1
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Hjalte J, Diehl C, Leung AE, Poon JF, Porcar L, Dalgliesh R, Sjögren H, Wahlgren M, Sanchez-Fernandez A. Modulating protein unfolding and refolding via the synergistic association of an anionic and a nonionic surfactant. J Colloid Interface Sci 2024; 672:244-255. [PMID: 38838632 DOI: 10.1016/j.jcis.2024.05.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
HYPOTHESIS Nonionic surfactants can counter the deleterious effect that anionic surfactants have on proteins, where the folded states are retrieved from a previously unfolded state. However, further studies are required to refine our understanding of the underlying mechanism of the refolding process. While interactions between nonionic surfactants and tightly folded proteins are not anticipated, we hypothesized that intermediate stages of surfactant-induced unfolding could define new interaction mechanisms by which nonionic surfactants can further alter protein conformation. EXPERIMENTS In this work, the behavior of three model proteins (human growth hormone, bovine serum albumin, and β-lactoglobulin) was investigated in the presence of the anionic surfactant sodium dodecylsulfate, the nonionic surfactant β-dodecylmaltoside, and mixtures of both surfactants. The transitions occurring to the proteins were determined using intrinsic fluorescence spectroscopy and far-UV circular dichroism. Based on these results, we developed a detailed interaction model for human growth hormone. Using nuclear magnetic resonance and contrast-variation small-angle neutron scattering, we studied the amino acid environment and the conformational state of the protein. FINDINGS The results demonstrate the key role of surfactant cooperation in defining the conformational state of the proteins, which can shift away or toward the folded state depending on the nonionic-to-ionic surfactant ratio. Dodecylmaltoside, initially a non-interacting surfactant, can unexpectedly associate with sodium dodecylsulfate-unfolded proteins to further impact their conformation at low nonionic-to-ionic surfactant ratio. When this ratio increases, the protein begins to retrieve the folded state. However, the native conformation cannot be fully recovered due to remnant surfactant molecules still adsorbed to the protein. This study demonstrates that the conformational landscape of the protein depends on a delicate interplay between the surfactants, ultimately controlled by the ratio between them, resulting in unpredictable changes in the protein conformation.
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Affiliation(s)
- Johanna Hjalte
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Carl Diehl
- SARomics Biostructures AB, Medicon Village, Scheelevägen 2, 223 81 Lund, Sweden
| | - Anna E Leung
- European Spallation Source, Box 176, 221 00 Lund, Sweden
| | - Jia-Fei Poon
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden; European Spallation Source, Box 176, 221 00 Lund, Sweden
| | - Lionel Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Rob Dalgliesh
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Helen Sjögren
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Adrian Sanchez-Fernandez
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain.
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2
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Keller MJ, Zhang Q, Qian S, Sanders BC, O'Neill HM, Hettich RL. Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization. Anal Chem 2024; 96:212-219. [PMID: 38150504 DOI: 10.1021/acs.analchem.3c03750] [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: 12/29/2023]
Abstract
Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.
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Affiliation(s)
- Matthew J Keller
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- The Second Target Station Project of SNS, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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3
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Golub M, Pieper J. Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods. Molecules 2023; 28:7414. [PMID: 37959833 PMCID: PMC10650700 DOI: 10.3390/molecules28217414] [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: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.
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Affiliation(s)
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald Str. 1, 50411 Tartu, Estonia;
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4
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Lenz J, Larsen AH, Keller S, Luchini A. Effect of Cholesterol on the Structure and Composition of Glyco-DIBMA Lipid Particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:3569-3579. [PMID: 36854196 PMCID: PMC10018766 DOI: 10.1021/acs.langmuir.2c03019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Different amphiphilic co-polymers have been introduced to produce polymer-lipid particles with nanodisc structure composed of an inner lipid bilayer and polymer chains self-assembled as an outer belt. These particles can be used to stabilize membrane proteins in solution and enable their characterization by means of biophysical methods, including small-angle X-ray scattering (SAXS). Some of these co-polymers have also been used to directly extract membrane proteins together with their associated lipids from native membranes. Styrene/maleic acid and diisobutylene/maleic acid are among the most commonly used co-polymers for producing polymer-lipid particles, named SMALPs and DIBMALPs, respectively. Recently, a new co-polymer, named Glyco-DIBMA, was produced by partial amidation of DIBMA with the amino sugar N-methyl-d-glucosamine. Polymer-lipid particles produced with Glyco-DIBMA, named Glyco-DIBMALPs, exhibit improved structural properties and stability compared to those of SMALPs and DIBMALPs while retaining the capability of directly extracting membrane proteins from native membranes. Here, we characterize the structure and lipid composition of Glyco-DIBMALPs produced with either 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Glyco-DIBMALPs were also prepared with mixtures of either POPC or DMPC and cholesterol at different mole fractions. We estimated the lipid content in the Glyco-DIBMALPs and determined the particle structure and morphology by SAXS. We show that the Glyco-DIBMALPs are nanodisc-like particles whose size and shape depend on the polymer/lipid ratio. This is relevant for designing nanodisc particles with a tunable diameter according to the size of the membrane protein to be incorporated. We also report that the addition of >20 mol % cholesterol strongly perturbed the formation of Glyco-DIBMALPs. Altogether, we describe a detailed characterization of the Glyco-DIBMALPs, which provides relevant inputs for future application of these particles in the biophysical investigation of membrane proteins.
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Affiliation(s)
- Julia Lenz
- Molecular
Biophysics, Technische Universität
Kaiserslautern, Erwin-Schrödinger-Strasse
13, 67663 Kaiserslautern, Germany
| | | | - Sandro Keller
- Biophysics,
Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
- Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Alessandra Luchini
- European
Spallation Source - ERIC, Partikel Gatan, Lund 224
84, Sweden
- Department
of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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5
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Golub M, Moldenhauer M, Matsarskaia O, Martel A, Grudinin S, Soloviov D, Kuklin A, Maksimov EG, Friedrich T, Pieper J. Stages of OCP-FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 2: Small-Angle Neutron Scattering with Partial Deuteration. J Phys Chem B 2023; 127:1901-1913. [PMID: 36815674 DOI: 10.1021/acs.jpcb.2c07182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We used small-angle neutron scattering partially coupled with size-exclusion chromatography to unravel the solution structures of two variants of the Orange Carotenoid Protein (OCP) lacking the N-terminal extension (OCP-ΔNTE) and its complex formation with the Fluorescence Recovery Protein (FRP). The dark-adapted, orange form OCP-ΔNTEO is fully photoswitchable and preferentially binds the pigment echinenone. Its complex with FRP consists of a monomeric OCP component, which closely resembles the compact structure expected for the OCP ground state, OCPO. In contrast, the pink form OCP-ΔNTEP, preferentially binding the pigment canthaxanthin, is mostly nonswitchable. The pink OCP form appears to occur as a dimer and is characterized by a separation of the N- and C-terminal domains, with the canthaxanthin embedded only into the N-terminal domain. Therefore, OCP-ΔNTEP can be viewed as a prototypical model system for the active, spectrally red-shifted state of OCP, OCPR. The dimeric structure of OCP-ΔNTEP is retained in its complex with FRP. Small-angle neutron scattering using partially deuterated OCP-FRP complexes reveals that FRP undergoes significant structural changes upon complex formation with OCP. The observed structures are assigned to individual intermediates of the OCP photocycle in the presence of FRP.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Marcus Moldenhauer
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Olga Matsarskaia
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Sergei Grudinin
- Université Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000 Grenoble, France
| | - Dmytro Soloviov
- Faculty of Physics, Adam Mickiewicz University, ul. Wieniawskiego 1, 61-712 Poznan, Poland.,Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kirova 36a, 07270 Chornobyl, Ukraine
| | - Alexander Kuklin
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia.,Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - Eugene G Maksimov
- Department of Biophysics, M. V. Lomonosov Moscow State University, Vorob'jovy Gory 1-12, 119899 Moscow, Russia
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
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6
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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7
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Brady NG, Qian S, Nguyen J, O'Neill HM, Bruce BD. Small angle neutron scattering and lipidomic analysis of a native, trimeric PSI-SMALP from a thermophilic cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148596. [PMID: 35853496 PMCID: PMC10228149 DOI: 10.1016/j.bbabio.2022.148596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 06/05/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2023]
Abstract
The use of styrene-maleic acid copolymers (SMAs) to produce membrane protein-containing nanodiscs without the initial detergent isolation has gained significant interest over the last decade. We have previously shown that a Photosystem I SMALP from the thermophilic cyanobacterium, Thermosynechococcus elongatus (PSI-SMALP), has much more rapid energy transfer and charge separation in vitro than detergent isolated PSI complexes. In this study, we have utilized small-angle neutron scattering (SANS) to better understand the geometry of these SMALPs. These techniques allow us to investigate the size and shape of these particles in their fully solvated state. Further, the particle's proteolipid core and detergent shell or copolymer belt can be interrogated separately using contrast variation, a capability unique to SANS. Here we report the dimensions of the Thermosynechococcus elongatus PSI-SMALP containing a PSI trimer. At ~1.5 MDa, PSI-SMALP is the largest SMALP to be isolated; our lipidomic analysis indicates it contains ~1300 lipids/per trimeric particle, >40-fold more than the PSI-DDM particle and > 100 fold more than identified in the 1JB0 crystal structure. Interestingly, the lipid composition to the PSI trimer in the PSI-SMALP differs significantly from bulk thylakoid composition, being enriched ~50 % in the anionic sulfolipid, SQDG. Finally, utilizing the contrast match point for the SMA 1440 copolymer, we also can observe the ~1 nm SMA copolymer belt surrounding this SMALP for the first time, consistent with most models of SMA organization.
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Affiliation(s)
- Nathan G Brady
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jon Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Barry D Bruce
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA; Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
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8
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Ruskamo S, Raasakka A, Pedersen JS, Martel A, Škubník K, Darwish T, Porcar L, Kursula P. Human myelin proteolipid protein structure and lipid bilayer stacking. Cell Mol Life Sci 2022; 79:419. [PMID: 35829923 PMCID: PMC9279222 DOI: 10.1007/s00018-022-04428-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 11/03/2022]
Abstract
The myelin sheath is an essential, multilayered membrane structure that insulates axons, enabling the rapid transmission of nerve impulses. The tetraspan myelin proteolipid protein (PLP) is the most abundant protein of compact myelin in the central nervous system (CNS). The integral membrane protein PLP adheres myelin membranes together and enhances the compaction of myelin, having a fundamental role in myelin stability and axonal support. PLP is linked to severe CNS neuropathies, including inherited Pelizaeus-Merzbacher disease and spastic paraplegia type 2, as well as multiple sclerosis. Nevertheless, the structure, lipid interaction properties, and membrane organization mechanisms of PLP have remained unidentified. We expressed, purified, and structurally characterized human PLP and its shorter isoform DM20. Synchrotron radiation circular dichroism spectroscopy and small-angle X-ray and neutron scattering revealed a dimeric, α-helical conformation for both PLP and DM20 in detergent complexes, and pinpoint structural variations between the isoforms and their influence on protein function. In phosphatidylcholine membranes, reconstituted PLP and DM20 spontaneously induced formation of multilamellar myelin-like membrane assemblies. Cholesterol and sphingomyelin enhanced the membrane organization but were not crucial for membrane stacking. Electron cryomicroscopy, atomic force microscopy, and X-ray diffraction experiments for membrane-embedded PLP/DM20 illustrated effective membrane stacking and ordered organization of membrane assemblies with a repeat distance in line with CNS myelin. Our results shed light on the 3D structure of myelin PLP and DM20, their structure-function differences, as well as fundamental protein-lipid interplay in CNS compact myelin.
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Affiliation(s)
- Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Anne Martel
- Institut Laue-Langevin (ILL), Grenoble, France
| | - Karel Škubník
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tamim Darwish
- National Deuteration Facility, The Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, Sydney, NSW, 2232, Australia
| | | | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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9
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Larsen A, John L, Sansom M, Corey R. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us? Biosci Rep 2022; 42:BSR20211406. [PMID: 35297484 PMCID: PMC9008707 DOI: 10.1042/bsr20211406] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
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Affiliation(s)
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford, U.K
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10
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Golub M, Gätcke J, Subramanian S, Kölsch A, Darwish T, Howard JK, Feoktystov A, Matsarskaia O, Martel A, Porcar L, Zouni A, Pieper J. "Invisible" Detergents Enable a Reliable Determination of Solution Structures of Native Photosystems by Small-Angle Neutron Scattering. J Phys Chem B 2022; 126:2824-2833. [PMID: 35384657 DOI: 10.1021/acs.jpcb.2c01591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photosystems I (PSI) and II (PSII) are pigment-protein complexes capable of performing the light-induced charge separation necessary to convert solar energy into a biochemically storable form, an essential step in photosynthesis. Small-angle neutron scattering (SANS) is unique in providing structural information on PSI and PSII in solution under nearly physiological conditions without the need for crystallization or temperature decrease. We show that the reliability of the solution structure critically depends on proper contrast matching of the detergent belt surrounding the protein. Especially, specifically deuterated ("invisible") detergents are shown to be properly matched out in SANS experiments by a direct, quantitative comparison with conventional matching strategies. In contrast, protonated detergents necessarily exhibit incomplete matching so that related SANS results systematically overestimate the size of the membrane protein under study. While the solution structures obtained are close to corresponding high-resolution structures, we show that temperature and solution state lead to individual structural differences compared with high-resolution structures. We attribute these differences to the presence of a manifold of conformational substates accessible by protein dynamics under physiological conditions.
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Affiliation(s)
- M Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | - J Gätcke
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - S Subramanian
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - A Kölsch
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - T Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - J K Howard
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - A Feoktystov
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748 Garching, Germany
| | - O Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs CS 20156, 38042 Grenoble Cedex 9, France
| | - A Martel
- Institut Laue-Langevin, 71 Avenue des Martyrs CS 20156, 38042 Grenoble Cedex 9, France
| | - L Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs CS 20156, 38042 Grenoble Cedex 9, France
| | - A Zouni
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - J Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
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11
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Golub M, Lokstein H, Soloviov D, Kuklin A, Wieland DCF, Pieper J. Light-Harvesting Complex II Adopts Different Quaternary Structures in Solution as Observed Using Small-Angle Scattering. J Phys Chem Lett 2022; 13:1258-1265. [PMID: 35089716 DOI: 10.1021/acs.jpclett.1c03614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The high-resolution crystal structure of the trimeric major light-harvesting complex of photosystem II (LHCII) is often perceived as the basis for understanding its light-harvesting and photoprotective functions. However, the LHCII solution structure and its oligomerization or aggregation state may generally differ from the crystal structure and, moreover, also depend on its functional state. In this regard, small-angle scattering experiments provide the missing link by offering structural information in aqueous solution at physiological temperatures. Herein, we use small-angle scattering to investigate the solution structures of two different preparations of solubilized LHCII employing the nonionic detergents n-octyl-β-d-glucoside (OG) and n-dodecyl-β-D-maltoside (β-DM). The data reveal that the LHCII-OG complex is equivalent to the trimeric crystal structure. Remarkably, however, we observe─for the first time─a stable oligomer composed of three LHCII trimers in the case of the LHCII-β-DM preparation, implying additional pigment-pigment interactions. The latter complex is assumed to mimic trimer-trimer interactions which play an important role in the context of photoprotective nonphotochemical quenching.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 121 16 Prague, Czech Republic
| | - Dmytro Soloviov
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia
- Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
- Institute for Safety Problems of Nuclear Power Plants NAS of Ukraine, Lysogirska str. 12, 03028 Kyiv, Ukraine
| | - Alexander Kuklin
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia
- Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - D C Florian Wieland
- Helmholtz Zentrum Geesthacht, Institute for Materials Research, Department for Metallic Biomaterials, 21502 Geesthacht, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
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12
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Johansen NT, Bonaccorsi M, Bengtsen T, Larsen AH, Tidemand FG, Pedersen MC, Huda P, Berndtsson J, Darwish T, Yepuri NR, Martel A, Pomorski TG, Bertarello A, Sansom MS, Rapp M, Crehuet R, Schubeis T, Lindorff-Larsen K, Pintacuda G, Arleth L. Mg 2+-dependent conformational equilibria in CorA and an integrated view on transport regulation. eLife 2022; 11:71887. [PMID: 35129435 PMCID: PMC8865849 DOI: 10.7554/elife.71887] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.
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Affiliation(s)
| | - Marta Bonaccorsi
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Tone Bengtsen
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Andreas Haahr Larsen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen E, Denmark
| | | | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen E, Denmark
| | - Pie Huda
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Australia
| | - Jens Berndtsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Tamim Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, Australia
| | - Nageshewar Rao Yepuri
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, Australia
| | | | - Thomas Günther Pomorski
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Andrea Bertarello
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Mark Sp Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mikaela Rapp
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ramon Crehuet
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Tobias Schubeis
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | | | - Guido Pintacuda
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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13
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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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14
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Duff AP, Cagnes M, Darwish TA, Krause-Heuer AM, Moir M, Recsei C, Rekas A, Russell RA, Wilde KL, Yepuri NR. Deuteration for biological SANS: Case studies, success and challenges in chemistry and biology. Methods Enzymol 2022; 677:85-126. [DOI: 10.1016/bs.mie.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Cisse A, Schachner-Nedherer AL, Appel M, Beck C, Ollivier J, Leitinger G, Prassl R, Kornmueller K, Peters J. Dynamics of Apolipoprotein B-100 in Interaction with Detergent Probed by Incoherent Neutron Scattering. J Phys Chem Lett 2021; 12:12402-12410. [PMID: 34939807 DOI: 10.1021/acs.jpclett.1c03141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Apolipoprotein B-100 (apo B-100) is the protein moiety of both low- and very-low-density lipoproteins, whose role is crucial to cholesterol and triglyceride transport. Aiming at the molecular dynamics' details of apo B-100, scarcely studied, we performed elastic and quasi-elastic incoherent neutron scattering (EINS, QENS) experiments combining different instruments and time scales. Similar to classical membrane proteins, the solubilization results in remaining detergent, here Nonidet P-40 (NP40). Therefore, we propose a framework for QENS studies of protein-detergent complexes, with the introduction of a combined model, including the experimental apo B-100/NP40 ratio. Relying on the simultaneous analysis of all QENS amplitudes, this approach is sensitive enough to separate both contributions. Its application identified two points: (i) apo B-100 slow dynamics and (ii) the acceleration of NP40 dynamics in the presence of apo B-100. Direct translation of the exposed methodology now makes the investigation of more membrane proteins by neutron spectroscopy achievable.
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Affiliation(s)
- Aline Cisse
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
| | | | | | - Christian Beck
- Institut Laue Langevin, 38042 Grenoble, France
- Institut of Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | | | | | | | | | - Judith Peters
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
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16
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Lycksell M, Rovšnik U, Bergh C, Johansen NT, Martel A, Porcar L, Arleth L, Howard RJ, Lindahl E. Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering. Proc Natl Acad Sci U S A 2021; 118:e2108006118. [PMID: 34504004 PMCID: PMC8449418 DOI: 10.1073/pnas.2108006118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 02/03/2023] Open
Abstract
Pentameric ligand-gated ion channels undergo subtle conformational cycling to control electrochemical signal transduction in many kingdoms of life. Several crystal structures have now been reported in this family, but the functional relevance of such models remains unclear. Here, we used small-angle neutron scattering (SANS) to probe ambient solution-phase properties of the pH-gated bacterial ion channel GLIC under resting and activating conditions. Data collection was optimized by inline paused-flow size-exclusion chromatography, and exchanging into deuterated detergent to hide the micelle contribution. Resting-state GLIC was the best-fit crystal structure to SANS curves, with no evidence for divergent mechanisms. Moreover, enhanced-sampling molecular-dynamics simulations enabled differential modeling in resting versus activating conditions, with the latter corresponding to an intermediate ensemble of both the extracellular and transmembrane domains. This work demonstrates state-dependent changes in a pentameric ion channel by SANS, an increasingly accessible method for macromolecular characterization with the coming generation of neutron sources.
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Affiliation(s)
- Marie Lycksell
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Urška Rovšnik
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Cathrine Bergh
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Nicolai T Johansen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anne Martel
- Institut Laue-Langevin, 38042 Grenoble, France
| | | | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden;
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
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17
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Preparation of a Deuterated Membrane Protein for Small-Angle Neutron Scattering. Methods Mol Biol 2021. [PMID: 33877630 DOI: 10.1007/978-1-0716-1394-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter outlines a protocol developed to prepare a purified deuterated membrane protein for a small-angle neutron scattering (SANS) experiment. SANS is a noninvasive technique well suited to studying membrane protein solution structures, and deuteration enhances the signal from the protein over the background (Breyton et al., Eur Phys J E Soft Matter 36 (7):71, 2013; Garg et al., Biophys J 101 (2):370-377, 2011). We present our workflow: transformation of our plasmid into E. coli, cell growth and expression of our deuterated protein, membrane isolation, detergent solubilization, protein purification, purity assessment, and final preparation for SANS.
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18
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Larsson J, Leung AE, Lang C, Wu B, Wahlgren M, Nylander T, Ulvenlund S, Sanchez-Fernandez A. Tail unsaturation tailors the thermodynamics and rheology of a self-assembled sugar-based surfactant. J Colloid Interface Sci 2021; 585:178-183. [DOI: 10.1016/j.jcis.2020.11.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022]
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19
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Insights into Solution Structures of Photosynthetic Protein Complexes from Small-Angle Scattering Methods. CRYSTALS 2021. [DOI: 10.3390/cryst11020203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
High-resolution structures of photosynthetic pigment–protein complexes are often determined using crystallography or cryo-electron microscopy (cryo-EM), which are restricted to the use of protein crystals or to low temperatures, respectively. However, functional studies and biotechnological applications of photosystems necessitate the use of proteins isolated in aqueous solution, so that the relevance of high-resolution structures has to be independently verified. In this regard, small-angle neutron and X-ray scattering (SANS and SAXS, respectively) can serve as the missing link because of their capability to provide structural information for proteins in aqueous solution at physiological temperatures. In the present review, we discuss the principles and prototypical applications of SANS and SAXS using the photosynthetic pigment–protein complexes phycocyanin (PC) and Photosystem I (PSI) as model systems for a water-soluble and for a membrane protein, respectively. For example, the solution structure of PSI was studied using SAXS and SANS with contrast matching. A Guinier analysis reveals that PSI in solution is virtually free of aggregation and characterized by a radius of gyration of about 75 Å. The latter value is about 10% larger than expected from the crystal structure. This is corroborated by an ab initio structure reconstitution, which also shows a slight expansion of Photosystem I in buffer solution at room temperature. In part, this may be due to conformational states accessible by thermally activated protein dynamics in solution at physiological temperatures. The size of the detergent belt is derived by comparison with SANS measurements without detergent match, revealing a monolayer of detergent molecules under proper solubilization conditions.
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20
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Sakakibara Y, Osada K, Uraki Y, Ubukata M, Shigetomi K. Direct deuteration of hinokitiol and its mechanistic study. Biosci Biotechnol Biochem 2021; 85:215-222. [PMID: 33590006 DOI: 10.1093/bbb/zbaa031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/05/2020] [Indexed: 11/14/2022]
Abstract
Hinokitiol has a broad antibacterial activity against bacteria and fungi. While its biosynthetic pathway has been intensively studied, its dynamics in natural environments, such as biodegradation pathway, remain unclear. In this study, the authors report a direct deuterium labeling of hinokitiol as a traceable molecular probe to serve those studies. Hinokitiol was subjected to the H2-Pd/C-D2O conditions and deuterated hinokitiol was obtained with excellent deuteration efficiencies and in moderate yield. The 1H and 2H NMR spectra indicated that all ring- and aliphatic hydrogens except that on C-6 were substituted by deuterium. According to the substrate scope and computational chemistry, deuteration on tropolone ring was suggested to proceed via D+-mediated process, and which was supported by the results of the experiment with trifluoroacetic acid and Pd(TPP)4. On the other hand, the deuteration on aliphatic group was predicted to be catalyzed by Pd(II) species.
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Affiliation(s)
| | - Kota Osada
- School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yasumitsu Uraki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Makoto Ubukata
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kengo Shigetomi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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21
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Conn CE, de Campo L, Whitten AE, Garvey CJ, Krause-Heuer AM, van 't Hag L. Membrane Protein Structures in Lipid Bilayers; Small-Angle Neutron Scattering With Contrast-Matched Bicontinuous Cubic Phases. Front Chem 2021; 8:619470. [PMID: 33644002 PMCID: PMC7903247 DOI: 10.3389/fchem.2020.619470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/02/2020] [Indexed: 01/12/2023] Open
Abstract
This perspective describes advances in determining membrane protein structures in lipid bilayers using small-angle neutron scattering (SANS). Differentially labeled detergents with a homogeneous scattering length density facilitate contrast matching of detergent micelles; this has previously been used successfully to obtain the structures of membrane proteins. However, detergent micelles do not mimic the lipid bilayer environment of the cell membrane in vivo. Deuterated vesicles can be used to obtain the radius of gyration of membrane proteins, but protein-protein interference effects within the vesicles severely limits this method such that the protein structure cannot be modeled. We show herein that different membrane protein conformations can be distinguished within the lipid bilayer of the bicontinuous cubic phase using contrast-matching. Time-resolved studies performed using SANS illustrate the complex phase behavior in lyotropic liquid crystalline systems and emphasize the importance of this development. We believe that studying membrane protein structures and phase behavior in contrast-matched lipid bilayers will advance both biological and pharmaceutical applications of membrane-associated proteins, biosensors and food science.
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Affiliation(s)
- Charlotte E. Conn
- School of Science, STEM College, RMIT University, Melbourne, VIC, Australia
| | - Liliana de Campo
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Andrew E. Whitten
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Christopher J. Garvey
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
- Lund Institute for Advanced Neutron and X-Ray Science, Lund, Sweden
- Biolfim-Research Center for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | - Anwen M. Krause-Heuer
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Leonie van 't Hag
- Department of Chemical Engineering, Monash University, Clayton, VIC, Australia
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22
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Fischer J, Radulescu A, Falus P, Richter D, Biehl R. Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model. J Phys Chem B 2021; 125:780-788. [PMID: 33470118 DOI: 10.1021/acs.jpcb.0c09476] [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
Disordered regions as found in intrinsically disordered proteins (IDP) or during protein folding define response time to stimuli and protein folding times. Neutron spin-echo spectroscopy is a powerful tool to directly access the collective motions of the unfolded chain to enlighten the physical origin of basic conformational relaxation. During the thermal unfolding of native ribonuclease A, we examine the structure and dynamics of the disordered state within a two-state transition model using polymer models, including internal friction, to describe the chain dynamics. The presence of four disulfide bonds alters the disordered configuration to a more compact configuration compared to a Gaussian chain that is defined by the additional links, as demonstrated by coarse-grained simulation. The dynamics of the disordered chain is described by Zimm dynamics with internal friction (ZIF) between neighboring amino acids. Relaxation times are dominated by mode-independent internal friction. Internal friction relaxation times show an Arrhenius-like behavior with an activation energy of 33 kJ/mol. The Zimm dynamics is dominated by internal friction and suggest that the characteristic motions correspond to overdamped elastic modes similar to the motions observed for folded proteins but within a pool of disordered configurations spanning the configurational space. For IDP, internal friction dominates while solvent friction and hydrodynamic interactions are smaller corrections.
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Affiliation(s)
- Jennifer Fischer
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, 85748 Garching, Germany
| | - Peter Falus
- Institut Laue-Langevin (ILL), 71 rue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Dieter Richter
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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23
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Orioli S, Henning Hansen CG, Arleth L. Ab initio determination of the shape of membrane proteins in a nanodisc. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:176-193. [DOI: 10.1107/s2059798320015405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/20/2020] [Indexed: 11/10/2022]
Abstract
New software, called Marbles, is introduced that employs SAXS intensities to predict the shape of membrane proteins embedded into membrane nanodiscs. To gain computational speed and efficient convergence, the strategy is based on a hybrid approach that allows one to account for the contribution of the nanodisc to the SAXS intensity through a semi-analytical model, while the embedded membrane protein is treated as a set of beads, similarly to as in well known ab initio methods. The reliability and flexibility of this approach is proved by benchmarking the code, implemented in C++ with a Python interface, on a toy model and two proteins with very different geometry and size.
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24
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Larsson J, Sanchez-Fernandez A, Leung AE, Schweins R, Wu B, Nylander T, Ulvenlund S, Wahlgren M. Molecular structure of maltoside surfactants controls micelle formation and rheological behavior. J Colloid Interface Sci 2021; 581:895-904. [DOI: 10.1016/j.jcis.2020.08.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
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25
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Golub M, Hussein R, Ibrahim M, Hecht M, Wieland DCF, Martel A, Machado B, Zouni A, Pieper J. Solution Structure of the Detergent-Photosystem II Core Complex Investigated by Small-Angle Scattering Techniques. J Phys Chem B 2020; 124:8583-8592. [PMID: 32816484 DOI: 10.1021/acs.jpcb.0c07169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Albeit achieving the X-ray diffraction structure of dimeric photosystem II core complexes (dPSIIcc) at the atomic resolution, the nature of the detergent belt surrounding dPSIIcc remains ambiguous. Therefore, the solution structure of the whole detergent-protein complex of dPSIIcc of Thermosynechococcus elongatus (T. elongatus) solubilized in n-dodecyl-ß-d-maltoside (ßDM) was investigated by a combination of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) with contrast variation. First, the structure of dPSIIcc was studied separately in SANS experiments using a contrast of 5% D2O. Guinier analysis reveals that the dPSIIcc solution is virtually free of aggregation in the studied concentration range of 2-10 mg/mL dPSIIcc, and characterized by a radius of gyration of 62 Å. A structure reconstitution shows that dPSIIcc in buffer solution widely retains the crystal structure reported by X-ray free electron laser studies at room temperature with a slight expansion of the entire protein. Additional SANS experiments on dPSIIcc samples in a buffer solution containing 75% D2O provide information about the size and shape of the whole detergent-dPSIIcc. The maximum position of P(r) function increases to 68 Å, i.e., it is about 6 Å larger than that of dPSIIcc only, thus indicating the presence of an additional structure. Thus, it can be concluded that dPSIIcc is surrounded by a monomolecular belt of detergent molecules under appropriate solubilization conditions. The homogeneity of the ßDM-dPSIIcc solutions was also verified using dynamic light scattering. Complementary SAXS experiments indicate the presence of unbound detergent micelles by a separate peak consistent with a spherical shape possessing a radius of about 40 Å. The latter structure also contributes to the SANS data but rather broadens the SANS curve artificially. Without the simultaneous inspection of SANS and SAXS data, this effect may lead to an apparent underestimation of the size of the PS II-detergent complex. The formation of larger unbound detergent aggregates in solution prior to crystallization may have a significant effect on the crystal formation or quality of the ßDM-dPSIIcc.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | - Rana Hussein
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115 Berlin, Germany
| | - Mohamed Ibrahim
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115 Berlin, Germany
| | - Max Hecht
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | | | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Barbara Machado
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Athina Zouni
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
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26
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Sanchez-Fernandez A, Diehl C, Houston JE, Leung AE, Tellam JP, Rogers SE, Prevost S, Ulvenlund S, Sjögren H, Wahlgren M. An integrative toolbox to unlock the structure and dynamics of protein-surfactant complexes. NANOSCALE ADVANCES 2020; 2:4011-4023. [PMID: 36132802 PMCID: PMC9417085 DOI: 10.1039/d0na00194e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/11/2020] [Indexed: 05/06/2023]
Abstract
The interactions between protein and surfactants play an important role in the stability and performance of formulated products. Due to the high complexity of such interactions, multi-technique approaches are required to study these systems. Here, an integrative approach is used to investigate the various interactions in a model system composed of human growth hormone and sodium dodecyl sulfate. Contrast variation small-angle neutron scattering was used to obtain information on the structure of the protein, surfactant aggregates and surfactant-protein complexes. 1H and 1H-13C HSQC nuclear magnetic resonance spectroscopy was employed to probe the local structure and dynamics of specific amino acids upon surfactant addition. Through the combination of these advanced methods with fluorescence spectroscopy, circular dichroism and isothermal titration calorimetry, it was possible to identify the interaction mechanisms between the surfactant and the protein in the pre- and post-micellar regimes, and interconnect the results from different techniques. As such, the protein was revealed to evolve from a partially unfolded conformation at low SDS concentration to a molten globule at intermediate concentrations, where the protein conformation and local dynamics of hydrophobic amino acids are partially affected compared to the native state. At higher surfactant concentrations the local structure of the protein appears disrupted, and a decorated micelle structure is observed, where the protein is wrapped around a surfactant assembly. Importantly, this integrative approach allows for the identification of the characteristic fingerprints of complex transitions as seen by each technique, and establishes a methodology for an in-detail study of surfactant-protein systems.
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Affiliation(s)
| | - Carl Diehl
- SARomics Biostructures AB Medicon Village, Scheelevägen 2 223 81 Lund Sweden
| | | | - Anna E Leung
- European Spallation Source Box 176 221 00 Lund Sweden
| | - James P Tellam
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory Didcot OX11 0QX UK
| | - Sarah E Rogers
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory Didcot OX11 0QX UK
| | - Sylvain Prevost
- Institut Laue-Langevin 71 Avenue des Martyrs 38000 Grenoble France
| | - Stefan Ulvenlund
- Food Technology, Engineering and Nutrition, Lund University Box 124 221 00 Lund Sweden
- EnzaBiotech AB Scheelevägen 22 223 63 Lund Sweden
| | - Helen Sjögren
- Ferring Pharmaceuticals A/S Kay Fiskers Plads 11 2300 Copenhagen S Denmark
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Lund University Box 124 221 00 Lund Sweden
- EnzaBiotech AB Scheelevägen 22 223 63 Lund Sweden
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27
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Andersson J, Bilotto P, Mears LLE, Fossati S, Ramach U, Köper I, Valtiner M, Knoll W. Solid-supported lipid bilayers - A versatile tool for the structural and functional characterization of membrane proteins. Methods 2020; 180:56-68. [PMID: 32920130 DOI: 10.1016/j.ymeth.2020.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The cellular membrane is central to the development of single-and multicellular life, as it separates the delicate cellular interior from the hostile environment. It exerts tight control over entry and exit of substances, is responsible for signaling with other cells in multicellular organisms and prevents pathogens from entering the cell. In the case of bacteria and viruses, the cellular membrane also hosts the proteins enabling invasion of the host organism. In a very real sense therefore, the cellular membrane is central to all life. The study of the cell membrane and membrane proteins in particular has therefore attracted significant attention. Due to the enormous variety of tasks performed by the membrane, it is a highly complex and challenging structure to study. Ideally, membrane components would be studied in isolation from this environment, but unlike water soluble proteins, the amphiphilic environment provided by the cellular membrane is key to the structure and function of the cell membrane. Therefore, model membranes have been developed to provide an environment in which a membrane protein can be studied. This review presents a set of tools that enable the comprehensive characterization of membrane proteins: electrochemical tools, surface plasmon resonance, neutron scattering, the surface forces apparatus and atomic force microscopy are discussed, with a particular focus on experimental technique and data evaluation.
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Affiliation(s)
| | - Pierluigi Bilotto
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Laura L E Mears
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Stefan Fossati
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Ulrich Ramach
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Ingo Köper
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Markus Valtiner
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
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28
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Larsen AH, Pedersen JS, Arleth L. Assessment of structure factors for analysis of small-angle scattering data from desired or undesired aggregates. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720006500] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aggregation processes are central features of many systems ranging from colloids and polymers to inorganic nanoparticles and biological systems. Some aggregated structures are controlled and desirable, e.g. in the design of size-controlled clustered nanoparticles or some protein-based drugs. In other cases, the aggregates are undesirable, e.g. protein aggregation involved in neurodegenerative diseases or in vitro studies of single protein structures. In either case, experimental and analytical tools are needed to cast light on the aggregation processes. Aggregation processes can be studied with small-angle scattering, but analytical descriptions of the aggregates are needed for detailed structural analysis. This paper presents a list of useful small-angle scattering structure factors, including a novel structure factor for a spherical cluster with local correlations between the constituent particles. Several of the structure factors were renormalized to get correct limit values in both the high-q and low-q limit, where q is the modulus of the scattering vector. The structure factors were critically evaluated against simulated data. Structure factors describing fractal aggregates provided approximate descriptions of the simulated data for all tested structures, from linear to globular aggregates. The addition of a correlation hole for the constituent particles in the fractal structure factors significantly improved the fits in all cases. Linear aggregates were best described by a linear structure factor and globular aggregates by the newly derived spherical cluster structure factor. As a central point, it is shown that the structure factors could be used to take aggregation contributions into account for samples of monomeric protein containing a minor fraction of aggregated protein. After applying structure factors in the analysis, the correct structure and oligomeric state of the protein were determined. Thus, by careful use of the presented structure factors, important structural information can be retrieved from small-angle scattering data, both when aggregates are desired and when they are undesired.
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29
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Larsen AH, Wang Y, Bottaro S, Grudinin S, Arleth L, Lindorff-Larsen K. Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. PLoS Comput Biol 2020; 16:e1007870. [PMID: 32339173 PMCID: PMC7205321 DOI: 10.1371/journal.pcbi.1007870] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/07/2020] [Accepted: 04/13/2020] [Indexed: 11/18/2022] Open
Abstract
Many proteins contain multiple folded domains separated by flexible linkers, and the ability to describe the structure and conformational heterogeneity of such flexible systems pushes the limits of structural biology. Using the three-domain protein TIA-1 as an example, we here combine coarse-grained molecular dynamics simulations with previously measured small-angle scattering data to study the conformation of TIA-1 in solution. We show that while the coarse-grained potential (Martini) in itself leads to too compact conformations, increasing the strength of protein-water interactions results in ensembles that are in very good agreement with experiments. We show how these ensembles can be refined further using a Bayesian/Maximum Entropy approach, and examine the robustness to errors in the energy function. In particular we find that as long as the initial simulation is relatively good, reweighting against experiments is very robust. We also study the relative information in X-ray and neutron scattering experiments and find that refining against the SAXS experiments leads to improvement in the SANS data. Our results suggest a general strategy for studying the conformation of multi-domain proteins in solution that combines coarse-grained simulations with small-angle X-ray scattering data that are generally most easy to obtain. These results may in turn be used to design further small-angle neutron scattering experiments that exploit contrast variation through 1H/2H isotope substitutions.
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Affiliation(s)
- Andreas Haahr Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- X-ray and Neutron Science, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sergei Grudinin
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France
| | - Lise Arleth
- X-ray and Neutron Science, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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30
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Ravishankar H, Pedersen MN, Eklund M, Sitsel A, Li C, Duelli A, Levantino M, Wulff M, Barth A, Olesen C, Nissen P, Andersson M. Tracking Ca 2+ ATPase intermediates in real time by x-ray solution scattering. SCIENCE ADVANCES 2020; 6:eaaz0981. [PMID: 32219166 PMCID: PMC7083613 DOI: 10.1126/sciadv.aaz0981] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/23/2019] [Indexed: 05/14/2023]
Abstract
Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2]E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release of caged ATP, a 1.5-ms intermediate was formed that showed closure of the cytoplasmic domains typical of E1 states with bound Ca2+ and ATP. A subsequent 13-ms transient state showed a previously unresolved actuator (A) domain arrangement that exposed the ADP-binding site after phosphorylation. Hence, the obtained TR-XSS models determine the relative timing of so-far elusive domain rearrangements in a native environment.
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Affiliation(s)
- Harsha Ravishankar
- Department of Chemistry, Umeå University. Linnaeus Väg 10, 901 87 Umeå, Sweden
| | | | | | - Aljona Sitsel
- DANDRITE–Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University. Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Chenge Li
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius Väg 16C, 106 91 Stockholm, Sweden
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen. Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Matteo Levantino
- European Synchrotron Radiation Facility, Grenoble, Cedex 38043, BP 220, France
- Department of Physics and Chemistry, University of Palermo, Viale delle Scienze -Ed 18, 90128 Palermo, Italy
| | - Michael Wulff
- European Synchrotron Radiation Facility, Grenoble, Cedex 38043, BP 220, France
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius Väg 16C, 106 91 Stockholm, Sweden
| | - Claus Olesen
- Department of Biomedicine, Aarhus University, Vest Ole Worms Allé 3, 113 8000 Aarhus C, Denmark
| | - Poul Nissen
- DANDRITE–Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University. Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Magnus Andersson
- Department of Chemistry, Umeå University. Linnaeus Väg 10, 901 87 Umeå, Sweden
- Corresponding author.
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31
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Structural dynamics of P-type ATPase ion pumps. Biochem Soc Trans 2020; 47:1247-1257. [PMID: 31671180 DOI: 10.1042/bst20190124] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 02/04/2023]
Abstract
P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.
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32
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Pedersen MC, Wang Y, Tidemand FG, Martel A, Lindorff-Larsen K, Arleth L. PSX, Protein–Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719012469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Recent developments in neutron scattering instrumentation and sample handling have enabled studies of more complex biological samples and measurements at shorter exposure times. The experiments are typically conducted in D2O-based buffers to emphasize or diminish scattering from a particular component or to minimize background noise in the experiment. To extract most information from such experiments it is thus desirable to determine accurate estimates of how and when closely bound hydrogen atoms from the biomolecule exchange with the deuterium in the solvent. This article introduces and documents software, PSX, for exploring the effect of hydrogen–deuterium exchange for proteins solubilized in D2O as well as the underlying bioinformatical models. The software aims to be generally applicable for any atomistic structure of a protein and its surrounding environment, and thus captures effects of both heterogenous exchange rates throughout the protein structure and varying the experimental conditions such as pH and temperature. The paper concludes with examples of applications and estimates of the effect in typical scenarios emerging in small-angle neutron scattering on biological macromolecules in solution. The analysis presented here suggests that the common assumption of 90% exchange is in many cases an overestimate with the rapid sample handling systems currently available, which leads to fitting and calibration issues when analysing the data. Source code for the presented software is available from an online repository in which it is published under version 3 of the GNU publishing licence.
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33
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Structure and Dynamics of the Central Lipid Pool and Proteins of the Bacterial Holo-Translocon. Biophys J 2019; 116:1931-1940. [PMID: 31053257 PMCID: PMC6531790 DOI: 10.1016/j.bpj.2019.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/11/2019] [Accepted: 04/02/2019] [Indexed: 01/01/2023] Open
Abstract
The bacterial Sec translocon, SecYEG, associates with accessory proteins YidC and the SecDF-YajC subcomplex to form the bacterial holo-translocon (HTL). The HTL is a dynamic and flexible protein transport machine capable of coordinating protein secretion across the membrane and efficient lateral insertion of nascent membrane proteins. It has been hypothesized that a central lipid core facilitates the controlled passage of membrane proteins into the bilayer, ensuring the efficient formation of their native state. By performing small-angle neutron scattering on protein solubilized in “match-out” deuterated detergent, we have been able to interrogate a “naked” HTL complex, with the scattering contribution of the surrounding detergent micelle rendered invisible. Such an approach has allowed the confirmation of a lipid core within the HTL, which accommodates between 8 and 29 lipids. Coarse-grained molecular dynamics simulations of the HTL also demonstrate a dynamic, central pool of lipids. An opening at this lipid-rich region between YidC and the SecY lateral gate may provide an exit gateway for newly synthesized, correctly oriented, membrane protein helices, or even small bundles of helices, to emerge from the HTL.
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34
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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35
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Bucciarelli S, Midtgaard SR, Nors Pedersen M, Skou S, Arleth L, Vestergaard B. Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument. J Appl Crystallogr 2018; 51:1623-1632. [PMID: 30546289 PMCID: PMC6276278 DOI: 10.1107/s1600576718014462] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/13/2018] [Indexed: 11/16/2022] Open
Abstract
Coupling of size-exclusion chromatography with biological solution small-angle X-ray scattering (SEC-SAXS) on dedicated synchrotron beamlines enables structural analysis of challenging samples such as labile proteins and low-affinity complexes. For this reason, the approach has gained increased popularity during the past decade. Transportation of perishable samples to synchrotrons might, however, compromise the experiments, and the limited availability of synchrotron beamtime renders iterative sample optimization tedious and lengthy. Here, the successful setup of laboratory-based SEC-SAXS is described in a proof-of-concept study. It is demonstrated that sufficient quality data can be obtained on a laboratory instrument with small sample consumption, comparable to typical synchrotron SEC-SAXS demands. UV/vis measurements directly on the SAXS exposure cell ensure accurate concentration determination, crucial for direct molecular weight determination from the scattering data. The absence of radiation damage implies that the sample can be fractionated and subjected to complementary analysis available at the home institution after SEC-SAXS. Laboratory-based SEC-SAXS opens the field for analysis of biological samples at the home institution, thus increasing productivity of biostructural research. It may further ensure that synchrotron beamtime is used primarily for the most suitable and optimized samples.
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Affiliation(s)
- Saskia Bucciarelli
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Søren Roi Midtgaard
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Martin Nors Pedersen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | | | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
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36
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Johansen NT, Pedersen MC, Porcar L, Martel A, Arleth L. Introducing SEC–SANS for studies of complex self-organized biological systems. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1178-1191. [DOI: 10.1107/s2059798318007180] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/14/2018] [Indexed: 01/11/2023]
Abstract
Small-angle neutron scattering (SANS) is maturing as a method for studying complex biological structures. Owing to the intrinsic ability of the technique to discern between 1H- and 2H-labelled particles, it is especially useful for contrast-variation studies of biological systems containing multiple components. SANS is complementary to small-angle X-ray scattering (SAXS), in which similar contrast variation is not easily performed but in which data with superior counting statistics are more easily obtained. Obtaining small-angle scattering (SAS) data on monodisperse complex biological structures is often challenging owing to sample degradation and/or aggregation. This problem is enhanced in the D2O-based buffers that are typically used in SANS. In SAXS, such problems are solved using an online size-exclusion chromatography (SEC) setup. In the present work, the feasibility of SEC–SANS was investigated using a series of complex and difficult samples of membrane proteins embedded in nanodisc particles that consist of both phospholipid and protein components. It is demonstrated that SEC–SANS provides data of sufficient signal-to-noise ratio for these systems, while at the same time circumventing aggregation. By combining SEC–SANS and SEC–SAXS data, an optimized basis for refining structural models of the investigated structures is obtained.
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Larsen AH, Dorosz J, Thorsen TS, Johansen NT, Darwish T, Midtgaard SR, Arleth L, Kastrup JS. Small-angle neutron scattering studies on the AMPA receptor GluA2 in the resting, AMPA-bound and GYKI-53655-bound states. IUCRJ 2018; 5:780-793. [PMID: 30443361 PMCID: PMC6211538 DOI: 10.1107/s2052252518012186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/28/2018] [Indexed: 06/09/2023]
Abstract
The AMPA receptor GluA2 belongs to the family of ionotropic glutamate receptors, which are responsible for most of the fast excitatory neuronal signalling in the central nervous system. These receptors are important for memory and learning, but have also been associated with brain diseases such as Alzheimer's disease and epilepsy. Today, one drug is on the market for the treatment of epilepsy targeting AMPA receptors, i.e. a negative allosteric modulator of these receptors. Recently, crystal structures and cryo-electron microscopy (cryo-EM) structures of full-length GluA2 in the resting (apo), activated and desensitized states have been reported. Here, solution structures of full-length GluA2 are reported using small-angle neutron scattering (SANS) with a novel, fully matched-out detergent. The GluA2 solution structure was investigated in the resting state as well as in the presence of AMPA and of the negative allosteric modulator GYKI-53655. In solution and at neutral pH, the SANS data clearly indicate that GluA2 is in a compact form in the resting state. The solution structure resembles the crystal structure of GluA2 in the resting state, with an estimated maximum distance (D max) of 179 ± 11 Å and a radius of gyration (R g) of 61.9 ± 0.4 Å. An ab initio model of GluA2 in solution generated using DAMMIF clearly showed the individual domains, i.e. the extracellular N-terminal domains and ligand-binding domains as well as the transmembrane domain. Solution structures revealed that GluA2 remained in a compact form in the presence of AMPA or GYKI-53655. At acidic pH only, GluA2 in the presence of AMPA adopted a more open conformation of the extracellular part (estimated D max of 189 ± 5 Å and R g of 65.2 ± 0.5 Å), resembling the most open, desensitized class 3 cryo-EM structure of GluA2 in the presence of quisqualate. In conclusion, this methodological study may serve as an example for future SANS studies on membrane proteins.
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Affiliation(s)
- Andreas Haahr Larsen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thor Seneca Thorsen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Nicolai Tidemand Johansen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Tamim Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Australia
| | - Søren Roi Midtgaard
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Oliver RC, Naing SH, Weiss KL, Pingali SV, Lieberman RL, Urban VS. Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling. J Vis Exp 2018:57901. [PMID: 30394373 PMCID: PMC6235576 DOI: 10.3791/57901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The biological small-angle neutron scattering instrument at the High-Flux Isotope Reactor of Oak Ridge National Laboratory is dedicated to the investigation of biological materials, biofuel processing, and bio-inspired materials covering nanometer to micrometer length scales. The methods presented here for investigating physical properties (i.e., size and shape) of membrane proteins (here, MmIAP, an intramembrane aspartyl protease from Methanoculleus marisnigri) in solutions of micelle-forming detergents are well-suited for this small-angle neutron scattering instrument, among others. Other biophysical characterization techniques are hindered by their inability to address the detergent contributions in a protein-detergent complex structure. Additionally, access to the Bio-Deuteration Lab provides unique capabilities for preparing large-scale cultivations and expressing deuterium-labeled proteins for enhanced scattering signal from the protein. While this technique does not provide structural details at high-resolution, the structural knowledge gap for membrane proteins contains many addressable areas of research without requiring near-atomic resolution. For example, these areas include determination of oligomeric states, complex formation, conformational changes during perturbation, and folding/unfolding events. These investigations can be readily accomplished through applications of this method.
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Affiliation(s)
- Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory
| | - Swe-Htet Naing
- School of Chemistry and Biochemistry, Georgia Institute of Technology
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory
| | | | | | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory;
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Dos Santos Morais R, Delalande O, Pérez J, Mias-Lucquin D, Lagarrigue M, Martel A, Molza AE, Chéron A, Raguénès-Nicol C, Chenuel T, Bondon A, Appavou MS, Le Rumeur E, Combet S, Hubert JF. Human Dystrophin Structural Changes upon Binding to Anionic Membrane Lipids. Biophys J 2018; 115:1231-1239. [PMID: 30197181 DOI: 10.1016/j.bpj.2018.07.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/16/2018] [Accepted: 07/31/2018] [Indexed: 11/19/2022] Open
Abstract
Scaffolding proteins play important roles in supporting the plasma membrane (sarcolemma) of muscle cells. Among them, dystrophin strengthens the sarcolemma through protein-lipid interactions, and its absence due to gene mutations leads to the severe Duchenne muscular dystrophy. Most of the dystrophin protein consists of a central domain made of 24 spectrin-like coiled-coil repeats (R). Using small angle neutron scattering (SANS) and the contrast variation technique, we specifically probed the structure of the three first consecutive repeats 1-3 (R1-3), a part of dystrophin known to physiologically interact with membrane lipids. R1-3 free in solution was compared to its structure adopted in the presence of phospholipid-based bicelles. SANS data for the protein/lipid complexes were obtained with contrast-matched bicelles under various phospholipid compositions to probe the role of electrostatic interactions. When bound to anionic bicelles, large modifications of the protein three-dimensional structure were detected, as revealed by a significant increase of the protein gyration radius from 42 ± 1 to 60 ± 4 Å. R1-3/anionic bicelle complexes were further analyzed by coarse-grained molecular dynamics simulations. From these studies, we report an all-atom model of R1-3 that highlights the opening of the R1 coiled-coil repeat when bound to the membrane lipids. This model is totally in agreement with SANS and click chemistry/mass spectrometry data. We conclude that the sarcolemma membrane anchoring that occurs during the contraction/elongation process of muscles could be ensured by this coiled-coil opening. Therefore, understanding these structural changes may help in the design of rationalized shortened dystrophins for gene therapy. Finally, our strategy opens up new possibilities for structure determination of peripheral and integral membrane proteins not compatible with different high-resolution structural methods.
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Affiliation(s)
- Raphael Dos Santos Morais
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France; Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, France; SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France
| | - Olivier Delalande
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Javier Pérez
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France
| | - Dominique Mias-Lucquin
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Mélanie Lagarrigue
- Université de Rennes, Rennes, France; Inserm U1085, Protim-Plate-forme Protéomique, Rennes, France
| | | | - Anne-Elisabeth Molza
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Angélique Chéron
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Céline Raguénès-Nicol
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Thomas Chenuel
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Arnaud Bondon
- CNRS 6226, Institut des Sciences Chimiques de Rennes, PRISM, Rennes, France
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Garching, Germany
| | - Elisabeth Le Rumeur
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Sophie Combet
- Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, France.
| | - Jean-François Hubert
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France.
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Larsen AH, Arleth L, Hansen S. Analysis of small-angle scattering data using model fitting and Bayesian regularization. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718008956] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The structure of macromolecules can be studied by small-angle scattering (SAS), but as this is an ill-posed problem, prior knowledge about the sample must be included in the analysis. Regularization methods are used for this purpose, as already implemented in indirect Fourier transformation and bead-modeling-based analysis of SAS data, but not yet in the analysis of SAS data with analytical form factors. To fill this gap, a Bayesian regularization method was implemented, where the prior information was quantified as probability distributions for the model parameters and included via a functional S. The quantity Q = χ2 + αS was then minimized and the value of the regularization parameter α determined by probability maximization. The method was tested on small-angle X-ray scattering data from a sample of nanodiscs and a sample of micelles. The parameters refined with the Bayesian regularization method were closer to the prior values as compared with conventional χ2 minimization. Moreover, the errors on the refined parameters were generally smaller, owing to the inclusion of prior information. The Bayesian method stabilized the refined values of the fitted model upon addition of noise and can thus be used to retrieve information from data with low signal-to-noise ratio without risk of overfitting. Finally, the method provides a measure for the information content in data, N
g, which represents the effective number of retrievable parameters, taking into account the imposed prior knowledge as well as the noise level in data.
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