, Wassenaar TA, Abdizadeh H, Marrink SJ, Ferkinghoff-Borg J, Schiøtt B. General Protocol for Constructing Molecular Models of Nanodiscs. J Chem Inf Model 2021; 61:2869-2883. [PMID: 34048229 DOI: 10.1021/acs.jcim.1c00157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanodisc technology is increasingly being applied for structural and biophysical studies of membrane proteins. In this work, we present a general protocol for constructing molecular models of nanodiscs for molecular dynamics simulations. The protocol is written in python and based on geometric equations, making it fast and easy to modify, enabling automation and customization of nanodiscs in silico. The novelty being the ability to construct any membrane scaffold protein (MSP) variant fast and easy given only an input sequence. We validated and tested the protocol by simulating seven different nanodiscs of various sizes and with different membrane scaffold proteins, both circularized and noncircularized. The structural and biophysical properties were analyzed and shown to be in good agreement with previously reported experimental data and simulation studies.
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Affiliation(s)
- Lisbeth R Kjølbye
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.,Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | | | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C, Denmark
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12
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Chmielińska A, Stepien P, Bonarek P, Girych M, Enkavi G, Rog T, Dziedzicka-Wasylewska M, Polit A. Can di-4-ANEPPDHQ reveal the structural differences between nanodiscs and liposomes? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183649. [PMID: 33991503 DOI: 10.1016/j.bbamem.2021.183649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/15/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022]
Abstract
The potential-sensitive di-4-ANEPPDHQ dye is presently gaining popularity in structural studies of the lipid bilayer. Within the bilayer, dye environmental sensitivity originates from the excitation induced charge redistribution and is usually attributed to solvent relaxation. Here, di-4-ANEPPDHQ is utilized to compare the structure of neutral and negatively charged lipid bilayers between two model systems: the nanodiscs and the liposomes. Using the well-established approach of measuring solvatochromic shifts of the steady-state spectra to study the bilayer structural changes has proved insufficient in this case. By applying an in-depth analysis of time-resolved fluorescence decays and emission spectra, we distinguished and characterized two and three distinct emissive di-4-ANEPPDHQ species in the liposomes and the nanodiscs, respectively. These emissive species were ascribed to the dual emission of the dye rather than to solvent relaxation. An additional, long-lived component present in the nanodiscs was associated with a unique domain of high order, postulated recently. Our results reveal that the di-4-ANEPPDHQ steady-state fluorescence should be interpreted with caution. With the experimental approach presented here, the di-4-ANEPPDHQ sensitivity was improved. We confirmed that the bilayer structure is, indeed, altered in the nanodiscs. Moreover, molecular dynamic simulations showed a distribution of the probe in the nanodiscs plane, which is sensitive to lipid composition. In POPC nanodiscs, probe frequently interacts with MSP, while in POPC-POPG nanodiscs, such interactions are rare. We did not observe, however, any impact of those interactions on the probe fluorescence.
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Affiliation(s)
- Anna Chmielińska
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Piotr Stepien
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Piotr Bonarek
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Tomasz Rog
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Marta Dziedzicka-Wasylewska
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Agnieszka Polit
- Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
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13
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Abstract
The properties of natural lipid bilayers are vital to the regulation of many membrane proteins. Scaffolded nanodiscs provide an in vitro lipid bilayer platform to host membrane proteins in an environment that approximates native lipid bilayers. However, the properties of scaffold-enclosed bilayers may depart significantly from those of bulk cellular membranes. Therefore, to improve the usefulness of nanodiscs it is essential to understand the properties of lipids restricted by scaffolds. We used computational molecular dynamics and modeling approaches to understand the effects of nanodisc size, scaffold type (DNA or protein), and hydrophobic modification of DNA scaffolds on bilayer stability and degree to which the properties of enclosed bilayers approximate bulk bilayers. With respect to achieving bulk bilayer behavior, we found that charge neutralization of DNA scaffolds was more important than the total hydrophobic content of their modifications: bilayer properties were better for scaffolds having a large number of short alkyl chains than those having fewer long alkyl chains. Further, complete charge neutralization of DNA scaffolds enabled better lipid binding, and more stable bilayers, as shown by steered molecular dynamics simulations that measured the force required to dislodge scaffolds from lipid bilayer patches. Considered together, our simulations provide a guide to the design of DNA-scaffolded nanodiscs suitable for studying membrane proteins.
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Affiliation(s)
- Vishal Maingi
- Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Paul W K Rothemund
- Departments of Bioengineering, Computing + Mathematical Sciences, and Computation & Neural Systems, California Institute of Technology, Pasadena, California 91125, United States
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14
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Iadanza MG, Schiffrin B, White P, Watson MA, Horne JE, Higgins AJ, Calabrese AN, Brockwell DJ, Tuma R, Kalli AC, Radford SE, Ranson NA. Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs. Commun Biol 2020; 3:766. [PMID: 33318620 PMCID: PMC7736308 DOI: 10.1038/s42003-020-01419-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/12/2020] [Indexed: 11/28/2022] Open
Abstract
The β-barrel assembly machinery (BAM) catalyses the folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria by mechanisms that remain unclear. Here, we present an ensemble of cryoEM structures of the E. coli BamABCDE (BAM) complex in lipid nanodiscs, determined using multi-body refinement techniques. These structures, supported by single-molecule FRET measurements, describe a range of motions in the BAM complex, mostly localised within the periplasmic region of the major subunit BamA. The β-barrel domain of BamA is in a 'lateral open' conformation in all of the determined structures, suggesting that this is the most energetically favourable species in this bilayer. Strikingly, the BAM-containing lipid nanodisc is deformed, especially around BAM's lateral gate. This distortion is also captured in molecular dynamics simulations, and provides direct structural evidence for the lipid 'disruptase' activity of BAM, suggested to be an important part of its functional mechanism.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew A Watson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Anna J Higgins
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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15
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Bunker A, Róg T. Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery. Front Mol Biosci 2020; 7:604770. [PMID: 33330633 PMCID: PMC7732618 DOI: 10.3389/fmolb.2020.604770] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.
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Affiliation(s)
- Alex Bunker
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
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16
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Sligar SG, Denisov IG. Nanodiscs: A toolkit for membrane protein science. Protein Sci 2020; 30:297-315. [PMID: 33165998 DOI: 10.1002/pro.3994] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes, including transport, signal transduction and the enzymes in a variety of metabolic pathways. Integral membrane proteins account for up to 30% of the human proteome and they make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists, and one is most often left with the challenge of finding inhibitors, activators and specific antibodies using a denatured or detergent solubilized aggregate. The Nanodisc platform circumvents these challenges by providing a self-assembled system that renders typically insoluble, yet biologically and pharmacologically significant, targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media in a native-like bilayer environment that maintain a target's functional activity. By providing a bilayer surface of defined composition and structure, Nanodiscs have found great utility in the study of cellular signaling complexes that assemble on a membrane surface. Nanodiscs provide a nanometer scale vehicle for the in vivo delivery of amphipathic drugs, therapeutic lipids, tethered nucleic acids, imaging agents and active protein complexes. This means for generating nanoscale lipid bilayers has spawned the successful use of numerous other polymer and peptide amphipathic systems. This review, in celebration of the Anfinsen Award, summarizes some recent results and provides an inroad into the current and historical literature.
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Affiliation(s)
- Stephen G Sligar
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Ilia G Denisov
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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17
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Complexity of seemingly simple lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183420. [DOI: 10.1016/j.bbamem.2020.183420] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
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18
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Rangubpit W, Paritanon P, Pandey RB, Sompornpisut P. Thermally induced structural organization of nanodiscs by coarse-grained molecular dynamics simulations. Biophys Chem 2020; 267:106464. [PMID: 32927312 DOI: 10.1016/j.bpc.2020.106464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Membrane scaffold proteins (MSP) nanodiscs have been extensively used in structural study of membrane proteins. In cryo-EM, an incorporation of target proteins into nanodiscs is conducted under a rapid change from cryogenic to ambient temperatures. We present a coarse-grained molecular dynamics (CGMD) study for investigating an effect of temperature on the structural organization of DPPC-nanodisc and POPC-nanodisc. A non-monotonic response of physical quantities (i.e. the lipid order parameter, nanodisc flatness, structural change, solvation property, radius of gyration) with increase in temperature (T = 200-350 K) is found to be associated with the gel-ripple-liquid crystalline phase change within nanodiscs. The reorganization of lipids upon temperature variation induced conformational changes of MSP to minimize hydrophobic exposure of the lipid membrane to an aqueous environment. Structural response to temperature is different to a certain extent between the saturated DPPC and unsaturated POPC.
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Affiliation(s)
- Warin Rangubpit
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, 10330, Thailand
| | - Pasawan Paritanon
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, 10330, Thailand
| | - Ras B Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pornthep Sompornpisut
- Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, 10330, Thailand.
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19
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Schachter I, Allolio C, Khelashvili G, Harries D. Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties. J Phys Chem B 2020; 124:7166-7175. [PMID: 32697588 PMCID: PMC7526989 DOI: 10.1021/acs.jpcb.0c03374] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Lipid
nanodiscs are small synthetic lipid bilayer structures that
are stabilized in solution by special circumscribing (or scaffolding)
proteins or polymers. Because they create native-like environments
for transmembrane proteins, lipid nanodiscs have become a powerful
tool for structural determination of this class of systems when combined
with cryo-electron microscopy or nuclear magnetic resonance. The elastic
properties of lipid bilayers determine how the lipid environment responds
to membrane protein perturbations, and how the lipid in turn modifies
the conformational state of the embedded protein. However, despite
the abundant use of nanodiscs in determining membrane protein structure,
the elastic material properties of even pure lipid nanodiscs (i.e.,
without embedded proteins) have not yet been quantitatively investigated.
A major hurdle is due to the inherently nonlocal treatment of the
elastic properties of lipid systems implemented by most existing methods,
both experimental and computational. In addition, these methods are
best suited for very large “infinite” size lipidic assemblies,
or ones that contain periodicity, in the case of simulations. We have
previously described a computational analysis of molecular dynamics
simulations designed to overcome these limitations, so it allows quantification
of the bending rigidity (KC) and tilt
modulus (κt) on a local scale even for finite, nonperiodic
systems, such as lipid nanodiscs. Here we use this computational approach
to extract values of KC and κt for a set of lipid nanodisc systems that vary in size and
lipid composition. We find that the material properties of lipid nanodiscs
are different from those of infinite bilayers of corresponding lipid
composition, highlighting the effect of nanodisc confinement. Nanodiscs
tend to show higher stiffness than their corresponding macroscopic
bilayers, and moreover, their material properties vary spatially within
them. For small-size MSP1 nanodiscs, the stiffness decreases radially,
from a value that is larger in their center than the moduli of the
corresponding bilayers by a factor of ∼2–3. The larger
nanodiscs (MSP1E3D1 and MSP2N2) show milder spatial changes of moduli
that are composition dependent and can be maximal in the center or
at some distance from it. These trends in moduli correlate with spatially
varying structural properties, including the area per lipid and the
nanodisc thickness. Finally, as has previously been reported, nanodiscs
tend to show deformations from perfectly flat circular geometries
to varying degrees, depending on size and lipid composition. The modulations
of lipid elastic properties that we find should be carefully considered
when making structural and functional inferences concerning embedded
proteins.
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Affiliation(s)
- Itay Schachter
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Christoph Allolio
- Institute of Mathematics, Faculty of Mathematics and Physics, Charles University, Prague 18674, Czech Republic
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States.,Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
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20
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McLean MA, Denisov IG, Grinkova YV, Sligar SG. Dark, Ultra-Dark and Ultra-Bright Nanodiscs for membrane protein investigations. Anal Biochem 2020; 607:113860. [PMID: 32750355 DOI: 10.1016/j.ab.2020.113860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 11/16/2022]
Abstract
We describe the construction, expression and purification of three new membrane scaffold proteins (MSP) for use in assembling Nanodiscs. These new MSPs have a variety of luminescent properties for use in combination with several analytical methods. "Dark" MSP has no tryptophan residues, "Ultra-Dark" replaces both tryptophan and tyrosine with non-fluorescent side chains, and "Ultra-Bright" adds additional tryptophans to the parent membrane scaffold protein to provide a dramatic increase in native tryptophan fluorescence. All MSPs were used to successfully assemble Nanodiscs nominally 10 nm in diameter, and the resultant bilayer structure was characterized. An example of the usefulness of these new scaffold proteins is provided.
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Affiliation(s)
- Mark A McLean
- Department of Biochemistry, University of Illinois, Urbana, IL, 16801, USA
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL, 16801, USA
| | - Yelena V Grinkova
- Department of Biochemistry, University of Illinois, Urbana, IL, 16801, USA
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL, 16801, USA; Department of Chemistry, University of Illinois, Urbana, IL, 16801, USA.
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21
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Bengtsen T, Holm VL, Kjølbye LR, Midtgaard SR, Johansen NT, Tesei G, Bottaro S, Schiøtt B, Arleth L, Lindorff-Larsen K. Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations. eLife 2020; 9:e56518. [PMID: 32729831 PMCID: PMC7426092 DOI: 10.7554/elife.56518] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
Nanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer, and are broadly used for characterization of membrane proteins. Here, we investigate the structure, dynamics and biophysical properties of two small nanodiscs, MSP1D1ΔH5 and ΔH4H5. We combine our SAXS and SANS experiments with molecular dynamics simulations and previously obtained NMR and EPR data to derive and validate a conformational ensemble that represents the structure and dynamics of the nanodisc. We find that it displays conformational heterogeneity with various elliptical shapes, and with substantial differences in lipid ordering in the centre and rim of the discs. Together, our results reconcile previous apparently conflicting observations about the shape of nanodiscs, and pave the way for future integrative studies of larger complex systems such as membrane proteins embedded in nanodiscs.
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Affiliation(s)
- Tone Bengtsen
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Viktor L Holm
- Structural Biophysics, X-ray and Neutron Science, Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
| | | | - Søren R Midtgaard
- Structural Biophysics, X-ray and Neutron Science, Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
| | - Nicolai Tidemand Johansen
- Structural Biophysics, X-ray and Neutron Science, Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
| | - Giulio Tesei
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | | | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
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22
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Abstract
The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.
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23
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Augustyn B, Stepien P, Poojari C, Mobarak E, Polit A, Wisniewska-Becker A, Róg T. Cholesteryl Hemisuccinate Is Not a Good Replacement for Cholesterol in Lipid Nanodiscs. J Phys Chem B 2019; 123:9839-9845. [DOI: 10.1021/acs.jpcb.9b07853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Piotr Stepien
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Chetan Poojari
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Edouard Mobarak
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | | | | | - Tomasz Róg
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
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24
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López CA, Swift MF, Xu XP, Hanein D, Volkmann N, Gnanakaran S. Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM. Structure 2019; 27:988-999.e4. [DOI: 10.1016/j.str.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 12/21/2018] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
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25
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Sahoo BR, Genjo T, Moharana KC, Ramamoorthy A. Self-Assembly of Polymer-Encased Lipid Nanodiscs and Membrane Protein Reconstitution. J Phys Chem B 2019; 123:4562-4570. [DOI: 10.1021/acs.jpcb.9b03681] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Kanhu C. Moharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha 751003, India
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26
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Qi Y, Lee J, Klauda JB, Im W. CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems. J Comput Chem 2019; 40:893-899. [PMID: 30677169 DOI: 10.1002/jcc.25773] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/05/2018] [Accepted: 12/11/2018] [Indexed: 01/13/2023]
Abstract
Nanodiscs are discoidal protein-lipid complexes that have wide applications in membrane protein studies. Modeling and simulation of nanodiscs are challenging due to the absence of structures of many membrane scaffold proteins (MSPs) that wrap around the membrane bilayer. We have developed CHARMM-GUI Nanodisc Builder (http://www.charmm-gui.org/input/nanodisc) to facilitate the setup of nanodisc simulation systems by modeling the MSPs with defined size and known structural features. A total of 11 different nanodiscs with a diameter from 80 to 180 Å are made available in both the all-atom CHARMM and two coarse-grained (PACE and Martini) force fields. The usage of the Nanodisc Builder is demonstrated with various simulation systems. The structures and dynamics of proteins and lipids in these systems were analyzed, showing similar behaviors to those from previous all-atom and coarse-grained nanodisc simulations. We expect the Nanodisc Builder to be a convenient and reliable tool for modeling and simulation of nanodisc systems. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Jumin Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland, College Park, Maryland
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania
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Molecular mechanism of fusion pore formation driven by the neuronal SNARE complex. Proc Natl Acad Sci U S A 2018; 115:12751-12756. [PMID: 30482862 DOI: 10.1073/pnas.1816495115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Release of neurotransmitters from synaptic vesicles begins with a narrow fusion pore, the structure of which remains unresolved. To obtain a structural model of the fusion pore, we performed coarse-grained molecular dynamics simulations of fusion between a nanodisc and a planar bilayer bridged by four partially unzipped SNARE complexes. The simulations revealed that zipping of SNARE complexes pulls the polar C-terminal residues of the synaptobrevin 2 and syntaxin 1A transmembrane domains to form a hydrophilic core between the two distal leaflets, inducing fusion pore formation. The estimated conductances of these fusion pores are in good agreement with experimental values. Two SNARE protein mutants inhibiting fusion experimentally produced no fusion pore formation. In simulations in which the nanodisc was replaced by a 40-nm vesicle, an extended hemifusion diaphragm formed but a fusion pore did not, indicating that restricted SNARE mobility is required for rapid fusion pore formation. Accordingly, rapid fusion pore formation also occurred in the 40-nm vesicle system when SNARE mobility was restricted by external forces. Removal of the restriction is required for fusion pore expansion.
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Graziano V, Miller L, Yang L. Interpretation of solution scattering data from lipid nanodiscs. J Appl Crystallogr 2018; 51:157-166. [PMID: 29507548 PMCID: PMC5822991 DOI: 10.1107/s1600576717018441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/24/2017] [Indexed: 05/29/2023] Open
Abstract
Solution scattering data from lipid nanodiscs are interpreted on the basis of X-ray scattering data in an extended range of scattering vectors. The structural information contained in solution scattering data from empty lipid nanodiscs is examined in the context of a multi-component geometric model. X-ray scattering data were collected on nanodiscs of different compositions at scattering vector magnitudes up to 2.0 Å−1. Through the calculation of the partial form factor for each of the nanodisc components before the isotropic average, structural parameters in the model were correlated to the features observed in the X-ray scattering data and to the corresponding distance distribution function. It is shown that, in general, the features at ∼0.3–0.6 Å−1 in the scattering data correlate to the bilayer structure. The data also support the argument that the elliptical shape of nanodiscs found in model fitting is physical, rather than an artefact due to the nanodisc size distribution. The lipid chain packing peak at ∼1.5 Å−1 is visible in the data and reflects the lipid bilayer phase transition. The shape change in the distance distribution function across the phase transition suggests that the nanodiscs are more circular in the fluid phase. The implication of these findings for model fitting of empty and protein-loaded nanodiscs is discussed.
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Affiliation(s)
- Vito Graziano
- Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Lisa Miller
- Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Lin Yang
- Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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Lu Y, Zhang H, Niedzwiedzki DM, Jiang J, Blankenship RE, Gross ML. Fast Photochemical Oxidation of Proteins Maps the Topology of Intrinsic Membrane Proteins: Light-Harvesting Complex 2 in a Nanodisc. Anal Chem 2016; 88:8827-34. [PMID: 27500903 PMCID: PMC5201186 DOI: 10.1021/acs.analchem.6b01945] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although membrane proteins are crucial participants in photosynthesis and other biological processes, many lack high-resolution structures. Prior to achieving a high-resolution structure, we are investigating whether MS-based footprinting can provide coarse-grained protein structure by following structural changes that occur upon ligand binding, pH change, and membrane binding. Our platform probes topology and conformation of membrane proteins by combining MS-based footprinting, specifically fast photochemical oxidation of proteins (FPOP), and lipid Nanodiscs, which are more similar to the native membrane environment than are the widely used detergent micelles. We describe here results that show a protein's outer membrane regions are more heavily footprinted by OH radicals whereas the regions spanning the lipid bilayer remain inert to the labeling. Nanodiscs generally exhibit more protection of membrane proteins compared to detergent micelles and less shielding to those protein residues that exist outside the membrane. The combination of immobilizing the protein in Nanodiscs and footprinting with FPOP is a feasible approach to map extra-membrane protein surfaces, even at the amino-acid level, and to illuminate intrinsic membrane protein topology.
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Affiliation(s)
- Yue Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Dariusz M. Niedzwiedzki
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jing Jiang
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E. Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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