1
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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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2
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Adrien V, Rayan G, Astafyeva K, Broutin I, Picard M, Fuchs P, Urbach W, Taulier N. How to best estimate the viscosity of lipid bilayers. Biophys Chem 2021; 281:106732. [PMID: 34844029 DOI: 10.1016/j.bpc.2021.106732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/19/2021] [Indexed: 11/02/2022]
Abstract
The viscosity of lipid bilayers is a property relevant to biological function, as it affects the diffusion of membrane macromolecules. To determine its value, and hence portray the membrane, various literature-reported techniques lead to significantly different results. Herein we compare the results issuing from two widely used techniques to determine the viscosity of membranes: the Fluorescence Lifetime Imaging Microscopy (FLIM), and Fluorescence Recovery After Photobleaching (FRAP). FLIM relates the time of rotation of a molecular rotor inserted into the membrane to the macroscopic viscosity of a fluid. Whereas FRAP measures molecular diffusion coefficients. This approach is based on a hydrodynamic model connecting the mobility of a membrane inclusion to the viscosity of the membrane. We show that: This article emphasizes the pitfalls to be avoided and the rules to be observed in order to obtain a value of the bilayer viscosity that characterizes the bilayer instead of interactions between the bilayer and the embedded probe.
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Affiliation(s)
- Vladimir Adrien
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France; Université de Paris, CNRS, Laboratoire CiTCoM, 75006 Paris, France; Sorbonne Université, AP-HP Department of Psychiatry, Hôpital Saint-Antoine, Paris, France
| | - Gamal Rayan
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France.
| | - Ksenia Astafyeva
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Isabelle Broutin
- Université de Paris, CNRS, Laboratoire CiTCoM, 75006 Paris, France
| | - Martin Picard
- Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, F-75005 Paris, France; Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, F-75005 Paris, France
| | - Patrick Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France; Université de Paris, UFR Sciences du Vivant, 75013 Paris, France
| | - Wladimir Urbach
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France; Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
| | - Nicolas Taulier
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
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3
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Anandan A, Dunstan NW, Ryan TM, Mertens HDT, Lim KYL, Evans GL, Kahler CM, Vrielink A. Conformational flexibility of EptA driven by an interdomain helix provides insights for enzyme-substrate recognition. IUCRJ 2021; 8:732-746. [PMID: 34584735 PMCID: PMC8420757 DOI: 10.1107/s2052252521005613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Many pathogenic gram-negative bacteria have developed mechanisms to increase resistance to cationic antimicrobial peptides by modifying the lipid A moiety. One modification is the addition of phospho-ethano-lamine to lipid A by the enzyme phospho-ethano-lamine transferase (EptA). Previously we reported the structure of EptA from Neisseria, revealing a two-domain architecture consisting of a periplasmic facing soluble domain and a transmembrane domain, linked together by a bridging helix. Here, the conformational flexibility of EptA in different detergent environments is probed by solution scattering and intrinsic fluorescence-quenching studies. The solution scattering studies reveal the enzyme in a more compact state with the two domains positioned close together in an n-do-decyl-β-d-maltoside micelle environment and an open extended structure in an n-do-decyl-phospho-choline micelle environment. Intrinsic fluorescence quenching studies localize the domain movements to the bridging helix. These results provide important insights into substrate binding and the molecular mechanism of endotoxin modification by EptA.
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Affiliation(s)
- Anandhi Anandan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Nicholas W. Dunstan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Unit, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Katherine Y. L. Lim
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Genevieve L. Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Charlene M. Kahler
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
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4
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Abel S, Marchi M, Solier J, Finet S, Brillet K, Bonneté F. Structural insights into the membrane receptor ShuA in DDM micelles and in a model of gram-negative bacteria outer membrane as seen by SAXS and MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183504. [PMID: 33157097 DOI: 10.1016/j.bbamem.2020.183504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/20/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022]
Abstract
Successful crystallization of membrane proteins in detergent micelles depends on key factors such as conformational stability of the protein in micellar assemblies, the protein-detergent complex (PDC) monodispersity and favorable protein crystal contacts by suitable shielding of the protein hydrophobic surface by the detergent belt. With the aim of studying the influence of amphiphilic environment on membrane protein structure, stability and crystallizability, we combine molecular dynamics (MD) simulations with SEC-MALLS and SEC-SAXS (Size Exclusion Chromatography in line with Multi Angle Laser Light Scattering or Small Angle X-ray Scattering) experiments to describe the protein-detergent interactions that could help to rationalize PDC crystallization. In this context, we compare the protein-detergent interactions of ShuA from Shigella dysenteriae in n-Dodecyl-β-D-Maltopyranoside (DDM) with ShuA inserted in a realistic model of gram-negative bacteria outer membrane (OM) containing a mixture of bacterial lipopolysaccharide and phospholipids. To evaluate the quality of the PDC models, we compute the corresponding SAXS curves from the MD trajectories and compare with the experimental ones. We show that computed SAXS curves obtained from the MD trajectories reproduce better the SAXS obtained from the SEC-SAXS experiments for ShuA surrounded by 268 DDM molecules. The MD results show that the DDM molecules form around ShuA a closed belt whose the hydrophobic thickness appears slightly smaller (~22 Å) than the hydrophobic transmembrane domain of the protein (24.6 Å) suggested by Orientations of Proteins in Membranes (OPM) database. The simulations also show that ShuA transmembrane domain is remarkably stable in all the systems except for the extracellular and periplasmic loops that exhibit larger movements due to specific molecular interactions with lipopolysaccharides (LPS). We finally point out that this detergent behavior may lead to the occlusion of the periplasmic hydrophilic surface and poor crystal contacts leading to difficulties in crystallization of ShuA in DDM.
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Affiliation(s)
- Stéphane Abel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Massimo Marchi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Justine Solier
- Laboratoire d'Electrochimie et de Physico-chimie des Matériaux et des Interfaces, UMR 5279 CNRS Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, INP, F38000 Grenoble, France
| | - Stéphanie Finet
- Institut de Minéralogie, de Physique de Matériaux et de Cosmochimie, UMR 7590 CNRS-Sorbonne université, Bioinformatique et Biophysique, 4 Place Jussieu, F75005 Paris, France
| | - Karl Brillet
- Institut de Biologie Moléculaire et Cellulaire UPR 9002 CNRS, Architecture et Réactivité de l'ARN, 2 allée Konrad Roentgen, F67000 Strasbourg, France
| | - Françoise Bonneté
- Institut de Biologie Physico-Chimique (IBPC) UMR 7099 CNRS Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, 13 rue Pierre et Marie Curie, F75005 Paris, France.
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5
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Ferens FG, Patel TR, Oriss G, Court DA, Stetefeld J. A Cholesterol Analog Induces an Oligomeric Reorganization of VDAC. Biophys J 2019; 116:847-859. [PMID: 30777305 DOI: 10.1016/j.bpj.2019.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/16/2018] [Accepted: 01/23/2019] [Indexed: 12/11/2022] Open
Abstract
The oligomeric organization of the voltage-dependent anion-selective channel (VDAC) and its interactions with hexokinase play integral roles in mitochondrially mediated apoptotic signaling. Various small to large assemblies of VDAC are observed in mitochondrial outer membranes, but they do not predominate in detergent-solubilized VDAC samples. In this study, a cholesterol analog, cholesteryl-hemisuccinate (CHS), was shown to induce the formation of detergent-soluble VDAC multimers. The various oligomeric states of VDAC induced by the addition of CHS were deciphered through an integrated biophysics approach using microscale thermophoresis, analytical ultracentrifugation, and size-exclusion chromatography small angle x-ray scattering. Furthermore, CHS stabilizes the interaction between VDAC and hexokinase (Kd of 27 ± 6 μM), confirming the biological relevance of oligomers generated. Thus, sterols such as cholesterol in higher eukaryotes or ergosterol in fungi may regulate the VDAC oligomeric state and may provide a potential target for the modulation of apoptotic signaling by effecting VDAC-VDAC and VDAC-hexokinase interactions. In addition, the integrated biophysical approach described provides a powerful platform for the study of membrane protein complexes in solution.
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Affiliation(s)
- Fraser G Ferens
- Departments of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, Alberta, Canada; Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - George Oriss
- Departments of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Deborah A Court
- Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jörg Stetefeld
- Departments of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.
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6
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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7
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Koutsioubas A. Low-Resolution Structure of Detergent-Solubilized Membrane Proteins from Small-Angle Scattering Data. Biophys J 2018; 113:2373-2382. [PMID: 29211991 DOI: 10.1016/j.bpj.2017.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/20/2017] [Accepted: 10/03/2017] [Indexed: 11/16/2022] Open
Abstract
Despite the ever-increasing usage of small-angle scattering as a valuable complementary method in the field of structural biology, applications concerning membrane proteins remain elusive mainly due to experimental challenges and the relative lack of theoretical tools for the treatment of scattering data. This fact adds up to general difficulties encountered also by other established methods (crystallography, NMR) for the study of membrane proteins. Following the general paradigm of ab initio methods for low-resolution restoration of soluble protein structure from small-angle scattering data, we construct a general multiphase model with a set of physical constraints, which, together with an appropriate minimization procedure, gives direct structural information concerning the different components (protein, detergent molecules) of detergent-solubilized membrane protein complexes. Assessment of the method's precision and robustness is evaluated by performing shape restorations from simulated data of a tetrameric α-helical membrane channel (Aquaporin-0) solubilized by n-Dodecyl β-D-Maltoside and from previously published small-angle neutron scattering experimental data of the filamentous hemagglutinin adhesin β-barrel protein transporter solubilized by n-Octyl β-D-glucopyranoside. It is shown that the acquisition of small-angle neutron scattering data at two different solvent contrasts, together with an estimation of detergent aggregation number around the protein, permits the reliable reconstruction of the shape of membrane proteins without the need for any prior structural information.
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Affiliation(s)
- Alexandros Koutsioubas
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Garching, Germany.
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8
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Gabel F. Applications of SANS to Study Membrane Protein Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:201-214. [DOI: 10.1007/978-981-10-6038-0_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Abstract
AbstractIn 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a revolution in structure determination, facilitated by the development of new methods. This review explores some of the frontier methods that are shaping the future of X-ray diffraction, including coherent diffractive imaging, serial femtosecond X-ray crystallography and small-angle X-ray scattering. Collectively, these methods expand the current limits of structure determination in biological systems across multiple length and time scales.
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10
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Gelisio L, Scardi P. 100 years of Debye's scattering equation. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2016; 72:608-620. [DOI: 10.1107/s2053273316014881] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/21/2016] [Indexed: 11/10/2022]
Abstract
Debye's scattering equation (DSE) has spanned a century of scientific development, from the dawn of quantum mechanics and the investigation of the structure of atoms and molecules to the era of nanotechnology, paving the way tototal scatteringmethods. The formulation offers the most accurate representation of the intensity scattered by randomly oriented atomic aggregates, constructed by superimposing the signal from each atomic distance in the molecule. The present paper reviews some of the milestone applications, from the interpretation of the intensity curves from gases and vapours, to aggregates of increasing size and more extended order. Important developments, aimed at mitigating the prohibitive computational complexity of the DSE, and state-of-the-art methods for the characterization of static and dynamic displacements are also discussed.
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11
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Marchi M. A first principle particle mesh method for solution SAXS of large bio-molecular systems. J Chem Phys 2016; 145:045101. [DOI: 10.1063/1.4959123] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Pollock NL, Satriano L, Zegarra-Moran O, Ford RC, Moran O. Structure of wild type and mutant F508del CFTR: A small-angle X-ray scattering study of the protein–detergent complexes. J Struct Biol 2016; 194:102-11. [DOI: 10.1016/j.jsb.2016.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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13
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Harris BJ, Cheng X, Frymier P. Structure and Function of Photosystem I–[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study. J Phys Chem B 2016; 120:599-609. [DOI: 10.1021/acs.jpcb.5b07812] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bradley J. Harris
- College
of Engineering and Computer Science, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Xiaolin Cheng
- Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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14
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Abstract
In experimental studies of solubilized membrane proteins, the detergent corona influences the protein behavior and the resulting measurement. Thus, combinations of experimental techniques with atomistic modeling have been used to resolve corona structural parameters and distributions. Here, we used small-angle X-ray scattering (SAXS) data and molecular dynamics simulations to study a model protein-detergent complex (PDC) consisting of aquaporin-0 and dodecyl-β-maltoside molecules (βDDM). The corona morphology of single snapshots was found to be rough, but it is smooth and compacted in 100-ns-scale ensemble averages. Individual snapshots therefore were unable to accurately represent the ensemble information as captured by experimental SAXS. Mimicking of annular lipids by detergent was also observed. SAXS prediction using different published methods was used to identify optimal βDDM numbers. Explicit-solvent methods predicted best agreement using 290-βDDM PDCs, but implicit-solvent methods gave unclear predictions due to overcompensation by free solvation-layer density parameters. Thus, ensemble-based approaches and physically motivated constraints will help to extract structural information from SAXS data.
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Affiliation(s)
- Po-Chia Chen
- Institute for Microbiology and Genetics, Georg-August-University Göttingen , Justus-von-Liebig weg 11, 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen , Justus-von-Liebig weg 11, 37077 Göttingen, Germany
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15
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Probing the conformation of FhaC with small-angle neutron scattering and molecular modeling. Biophys J 2015; 107:185-96. [PMID: 24988353 DOI: 10.1016/j.bpj.2014.05.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 04/20/2014] [Accepted: 05/05/2014] [Indexed: 11/22/2022] Open
Abstract
Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120-160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins.
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16
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Pérez J, Koutsioubas A. Memprot: a program to model the detergent corona around a membrane protein based on SEC-SAXS data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:86-93. [PMID: 25615863 PMCID: PMC4304689 DOI: 10.1107/s1399004714016678] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/18/2014] [Indexed: 11/10/2022]
Abstract
The application of small-angle X-ray scattering (SAXS) to structural investigations of transmembrane proteins in detergent solution has been hampered by two main inherent hurdles. On the one hand, the formation of a detergent corona around the hydrophobic region of the protein strongly modifies the scattering curve of the protein. On the other hand, free micelles of detergent without a precisely known concentration coexist with the protein-detergent complex in solution, therefore adding an uncontrolled signal. To gain robust structural information on such systems from SAXS data, in previous work, advantage was taken of the online combination of size-exclusion chromatography (SEC) and SAXS, and the detergent corona around aquaporin-0, a membrane protein of known structure, could be modelled. A precise geometrical model of the corona, shaped as an elliptical torus, was determined. Here, in order to better understand the correlations between the corona model parameters and to discuss the uniqueness of the model, this work was revisited by analyzing systematic SAXS simulations over a wide range of parameters of the torus.
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Affiliation(s)
- Javier Pérez
- Beamline SWING, Synchrotron SOLEIL, L’Orme des Merisiers, BP 48, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Alexandros Koutsioubas
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
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17
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18
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Harris BJ, Cheng X, Frymier P. All-atom molecular dynamics simulation of a photosystem i/detergent complex. J Phys Chem B 2014; 118:11633-45. [PMID: 25233289 DOI: 10.1021/jp507157e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.
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Affiliation(s)
- Bradley J Harris
- Department of Chemical and Biomolecular Engineering, ‡Department of Biochemistry and Cellular and Molecular Biology, §Sustainable Energy Education and Research Center, and ∥Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee , Knoxville, Tennessee 37996, United States
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19
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Døvling Kaspersen J, Moestrup Jessen C, Stougaard Vad B, Skipper Sørensen E, Kleiner Andersen K, Glasius M, Pinto Oliveira CL, Otzen DE, Pedersen JS. Low-Resolution Structures of OmpA⋅DDM Protein-Detergent Complexes. Chembiochem 2014; 15:2113-24. [DOI: 10.1002/cbic.201402162] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 11/07/2022]
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Koutsioubas A, Pérez J. Incorporation of a hydration layer in the `dummy atom'ab initiostructural modelling of biological macromolecules. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813025387] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Ab initioalgorithms for the restoration of biomacromolecular structure from small-angle scattering data have gained popularity in the past 15 years. In particular, `dummy atom' models that require minimal information about the system under study have been proven capable of recovering the low-resolution shape of proteins and nucleic acids in many published works. However, consideration of solvated biological molecules as particles of uniform electron density contrast relative to the solvent neglects the presence of a hydration layer around their surface, leading to an overall apparent swelling of the obtained models and to a large overestimation of the volume of the particle. Here this problem is addressed by the introduction of an additional type of `dummy atom', representing the hydration layer. Successful applications of this new approach are illustrated for several proteins, and related results are compared with those from the programDAMMIN[Svergun (1999).Biophys. J.76, 2879–2886].
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