151
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Moss FR, Boxer SG. Atomic Recombination in Dynamic Secondary Ion Mass Spectrometry Probes Distance in Lipid Assemblies: A Nanometer Chemical Ruler. J Am Chem Soc 2016; 138:16737-16744. [PMID: 27977192 DOI: 10.1021/jacs.6b10655] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The lateral organization of biological membranes is thought to take place on the nanometer length scale. However, this length scale and the dynamic nature of small lipid and protein domains have made characterization of such organization in biological membranes and model systems difficult. Here we introduce a new method for measuring the colocalization of lipids in monolayers and bilayers using stable isotope labeling. We take advantage of a process that occurs in dynamic SIMS called atomic recombination, in which atoms on different molecules combine to form diatomic ions that are detected with a NanoSIMS instrument. This process is highly sensitive to the distance between molecules. By measuring the efficiency of the formation of 13C15N- ions from 13C and 15N atoms on different lipid molecules, we measure variations in the lateral organization of bilayers even though these heterogeneities occur on a length scale of only a few nm, well below the diameter of the primary ion beam of the NanoSIMS instrument or even the best super-resolution fluorescence methods. Using this technique, we provide direct evidence for nanoscale phase separation in a model membrane, which may provide a better model for the organization of biological membranes than lipid mixtures with microscale phase separation. We expect this technique to be broadly applicable to any assembly where very short scale proximity is of interest or unknown, both in chemical and biological systems.
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Affiliation(s)
- Frank R Moss
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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152
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Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 2016; 118-119:146-162. [PMID: 27939506 DOI: 10.1016/j.ymeth.2016.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023] Open
Abstract
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
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153
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Kirby N, Cowieson N, Hawley AM, Mudie ST, McGillivray DJ, Kusel M, Samardzic-Boban V, Ryan TM. Improved radiation dose efficiency in solution SAXS using a sheath flow sample environment. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1254-1266. [PMID: 27917826 PMCID: PMC5137223 DOI: 10.1107/s2059798316017174] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 12/24/2022]
Abstract
Coflow is a new method for delivering radiation-sensitive biological and other solution-based samples to high-brightness X-ray beamlines that exploits laminar flow to ameliorate radiation-damage limitations and provides a host of practical improvements associated with these types of experiments. Radiation damage is a major limitation to synchrotron small-angle X-ray scattering analysis of biomacromolecules. Flowing the sample during exposure helps to reduce the problem, but its effectiveness in the laminar-flow regime is limited by slow flow velocity at the walls of sample cells. To overcome this limitation, the coflow method was developed, where the sample flows through the centre of its cell surrounded by a flow of matched buffer. The method permits an order-of-magnitude increase of X-ray incident flux before sample damage, improves measurement statistics and maintains low sample concentration limits. The method also efficiently handles sample volumes of a few microlitres, can increase sample throughput, is intrinsically resistant to capillary fouling by sample and is suited to static samples and size-exclusion chromatography applications. The method unlocks further potential of third-generation synchrotron beamlines to facilitate new and challenging applications in solution scattering.
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Affiliation(s)
- Nigel Kirby
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Nathan Cowieson
- B21 SAXS, Diamond Light Source Ltd, Hartwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Adrian M Hawley
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Stephen T Mudie
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Duncan J McGillivray
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Michael Kusel
- Kusel Design, 6 Hambleton Street, Albert Park, Victoria 3206, Australia
| | - Vesna Samardzic-Boban
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Timothy M Ryan
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
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154
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Silva ER, Cooney G, Hamley IW, Alves WA, Lee S, O'Connor BF, Reza M, Ruokolainen J, Walls D. Structural behaviour and gene delivery in complexes formed between DNA and arginine-containing peptide amphiphiles. SOFT MATTER 2016; 12:9158-9169. [PMID: 27714346 DOI: 10.1039/c6sm01618a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We describe in depth the structure of complexes formed between DNA and two classes of arginine-containing peptide amphiphiles, namely, the lipopeptide PRW-C16 (P = proline, R = arginine, W = tryptophan, C16 = C16 : 0 alkyl chain) and the bolaamphiphile RFL4FR (R = arginine, F = phenylalanine, L = leucine). A combination of X-ray and neutron scattering provided unprecedented insights into the local structure of these complexes. Lipopeptide-based complexes self-assembled into layered structures with large-scale fractal features, hosting DNA in the interstices. Bola-amphiphile scaffolds were characterized by planar structures with DNA strands presumably sandwiched in-between peptide nanotapes. Importantly, complexation did not affect the structural integrity of DNA in either of the two complexes. The bolaamphiphile conjugates displayed high levels of molecular ordering in contrast to the liquid-crystalline features observed in lipopeptide assemblies. Peptide-DNA complexes were assessed for their potential as a means to deliver the reporter vector pEGFP-N1 into SW480 human colon carcinoma cells. Successfully transfected cells expressed green fluorescent protein. The potentiating effect of PRW-C16 on the cellular uptake of ectopic DNA was found to be much greater than that observed with RFL4FR. In contrast to the bolaamphiphile-based conjugate, the liquid-crystalline nature of the lipopeptide complex is likely to play a key role in DNA release and transfection efficiency since these weakly bound structures require lower energy expenditure during disassembly and load release.
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Affiliation(s)
- Emerson R Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André-SP, 09210-580, Brazil. and Instituto de Física, Universidade Federal de Alagoas, Maceió-AL, 57072-900, Brazil
| | - Gary Cooney
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, RG6 6AD, UK
| | - Wendel A Alves
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André-SP, 09210-580, Brazil.
| | - Shannon Lee
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Brendan F O'Connor
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Mehedi Reza
- Department of Applied Physics, Aalto University School of Science, P. O. Box 15100, FI-00076, Finland
| | - Janne Ruokolainen
- Department of Applied Physics, Aalto University School of Science, P. O. Box 15100, FI-00076, Finland
| | - Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
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155
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Jeffries CM, Graewert MA, Blanchet CE, Langley DB, Whitten AE, Svergun DI. Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments. Nat Protoc 2016; 11:2122-2153. [PMID: 27711050 PMCID: PMC5402874 DOI: 10.1038/nprot.2016.113] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume, including the solvent and buffer components, as well as the macromolecules of interest. To obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample. In addition, sample heterogeneity caused by contaminants, aggregates, mismatched solvents, radiation damage or other factors can severely influence and complicate data analysis, so it is essential that the samples be pure and monodisperse for the duration of the experiment. This protocol outlines the basic physics of SAXS and SANS, and it reveals how the underlying conceptual principles of the techniques ultimately 'translate' into practical laboratory guidance for the production of samples of sufficiently high quality for scattering experiments. The procedure describes how to prepare and characterize protein and nucleic acid samples for both SAXS and SANS using gel electrophoresis, size-exclusion chromatography (SEC) and light scattering. Also included are procedures that are specific to X-rays (in-line SEC-SAXS) and neutrons, specifically preparing samples for contrast matching or variation experiments and deuterium labeling of proteins.
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Affiliation(s)
- Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
| | - Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
| | - Clément E. Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
| | - David B. Langley
- Victor Chang Cardiac Research and Garvan Institutes, Darlinghurst,
NSW, Australia
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, Lucas
Heights, NSW, Australia
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
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156
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Costa L, Andriatis A, Brennich M, Teulon JM, Chen SWW, Pellequer JL, Round A. Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules. BMC STRUCTURAL BIOLOGY 2016; 16:18. [PMID: 27788689 PMCID: PMC5081678 DOI: 10.1186/s12900-016-0068-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/06/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation facilities are pillars of modern structural biology. Small-Angle X-ray scattering performed at synchrotron sources is often used to characterize the shape of biological macromolecules. A major challenge with high-energy X-ray beam on such macromolecules is the perturbation of sample due to radiation damage. RESULTS By employing atomic force microscopy, another common technique to determine the shape of biological macromolecules when deposited on flat substrates, we present a protocol to evaluate and characterize consequences of radiation damage. It requires the acquisition of images of irradiated samples at the single molecule level in a timely manner while using minimal amounts of protein. The protocol has been tested on two different molecular systems: a large globular tetremeric enzyme (β-Amylase) and a rod-shape plant virus (tobacco mosaic virus). Radiation damage on the globular enzyme leads to an apparent increase in molecular sizes whereas the effect on the long virus is a breakage into smaller pieces resulting in a decrease of the average long-axis radius. CONCLUSIONS These results show that radiation damage can appear in different forms and strongly support the need to check the effect of radiation damage at synchrotron sources using the presented protocol.
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Affiliation(s)
- Luca Costa
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000 France
- Present Address: CBS, Centre de Biochimie Structurale, CNRS UMR 5048-INSERM UMR 1054, 29, Rue de Navacelles, Montpellier, 34090 France
| | - Alexander Andriatis
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000 France
- MIT, 77 Massachusetts Ave., Cambridge, 02139 MA USA
| | - Martha Brennich
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000 France
| | - Jean-Marie Teulon
- Univ. Grenoble Alpes, 71 Avenue des Martyrs, Grenoble, 38044 France
- CNRS, IBS, 71 Avenue des Martyrs, Grenoble, 38044 France
- CEA, IBS, 71 Avenue des Martyrs, Grenoble, France
| | - Shu-wen W. Chen
- Univ. Grenoble Alpes, 71 Avenue des Martyrs, Grenoble, 38044 France
- CNRS, IBS, 71 Avenue des Martyrs, Grenoble, 38044 France
- CEA, IBS, 71 Avenue des Martyrs, Grenoble, France
| | - Jean-Luc Pellequer
- Univ. Grenoble Alpes, 71 Avenue des Martyrs, Grenoble, 38044 France
- CNRS, IBS, 71 Avenue des Martyrs, Grenoble, 38044 France
- CEA, IBS, 71 Avenue des Martyrs, Grenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, 38000 France
- Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, Grenoble, 38000 France
- Faculty of Natural Sciences, Keele University, Keele, Staffordshire UK
- Present Address: European XFEL GmbH, Holzkoppel 4, Schenefeld, 22869 Germany
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157
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Small-angle scattering studies of intrinsically disordered proteins and their complexes. Curr Opin Struct Biol 2016; 42:15-23. [PMID: 27794210 DOI: 10.1016/j.sbi.2016.10.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/01/2022]
Abstract
Intrinsically Disordered Proteins (IDPs) perform a broad range of biological functions. Their relevance has motivated intense research activity seeking to characterize their sequence/structure/function relationships. However, the conformational plasticity of these molecules hampers the application of traditional structural approaches, and new tools and concepts are being developed to address the challenges they pose. Small-Angle Scattering (SAS) is a structural biology technique that probes the size and shape of disordered proteins and their complexes with other biomolecules. The low-resolution nature of SAS can be compensated with specially designed computational tools and its combined interpretation with complementary structural information. In this review, we describe recent advances in the application of SAS to disordered proteins and highly flexible complexes and discuss current challenges.
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Affiliation(s)
- Tiago N Cordeiro
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Fátima Herranz-Trillo
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annika Urbanek
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Alejandro Estaña
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France; LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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158
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Liu LK, Abdelwahab H, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. The Structure of the Antibiotic Deactivating, N-hydroxylating Rifampicin Monooxygenase. J Biol Chem 2016; 291:21553-21562. [PMID: 27557658 PMCID: PMC5076826 DOI: 10.1074/jbc.m116.745315] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Indexed: 11/06/2022] Open
Abstract
Rifampicin monooxygenase (RIFMO) catalyzes the N-hydroxylation of the natural product antibiotic rifampicin (RIF) to 2'-N-hydroxy-4-oxo-rifampicin, a metabolite with much lower antimicrobial activity. RIFMO shares moderate sequence similarity with well characterized flavoprotein monooxygenases, but the protein has not been isolated and characterized at the molecular level. Herein, we report crystal structures of RIFMO from Nocardia farcinica, the determination of the oligomeric state in solution with small angle x-ray scattering, and the spectrophotometric characterization of substrate binding. The structure identifies RIFMO as a class A flavoprotein monooxygenase and is similar in fold and quaternary structure to MtmOIV and OxyS, which are enzymes in the mithramycin and oxytetracycline biosynthetic pathways, respectively. RIFMO is distinguished from other class A flavoprotein monooxygenases by its unique middle domain, which is involved in binding RIF. Small angle x-ray scattering analysis shows that RIFMO dimerizes via the FAD-binding domain to form a bell-shaped homodimer in solution with a maximal dimension of 110 Å. RIF binding was monitored using absorbance at 525 nm to determine a dissociation constant of 13 μm Steady-state oxygen consumption assays show that NADPH efficiently reduces the FAD only when RIF is present, implying that RIF binds before NADPH in the catalytic scheme. The 1.8 Å resolution structure of RIFMO complexed with RIF represents the precatalytic conformation that occurs before formation of the ternary E-RIF-NADPH complex. The RIF naphthoquinone blocks access to the FAD N5 atom, implying that large conformational changes are required for NADPH to reduce the FAD. A model for these conformational changes is proposed.
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Affiliation(s)
- Li-Kai Liu
- From the Departments of Biochemistry and
| | - Heba Abdelwahab
- the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
- the Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
| | | | | | - Pablo Sobrado
- the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
| | - John J Tanner
- From the Departments of Biochemistry and
- Chemistry and
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159
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Hutin S, Brennich M, Maillot B, Round A. Online ion-exchange chromatography for small-angle X-ray scattering. Acta Crystallogr D Struct Biol 2016; 72:1090-1099. [PMID: 27710930 PMCID: PMC5053136 DOI: 10.1107/s2059798316012833] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 08/09/2016] [Indexed: 11/22/2022] Open
Abstract
Biological small-angle X-ray scattering (BioSAXS) is a powerful technique to determine the solution structure, particle size, shape and surface-to-volume ratio of macromolecules. However, a drawback is that the sample needs to be monodisperse. To ensure this, size-exclusion chromatography (SEC) has been implemented on many BioSAXS beamlines. Here, the integration of ion-exchange chromatography (IEC) using both continuous linear and step gradients on a beamline is described. Background subtraction for continuous gradients by shifting a reference measurement and two different approaches for step gradients, which are based on interpolating between two background measurements, are discussed. The results presented here serve as a proof of principle for online IEC and subsequent data treatment.
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Affiliation(s)
- Stephanie Hutin
- Institut de Biologie Structurale, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Martha Brennich
- European Synchrotron Radiation Facilty, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Benoit Maillot
- European Synchrotron Radiation Facilty, 71 Avenue des Martyrs, 38042 Grenoble, France
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, BP 10142, 67404 Illkirch, France
| | - Adam Round
- EMBL Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
- EPSAM, Keele University, Keele, England
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160
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Small-angle scattering and 3D structure interpretation. Curr Opin Struct Biol 2016; 40:1-7. [DOI: 10.1016/j.sbi.2016.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022]
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161
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Naughton KL, Phan L, Leung EM, Kautz R, Lin Q, Van Dyke Y, Marmiroli B, Sartori B, Arvai A, Li S, Pique ME, Naeim M, Kerr JP, Aquino MJ, Roberts VA, Getzoff ED, Zhu C, Bernstorff S, Gorodetsky AA. Self-Assembly of the Cephalopod Protein Reflectin. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:8405-8412. [PMID: 27454809 DOI: 10.1002/adma.201601666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 05/08/2016] [Indexed: 06/06/2023]
Abstract
Films from the cephalopod protein reflectin demonstrate multifaceted functionality as infrared camouflage coatings, proton transport media, and substrates for growth of neural stem cells. A detailed study of the in vitro formation, structural characteristics, and stimulus response of such films is presented. The reported observations hold implications for the design and development of advanced cephalopod-inspired functional materials.
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Affiliation(s)
- Kyle L Naughton
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, 92697, USA
| | - Long Phan
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Erica M Leung
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Rylan Kautz
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Qiyin Lin
- Laboratory for Electron and X-Ray Instrumentation, University of California, Irvine, Irvine, CA, 92697, USA
| | - Yegor Van Dyke
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Andy Arvai
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael E Pique
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Mahan Naeim
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Justin P Kerr
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mercedeez J Aquino
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Victoria A Roberts
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chenhui Zhu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sigrid Bernstorff
- Elettra - Sincrotrone Trieste, Strada Statale 14, km 163.5, 34149, Trieste, Italy
| | - Alon A Gorodetsky
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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162
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Putnam CD. Guinier peak analysis for visual and automated inspection of small-angle X-ray scattering data. J Appl Crystallogr 2016; 49:1412-1419. [PMID: 27738411 PMCID: PMC5045725 DOI: 10.1107/s1600576716010906] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/05/2016] [Indexed: 01/12/2023] Open
Abstract
The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration, Rg, and the forward scattering intensity, I(0). In Guinier peak analysis (GPA), the plot of qI(q) versus q2 transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution function P(r) after and before the P(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.
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Affiliation(s)
- Christopher D. Putnam
- Ludwig Institute for Cancer Research, Department of Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
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163
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Palamini M, Canciani A, Forneris F. Identifying and Visualizing Macromolecular Flexibility in Structural Biology. Front Mol Biosci 2016; 3:47. [PMID: 27668215 PMCID: PMC5016524 DOI: 10.3389/fmolb.2016.00047] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/22/2016] [Indexed: 12/29/2022] Open
Abstract
Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.
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Affiliation(s)
| | | | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of PaviaPavia, Italy
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164
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Li N, Li X, Wang Y, Liu G, Zhou P, Wu H, Hong C, Bian F, Zhang R. The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solution. J Appl Crystallogr 2016; 49:1428-1432. [PMID: 27738413 PMCID: PMC5045727 DOI: 10.1107/s160057671601195x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/21/2016] [Indexed: 11/12/2022] Open
Abstract
A new biological small-angle X-ray scattering beamline (BioSAXS, BL19U2) at the Shanghai Synchrotron Radiation Facility (SSRF) is dedicated exclusively to small-angle scattering experiments from biological macromolecules in solution. As part of the important facilities in the National Center for Protein Sciences Shanghai (NCPSS), this BioSAXS beamline is the first in China to serve the rapidly increasing biology communities. The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained.
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Affiliation(s)
- Na Li
- National Center for Protein Science Shanghai, Shanghai Institutes of Biological Sciences , No. 320, Yueyang Road, Shanghai, 200031, People's Republic of China
| | - Xiuhong Li
- Shanghai Synchrotron Radiation Facility, Shanghai Institutes of Applied Physics , No. 239, Zhangheng Road, Shanghai, 201204, People's Republic of China
| | - Yuzhu Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Institutes of Applied Physics , No. 239, Zhangheng Road, Shanghai, 201204, People's Republic of China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Institutes of Biological Sciences , No. 320, Yueyang Road, Shanghai, 200031, People's Republic of China
| | - Ping Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Institutes of Applied Physics , No. 239, Zhangheng Road, Shanghai, 201204, People's Republic of China
| | - Hongjin Wu
- National Center for Protein Science Shanghai, Shanghai Institutes of Biological Sciences , No. 320, Yueyang Road, Shanghai, 200031, People's Republic of China
| | - Chunxia Hong
- Shanghai Synchrotron Radiation Facility, Shanghai Institutes of Applied Physics , No. 239, Zhangheng Road, Shanghai, 201204, People's Republic of China
| | - Fenggang Bian
- Shanghai Synchrotron Radiation Facility, Shanghai Institutes of Applied Physics , No. 239, Zhangheng Road, Shanghai, 201204, People's Republic of China
| | - Rongguang Zhang
- National Center for Protein Science Shanghai, Shanghai Institutes of Biological Sciences , No. 320, Yueyang Road, Shanghai, 200031, People's Republic of China
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165
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Emanuelle S, Brewer MK, Meekins DA, Gentry MS. Unique carbohydrate binding platforms employed by the glucan phosphatases. Cell Mol Life Sci 2016; 73:2765-2778. [PMID: 27147465 PMCID: PMC4920694 DOI: 10.1007/s00018-016-2249-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Glucan phosphatases are a family of enzymes that are functionally conserved at the enzymatic level in animals and plants. These enzymes bind and dephosphorylate glycogen in animals and starch in plants. While the enzymatic function is conserved, the glucan phosphatases employ distinct mechanisms to bind and dephosphorylate glycogen or starch. The founding member of the family is a bimodular human protein called laforin that is comprised of a carbohydrate binding module 20 (CBM20) followed by a dual specificity phosphatase domain. Plants contain two glucan phosphatases: Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). SEX4 contains a chloroplast targeting peptide, dual specificity phosphatase (DSP) domain, a CBM45, and a carboxy-terminal motif. LSF2 is comprised of simply a chloroplast targeting peptide, DSP domain, and carboxy-terminal motif. SEX4 employs an integrated DSP-CBM glucan-binding platform to engage and dephosphorylate starch. LSF2 lacks a CBM and instead utilizes two surface binding sites to bind and dephosphorylate starch. Laforin is a dimeric protein in solution and it utilizes a tetramodular architecture and cooperativity to bind and dephosphorylate glycogen. This chapter describes the biological role of glucan phosphatases in glycogen and starch metabolism and compares and contrasts their ability to bind and dephosphorylate glucans.
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Affiliation(s)
- Shane Emanuelle
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - M. Kathryn Brewer
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - David A. Meekins
- Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
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166
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Badger J, Grover P, Shi H, Panjarian S, Engen JR, Smithgall T, Makowski L. c-Abl Tyrosine Kinase Adopts Multiple Active Conformational States in Solution. Biochemistry 2016; 55:3251-60. [PMID: 27166638 PMCID: PMC4910136 DOI: 10.1021/acs.biochem.6b00202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Indexed: 11/29/2022]
Abstract
Protein tyrosine kinases of the Abl family have diverse roles in normal cellular regulation and drive several forms of leukemia as oncogenic fusion proteins. In the crystal structure of the inactive c-Abl kinase core, the SH2 and SH3 domains dock onto the back of the kinase domain, resulting in a compact, assembled state. This inactive conformation is stabilized by the interaction of the myristoylated N-cap with a pocket in the C-lobe of the kinase domain. Mutations that perturb these intramolecular interactions result in kinase activation. Here, we present X-ray scattering solution structures of multidomain c-Abl kinase core proteins modeling diverse active states. Surprisingly, the relative positions of the regulatory N-cap, SH3, and SH2 domains in an active myristic acid binding pocket mutant (A356N) were virtually identical to those of the assembled wild-type kinase core, indicating that Abl kinase activation does not require dramatic reorganization of the downregulated core structure. In contrast, the positions of the SH2 and SH3 domains in a clinically relevant imatinib-resistant gatekeeper mutant (T315I) appear to be reconfigured relative to their positions in the wild-type protein. Our results demonstrate that c-Abl kinase activation can occur either with (T315I) or without (A356N) global allosteric changes in the core, revealing the potential for previously unrecognized signaling diversity.
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Affiliation(s)
- John Badger
- DeltaG
Technologies, San Diego, California 92122, United States
| | - Prerna Grover
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Haibin Shi
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Shoghag
B. Panjarian
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - John R. Engen
- Department of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas
E. Smithgall
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Lee Makowski
- Department of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
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167
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Tokuda JM, Pabit SA, Pollack L. Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS. Biophys Rev 2016; 8:139-149. [PMID: 27551324 PMCID: PMC4991782 DOI: 10.1007/s12551-016-0196-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/10/2016] [Indexed: 12/29/2022] Open
Abstract
Understanding how DNA carries out its biological roles requires knowledge of its interactions with biological partners. Since DNA is a polyanionic polymer, electrostatic interactions contribute significantly. These interactions are mediated by positively charged protein residues or charge compensating cations. Direct detection of these partners and/or their effect on DNA conformation poses challenges, especially for monitoring conformational dynamics in real time. Small-angle x-ray scattering (SAXS) is uniquely sensitive to both the conformation and local environment (i.e. protein partner and associated ions) of the DNA. The primary challenge of studying multi-component systems with SAXS lies in resolving how each component contributes to the measured scattering. Here, we review two contrast variation (CV) strategies that enable targeted studies of the structures of DNA or its associated partners. First, solution contrast variation enables measurement of DNA conformation within a protein-DNA complex by masking out the protein contribution to the scattering profile. We review a specific example, in which the real-time unwrapping of DNA from a nucleosome core particle is measured during salt-induced disassembly. The second method, heavy atom isomorphous replacement, reports the spatial distribution of the cation cloud around duplex DNA by exploiting changes in the scattering strength of cations with varying atomic numbers. We demonstrate the application of this approach to provide the spatial distribution of monovalent cations (Na+, K+, Rb+, Cs+) around a standard 25-base pair DNA. The CV strategies presented here are valuable tools for understanding DNA interactions with its biological partners.
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Affiliation(s)
- Joshua M. Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Suzette A. Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
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168
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Borges JC, Seraphim TV, Dores-Silva PR, Barbosa LRS. A review of multi-domain and flexible molecular chaperones studies by small-angle X-ray scattering. Biophys Rev 2016; 8:107-120. [PMID: 28510050 PMCID: PMC5425780 DOI: 10.1007/s12551-016-0194-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/02/2016] [Indexed: 02/06/2023] Open
Abstract
Intrinsic flexibility is closely related to protein function, and a plethora of important regulatory proteins have been found to be flexible, multi-domain or even intrinsically disordered. On the one hand, understanding such systems depends on how these proteins behave in solution. On the other, small-angle X-ray scattering (SAXS) is a technique that fulfills the requirements to study protein structure and dynamics relatively quickly with few experimental limitations. Molecular chaperones from Hsp70 and Hsp90 families are multi-domain proteins containing flexible and/or disordered regions that play central roles in cellular proteostasis. Here, we review the structure and function of these proteins by SAXS. Our general approach includes the use of SAXS data to determine size and shape parameters, as well as protein shape reconstruction and their validation by using accessory biophysical tools. Some remarkable examples are presented that exemplify the potential of the SAXS technique. Protein structure can be determined in solution even at limiting protein concentrations (for example, human mortalin, a mitochondrial Hsp70 chaperone). The protein organization, flexibility and function (for example, the J-protein co-chaperones), oligomeric status, domain organization, and flexibility (for the Hsp90 chaperone and the Hip and Hep1 co-chaperones) may also be determined. Lastly, the shape, structural conservation, and protein dynamics (for the Hsp90 chaperone and both p23 and Aha1 co-chaperones) may be studied by SAXS. We believe this review will enhance the application of the SAXS technique to the study of the molecular chaperones.
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Affiliation(s)
- Júlio C Borges
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil.
| | - Thiago V Seraphim
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Paulo R Dores-Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
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169
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Kim HS, Martel A, Girard E, Moulin M, Härtlein M, Madern D, Blackledge M, Franzetti B, Gabel F. SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell. Biophys J 2016; 110:2185-94. [PMID: 27224484 PMCID: PMC4880798 DOI: 10.1016/j.bpj.2016.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/09/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022] Open
Abstract
Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (+36, -6, and -29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.
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Affiliation(s)
- Henry S Kim
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | - Eric Girard
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | | | - Dominique Madern
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Martin Blackledge
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | - Bruno Franzetti
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Frank Gabel
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France.
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170
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Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering. Biophys J 2016; 109:793-805. [PMID: 26287631 DOI: 10.1016/j.bpj.2015.06.065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/22/2015] [Accepted: 06/30/2015] [Indexed: 10/23/2022] Open
Abstract
Aberrant self-assembly, induced by structural misfolding of the prion proteins, leads to a number of neurodegenerative disorders. In particular, misfolding of the mostly α-helical cellular prion protein (PrP(C)) into a β-sheet-rich disease-causing isoform (PrP(Sc)) is the key molecular event in the formation of PrP(Sc) aggregates. The molecular mechanisms underlying the PrP(C)-to-PrP(Sc) conversion and subsequent aggregation remain to be elucidated. However, in persistently prion-infected cell-culture models, it was shown that treatment with monoclonal antibodies against defined regions of the prion protein (PrP) led to the clearing of PrP(Sc) in cultured cells. To gain more insight into this process, we characterized PrP-antibody complexes in solution using a fast protein liquid chromatography coupled with small-angle x-ray scattering (FPLC-SAXS) procedure. High-quality SAXS data were collected for full-length recombinant mouse PrP [denoted recPrP(23-230)] and N-terminally truncated recPrP(89-230), as well as their complexes with each of two Fab fragments (HuM-P and HuM-R1), which recognize N- and C-terminal epitopes of PrP, respectively. In-line measurements by fast protein liquid chromatography coupled with SAXS minimized data artifacts caused by a non-monodispersed sample, allowing structural analysis of PrP alone and in complex with Fab antibodies. The resulting structural models suggest two mechanisms for how these Fabs may prevent the conversion of PrP(C) into PrP(Sc).
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Affiliation(s)
- Lester Carter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California; Department of Neurology, University of California San Francisco, San Francisco, California
| | - Guillaume Poncet-Montange
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Hiro Tsuruta
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California; Department of Neurology, University of California San Francisco, San Francisco, California.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California.
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171
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Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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172
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Combined pressure and temperature denaturation of ribonuclease A produces alternate denatured states. Biochem Biophys Res Commun 2016; 473:834-839. [DOI: 10.1016/j.bbrc.2016.03.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 03/29/2016] [Indexed: 01/12/2023]
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173
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The dynamic organization of fungal acetyl-CoA carboxylase. Nat Commun 2016; 7:11196. [PMID: 27073141 PMCID: PMC4833862 DOI: 10.1038/ncomms11196] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 03/01/2016] [Indexed: 12/12/2022] Open
Abstract
Acetyl-CoA carboxylases (ACCs) catalyse the committed step in fatty-acid biosynthesis: the ATP-dependent carboxylation of acetyl-CoA to malonyl-CoA. They are important regulatory hubs for metabolic control and relevant drug targets for the treatment of the metabolic syndrome and cancer. Eukaryotic ACCs are single-chain multienzymes characterized by a large, non-catalytic central domain (CD), whose role in ACC regulation remains poorly characterized. Here we report the crystal structure of the yeast ACC CD, revealing a unique four-domain organization. A regulatory loop, which is phosphorylated at the key functional phosphorylation site of fungal ACC, wedges into a crevice between two domains of CD. Combining the yeast CD structure with intermediate and low-resolution data of larger fragments up to intact ACCs provides a comprehensive characterization of the dynamic fungal ACC architecture. In contrast to related carboxylases, large-scale conformational changes are required for substrate turnover, and are mediated by the CD under phosphorylation control. Acetyl-CoA carboxylases are central regulatory hubs of fatty acid metabolism and are important targets for drug development in obesity and cancer. Here, the authors demonstrate that the regulation of these highly dynamic enzymes in fungi is governed by a mechanism based on phosphorylation-dependent conformational variability.
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174
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Chen Y, Pollack L. SAXS studies of RNA: structures, dynamics, and interactions with partners. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:512-26. [PMID: 27071649 DOI: 10.1002/wrna.1349] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/11/2016] [Accepted: 03/01/2016] [Indexed: 12/29/2022]
Abstract
Small-angle X-ray scattering, SAXS, is a powerful and easily employed experimental technique that provides solution structures of macromolecules. The size and shape parameters derived from SAXS provide global structural information about these molecules in solution and essentially complement data acquired by other biophysical methods. As applied to protein systems, SAXS is a relatively mature technology: sophisticated tools exist to acquire and analyze data, and to create structural models that include dynamically flexible ensembles. Given the expanding appreciation of RNA's biological roles, there is a need to develop comparable tools to characterize solution structures of RNA, including its interactions with important biological partners. We review the progress toward achieving this goal, focusing on experimental and computational innovations. The use of multiphase modeling, absolute calibration and contrast variation methods, among others, provides new and often unique ways of visualizing this important biological molecule and its essential partners: ions, other RNAs, or proteins. WIREs RNA 2016, 7:512-526. doi: 10.1002/wrna.1349 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
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175
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López A, Herranz-Trillo F, Kotev M, Gairí M, Guallar V, Bernadó P, Millet O, Tarragó T, Giralt E. Active-Site-Directed Inhibitors of Prolyl Oligopeptidase Abolish Its Conformational Dynamics. Chembiochem 2016; 17:913-7. [DOI: 10.1002/cbic.201600102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Abraham López
- Chemistry and Molecular Pharmacology Program; Institute for Research in Biomedicine; The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Department of Organic Chemistry; University of Barcelona; Martí i Franquès, 1-11 08028 Barcelona Spain
| | - Fátima Herranz-Trillo
- Centre de Biochimie Structurale; INSERM U1054; CNRS UMR 5048; Université de Montpellier 1 and 2; 29 rue de Navacelles 34090 Montpellier France
| | - Martin Kotev
- Joint BSC-CRG-IRB Research Program in Computational Biology; Barcelona Supercomputing Center; Jordi Girona 31 08034 Barcelona Spain
| | - Margarida Gairí
- NMR Facility; Scientific and Technological Centers University of Barcelona (CCiTUB); Baldiri Reixac 10 08028 Barcelona Spain
| | - Víctor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology; Barcelona Supercomputing Center; Jordi Girona 31 08034 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23; 08010 Barcelona Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale; INSERM U1054; CNRS UMR 5048; Université de Montpellier 1 and 2; 29 rue de Navacelles 34090 Montpellier France
| | - Oscar Millet
- Structural Biology Unit; CIC bioGUNE; Parque Tecnológico de Vizcaya, Ed. 800 48160 Derio Spain
| | - Teresa Tarragó
- Chemistry and Molecular Pharmacology Program; Institute for Research in Biomedicine; The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Iproteos; S L; Barcelona Science Park; Baldiri Reixac 10 08028 Barcelona Spain
| | - Ernest Giralt
- Chemistry and Molecular Pharmacology Program; Institute for Research in Biomedicine; The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Department of Organic Chemistry; University of Barcelona; Martí i Franquès, 1-11 08028 Barcelona Spain
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176
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Brennich ME, Kieffer J, Bonamis G, De Maria Antolinos A, Hutin S, Pernot P, Round A. Online data analysis at the ESRF bioSAXS beamline, BM29. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576715024462] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
High-throughput small-angle X-ray scattering on proteins in solution (bioSAXS) at synchrotron sources is a commonly used technique in structural biology, which relies on highly automated data acquisition. Data reduction and primary analysis for bioSAXS experiments consist of a well defined series of individual tasks, the automation of which allows a first easy assessment of the quality of collected data and the adjustment of collection strategies if necessary. This article describes both the logic and the technical implementation of the automated processing pipeline for bioSAXS data at the ESRF BM29 beamline using theEDNAframework.
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177
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Kang H, Weiss TM, Bang I, Weis WI, Choi HJ. Structure of the Intermediate Filament-Binding Region of Desmoplakin. PLoS One 2016; 11:e0147641. [PMID: 26808545 PMCID: PMC4726743 DOI: 10.1371/journal.pone.0147641] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/06/2016] [Indexed: 11/19/2022] Open
Abstract
Desmoplakin (DP) is a cytoskeletal linker protein that connects the desmosomal cadherin/plakoglobin/plakophilin complex to intermediate filaments (IFs). The C-terminal region of DP (DPCT) mediates IF binding, and contains three plakin repeat domains (PRDs), termed PRD-A, PRD-B and PRD-C. Previous crystal structures of PRDs B and C revealed that each is formed by 4.5 copies of a plakin repeat (PR) and has a conserved positively charged groove on its surface. Although PRDs A and B are linked by just four amino acids, B and C are separated by a 154 residue flexible linker, which has hindered crystallographic analysis of the full DPCT. Here we present the crystal structure of a DPCT fragment spanning PRDs A and B, and elucidate the overall architecture of DPCT by small angle X-ray scattering (SAXS) analysis. The structure of PRD-A is similar to that of PRD-B, and the two domains are arranged in a quasi-linear arrangement, and separated by a 4 amino acid linker. Analysis of the B-C linker region using secondary structure prediction and the crystal structure of a homologous linker from the cytolinker periplakin suggests that the N-terminal ~100 amino acids of the linker form two PR-like motifs. SAXS analysis of DPCT indicates an elongated but non-linear shape with Rg = 51.5 Å and Dmax = 178 Å. These data provide the first structural insights into an IF binding protein containing multiple PRDs and provide a foundation for studying the molecular basis of DP-IF interactions.
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Affiliation(s)
- Hyunook Kang
- Dept. of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Thomas M. Weiss
- SLAC National Laboratory, Menlo Park, California, United States of America
| | - Injin Bang
- Dept. of Biological Sciences, Seoul National University, Seoul, South Korea
| | - William I. Weis
- Depts. of Structural Biology and Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hee-Jung Choi
- Dept. of Biological Sciences, Seoul National University, Seoul, South Korea
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178
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Gogonea V. Structural Insights into High Density Lipoprotein: Old Models and New Facts. Front Pharmacol 2016; 6:318. [PMID: 26793109 PMCID: PMC4709926 DOI: 10.3389/fphar.2015.00318] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
The physiological link between circulating high density lipoprotein (HDL) levels and cardiovascular disease is well-documented, albeit its intricacies are not well-understood. An improved appreciation of HDL function and overall role in vascular health and disease requires at its foundation a better understanding of the lipoprotein's molecular structure, its formation, and its process of maturation through interactions with various plasma enzymes and cell receptors that intervene along the pathway of reverse cholesterol transport. This review focuses on summarizing recent developments in the field of lipid free apoA-I and HDL structure, with emphasis on new insights revealed by newly published nascent and spherical HDL models constructed by combining low resolution structures obtained from small angle neutron scattering (SANS) with contrast variation and geometrical constraints derived from hydrogen-deuterium exchange (HDX), crosslinking mass spectrometry, electron microscopy, Förster resonance energy transfer, and electron spin resonance. Recently published low resolution structures of nascent and spherical HDL obtained from SANS with contrast variation and isotopic labeling of apolipoprotein A-I (apoA-I) will be critically reviewed and discussed in terms of how they accommodate existing biophysical structural data from alternative approaches. The new low resolution structures revealed and also provided some answers to long standing questions concerning lipid organization and particle maturation of lipoproteins. The review will discuss the merits of newly proposed SANS based all atom models for nascent and spherical HDL, and compare them with accepted models. Finally, naturally occurring and bioengineered mutations in apoA-I, and their impact on HDL phenotype, are reviewed and discuss together with new therapeutics employed for restoring HDL function.
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Affiliation(s)
- Valentin Gogonea
- Department of Chemistry, Cleveland State UniversityCleveland, OH, USA; Departments of Cellular and Molecular Medicine and the Center for Cardiovascular Diagnostics and Prevention, Cleveland ClinicCleveland, OH, USA
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179
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Dynamic Viral Glycoprotein Machines: Approaches for Probing Transient States That Drive Membrane Fusion. Viruses 2016; 8:v8010015. [PMID: 26761026 PMCID: PMC4728575 DOI: 10.3390/v8010015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/11/2015] [Accepted: 12/31/2015] [Indexed: 01/10/2023] Open
Abstract
The fusion glycoproteins that decorate the surface of enveloped viruses undergo dramatic conformational changes in the course of engaging with target cells through receptor interactions and during cell entry. These refolding events ultimately drive the fusion of viral and cellular membranes leading to delivery of the genetic cargo. While well-established methods for structure determination such as X-ray crystallography have provided detailed structures of fusion proteins in the pre- and post-fusion fusion states, to understand mechanistically how these fusion glycoproteins perform their structural calisthenics and drive membrane fusion requires new analytical approaches that enable dynamic intermediate states to be probed. Methods including structural mass spectrometry, small-angle X-ray scattering, and electron microscopy have begun to provide new insight into pathways of conformational change and fusion protein function. In combination, the approaches provide a significantly richer portrait of viral fusion glycoprotein structural variation and fusion activation as well as inhibition by neutralizing agents. Here recent studies that highlight the utility of these complementary approaches will be reviewed with a focus on the well-characterized influenza virus hemagglutinin fusion glycoprotein system.
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180
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Dauter Z, Wlodawer A. Progress in protein crystallography. Protein Pept Lett 2016; 23:201-10. [PMID: 26732246 PMCID: PMC6287266 DOI: 10.2174/0929866523666160106153524] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/26/2015] [Accepted: 01/03/2016] [Indexed: 11/22/2022]
Abstract
Macromolecular crystallography evolved enormously from the pioneering days, when structures were solved by "wizards" performing all complicated procedures almost by hand. In the current situation crystal structures of large systems can be often solved very effectively by various powerful automatic programs in days or hours, or even minutes. Such progress is to a large extent coupled to the advances in many other fields, such as genetic engineering, computer technology, availability of synchrotron beam lines and many other techniques, creating the highly interdisciplinary science of macromolecular crystallography. Due to this unprecedented success crystallography is often treated as one of the analytical methods and practiced by researchers interested in structures of macromolecules, but not highly competent in the procedures involved in the process of structure determination. One should therefore take into account that the contemporary, highly automatic systems can produce results almost without human intervention, but the resulting structures must be carefully checked and validated before their release into the public domain.
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Affiliation(s)
- Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD and Argonne, IL, USA.
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181
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Mohsen Dehnavi S, Pazuki G, Vossoughi M. PEGylated silica-enzyme nanoconjugates: a new frontier in large scale separation of α-amylase. Sci Rep 2015; 5:18221. [PMID: 26656308 PMCID: PMC4677402 DOI: 10.1038/srep18221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 11/03/2015] [Indexed: 12/20/2022] Open
Abstract
High resolution is nearly lost at the expense of throughput in most conventional bioseparation methods. Nanoparticles, due to their high surface to volume ratio, are attractiveenzyme carriers, which can boost the performance of extraction manifold. Here, wereport design and application ofa method highly capable of improving the partitioning of α-amylase in aqueous two-phase system of polymer and salt. Silica nanoparticle introduced to the system acts as a bridge that connects the enzyme and polymer. Theconjugated nanoparticles form the major part of the upper phase and thus significantly enhance the protein recovery. A thorough investigation was performed on the structure of the nanoconjugatesas well as analyzing the conformational structure of the enzyme after conjugationto explore anypossible denaturation.
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Affiliation(s)
- Seyed Mohsen Dehnavi
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Gholamreza Pazuki
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Manouchehr Vossoughi
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
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182
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Rajapaksha A, Stanley CB, Todd BA. Effects of macromolecular crowding on the structure of a protein complex: a small-angle scattering study of superoxide dismutase. Biophys J 2015; 108:967-974. [PMID: 25692601 PMCID: PMC4336365 DOI: 10.1016/j.bpj.2014.12.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/19/2014] [Accepted: 12/29/2014] [Indexed: 11/19/2022] Open
Abstract
Macromolecular crowding can alter the structure and function of biological macromolecules. We used small-angle scattering to measure the effects of macromolecular crowding on the size of a protein complex, SOD (superoxide dismutase). Crowding was induced using 400 MW PEG (polyethylene glycol),TEG (triethylene glycol), α-MG (methyl-α-glucoside), and TMAO (trimethylamine n-oxide). Parallel small-angle neutron scattering and small-angle x-ray scattering allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. Considering the osmotic pressure due to PEG, this deformation corresponds to a highly compressible structure. Small-angle x-ray scattering done in the presence of TEG suggests that for further deformation-beyond a 9% decrease in volume-the resistance to deformation may increase dramatically.
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Affiliation(s)
- Ajith Rajapaksha
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana
| | - Christopher B Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Brian A Todd
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana.
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183
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Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering. Sci Rep 2015; 5:15485. [PMID: 26503463 PMCID: PMC4621412 DOI: 10.1038/srep15485] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/28/2015] [Indexed: 01/09/2023] Open
Abstract
The nucleation event of amyloid fibrils is one of the most crucial processes that dictate the timing and rate of the pathology of diseases; however, information regarding how protein molecules associate to produce fibril nuclei is currently limited. In order to explore this issue in more detail, we performed time-resolved small angle X-ray scattering (SAXS) measurements on insulin fibrillation, in combination with additional multidirectional analyses of thioflavin T fluorescence, FTIR spectroscopy, light scattering, and light transmittance, during the fibrillation process of bovine insulin. SAXS monitoring revealed that insulin molecules associated into rod-like prefibrillar aggregates in the very early stage of the reaction. After the formation of these early aggregates, they appeared to further coalesce mutually to form larger clusters, and the SAXS profiles subsequently showed the further time evolution of conformational development towards mature amyloid fibrils. Distinct types of structural units in terms of shape in a nano-scale order, cross-β content, and thioflavin T fluorescence intensity were observed in a manner that was dependent on the fibrillation pathways. These results suggest the presence of diverse substructures that characterize various fibrillation pathways, and eventually, manifest polymorphisms in mature amyloid fibrils.
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184
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Tanner JJ. SAXS fingerprints of aldehyde dehydrogenase oligomers. Data Brief 2015; 5:745-51. [PMID: 26693506 PMCID: PMC4659792 DOI: 10.1016/j.dib.2015.10.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/10/2015] [Accepted: 10/15/2015] [Indexed: 11/13/2022] Open
Abstract
Enzymes of the aldehyde dehydrogenase (ALDH) superfamily catalyze the nicotinamide adenine dinucleotide-dependent oxidation of aldehydes to carboxylic acids. ALDHs are important in detoxification of aldehydes, amino acid metabolism, embryogenesis and development, neurotransmission, oxidative stress, and cancer. Mutations in genes encoding ALDHs cause metabolic disorders, including alcohol flush reaction (ALDH2), Sjögren–Larsson syndrome (ALDH3A2), hyperprolinemia type II (ALDH4A1), γ-hydroxybutyric aciduria (ALDH5A1), methylmalonic aciduria (ALDH6A1), pyridoxine dependent epilepsy (ALDH7A1), and hyperammonemia (ALDH18A1). We previously reported crystal structures and small-angle X-ray scattering (SAXS) analyses of ALDHs exhibiting dimeric, tetrameric, and hexameric oligomeric states (Luo et al., Biochemistry 54 (2015) 5513–5522; Luo et al., J. Mol. Biol. 425 (2013) 3106–3120). Herein I provide the SAXS curves, radii of gyration, and distance distribution functions for the three types of ALDH oligomer. The SAXS curves and associated analysis provide diagnostic fingerprints that allow rapid identification of the type of ALDH oligomer that is present in solution. The data sets provided here serve as a benchmark for characterizing oligomerization of ALDHs.
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Affiliation(s)
- John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia, Columbia, MO 65211, United States
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185
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Insights into open/closed conformations of the catalytically active human guanylate kinase as investigated by small-angle X-ray scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:81-9. [PMID: 26446352 PMCID: PMC4698301 DOI: 10.1007/s00249-015-1079-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/31/2015] [Indexed: 02/05/2023]
Abstract
Abstract
Bio-catalysis is the outcome of a subtle interplay between internal motions in enzymes and chemical kinetics. Small-angle X-ray scattering (SAXS) investigation of an enzyme’s internal motions during catalysis offers an integral view of the protein’s structural plasticity, dynamics, and function, which is useful for understanding allosteric effects and developing novel medicines. Guanylate kinase (GMPK) is an essential enzyme involved in the guanine nucleotide metabolism of unicellular and multicellular organisms. It is also required for the intracellular activation of numerous antiviral and anticancer purine nucleoside analog prodrugs. Catalytically active recombinant human GMPK (hGMPK) was purified for the first time and changes in the size and shape of open/closed hGMPK were tracked by SAXS. The binding of substrates (GMP + AMPPNP or Ap5G or GMP + ADP) resulted in the compaction of size and shape of hGMPK. The structural changes between open and completely closed hGMPK conformation were confirmed by observing differences in the hGMPK secondary structures with circular dichroism spectroscopy. Graphical abstract ![]()
Electronic supplementary material The online version of this article (doi:10.1007/s00249-015-1079-9) contains supplementary material, which is available to authorized users.
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186
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Kikhney AG, Svergun DI. A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 2015; 589:2570-7. [PMID: 26320411 DOI: 10.1016/j.febslet.2015.08.027] [Citation(s) in RCA: 392] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/17/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a biophysical method to study the overall shape and structural transitions of biological macromolecules in solution. SAXS provides low resolution information on the shape, conformation and assembly state of proteins, nucleic acids and various macromolecular complexes. The technique also offers powerful means for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs). Here, the basic principles of SAXS are presented, and profits and pitfalls of the characterization of multidomain flexible proteins and IDPs using SAXS are discussed from the practical point of view. Examples of the synergistic use of SAXS with high resolution methods like X-ray crystallography and nuclear magnetic resonance (NMR), as well as other experimental and in silico techniques to characterize completely, or partially unstructured proteins, are presented.
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Affiliation(s)
- Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany.
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187
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Yadav RP, Majumder A, Gakhar L, Artemyev NO. Extended conformation of the proline-rich domain of human aryl hydrocarbon receptor-interacting protein-like 1: implications for retina disease. J Neurochem 2015; 135:165-75. [PMID: 26139345 DOI: 10.1111/jnc.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/29/2015] [Accepted: 06/25/2015] [Indexed: 12/18/2022]
Abstract
Mutations in the primate-specific proline-rich domain (PRD) of aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) are thought to cause Leber congenital amaurosis or dominant cone-rod dystrophy. The role of PRD and the mechanisms of PRD mutations are poorly understood. Here, we have examined properties of hAIPL1 and effects of the PRD mutations on protein structure and function. Solution structures of hAIPL1, hAIPL11-316 with PRD truncation, and the P351Δ12 and P376S mutants were examined by small angle X-ray scattering. Our analysis suggests that PRD assumes an extended conformation and does not interact with the FK506-binding and tetratricopeptide domains. The PRD truncation, but not PRD mutations, reduced the molecule's radius of gyration and maximum dimension. We demonstrate that hAIPL1 is a monomeric protein, and its secondary structure and stability are not affected by the PRD mutations. PRD itself is an extended monomeric random coil. The PRD mutations caused little or no changes in hAIPL1 binding to known partners, phosphodiesterase-6A and HSP90. We also identified the γ-subunit of phosphodiesterase-6 as a novel partner of hAIPL1 and hypothesize that this interaction is altered by P351Δ12. Our results highlight the complexity of mechanisms of PRD mutations in disease and the possibility that certain mutations are benign variants. Mutations in the proline-rich domain (PRD) of human AIPL1 cause severe retinal diseases, yet the role of PRD and the mechanisms of PRD mutations are unknown. Here, we describe a SAXS-derived solution structure of AIPL1 and functional properties of disease-linked AIPL1-PRD mutants. This structure and functional analyses provide a framework for understanding the mechanisms of PRD in disease.
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Affiliation(s)
- Ravi P Yadav
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa, USA
| | - Anurima Majumder
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa, USA
| | - Lokesh Gakhar
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA.,Protein Crystallography Facility, University of Iowa, Iowa City, Iowa, USA
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
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188
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Zaccai NR, Sandlin CW, Hoopes JT, Curtis JE, Fleming PJ, Fleming KG, Krueger S. Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins. Methods Enzymol 2015; 566:159-210. [PMID: 26791979 PMCID: PMC4913355 DOI: 10.1016/bs.mie.2015.06.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In Gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archaeal prefoldins and the mitochondrial Tim chaperones, that is the α-helical "tentacles" extend from a β-strand "body" to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis, and structure modeling.
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Affiliation(s)
- Nathan R Zaccai
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clifford W Sandlin
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - James T Hoopes
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Joseph E Curtis
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Patrick J Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Karen G Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Susan Krueger
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA.
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189
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Allec N, Choi M, Yesupriya N, Szychowski B, White MR, Kann MG, Garcin ED, Daniel MC, Badano A. Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept. Sci Rep 2015; 5:12085. [PMID: 26160052 PMCID: PMC4498188 DOI: 10.1038/srep12085] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 05/28/2015] [Indexed: 11/24/2022] Open
Abstract
Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species.
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Affiliation(s)
- Nicholas Allec
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Mina Choi
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA
| | - Nikhil Yesupriya
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Brian Szychowski
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Maryland, USA
| | - Michael R. White
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Maryland, USA
| | - Maricel G. Kann
- Department of Biological Sciences, University of Maryland, Baltimore County, Maryland, USA
| | - Elsa D. Garcin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Maryland, USA
| | - Marie-Christine Daniel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Maryland, USA
| | - Aldo Badano
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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190
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Graewert MA, Franke D, Jeffries CM, Blanchet CE, Ruskule D, Kuhle K, Flieger A, Schäfer B, Tartsch B, Meijers R, Svergun DI. Automated pipeline for purification, biophysical and x-ray analysis of biomacromolecular solutions. Sci Rep 2015; 5:10734. [PMID: 26030009 PMCID: PMC5377070 DOI: 10.1038/srep10734] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/22/2015] [Indexed: 01/16/2023] Open
Abstract
Small angle X-ray scattering (SAXS), an increasingly popular method for structural analysis of biological macromolecules in solution, is often hampered by inherent sample polydispersity. We developed an all-in-one system combining in-line sample component separation with parallel biophysical and SAXS characterization of the separated components. The system coupled to an automated data analysis pipeline provides a novel tool to study difficult samples at the P12 synchrotron beamline (PETRA-3, EMBL/DESY, Hamburg).
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Affiliation(s)
- Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Clement E. Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Darja Ruskule
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Katja Kuhle
- Robert Koch-Institut, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany
| | - Antje Flieger
- Robert Koch-Institut, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany
| | - Bernd Schäfer
- Malvern Instruments GmbH, Rigipsstr. 19, 71083 Herrenberg, Germany
| | - Bernd Tartsch
- Malvern Instruments GmbH, Rigipsstr. 19, 71083 Herrenberg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
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191
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ARIFIN GIRI-RACHMAN ERNAWATI, PRATAMA FENRYCO, ROKA AJI OKTIRA, PATRIATI ARUM, IHSANAWATI IHSANAWATI, RAMDANI MOEIS MAELITA, GIRI-RACHMAN PUTRA EDY, RAMDANI MOEIS MAELITA. Expression and Purification of PhoR Sensor-Domain Histidine Kinase of Mycobacterium tuberculosis in Eschericia coli. MICROBIOLOGY INDONESIA 2015. [DOI: 10.5454/mi.9.2.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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192
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Feinstein WP, Brylinski M. Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 2015; 7:18. [PMID: 26082804 PMCID: PMC4468813 DOI: 10.1186/s13321-015-0067-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/14/2015] [Indexed: 12/13/2022] Open
Abstract
Background Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come with a default protocol for calculating the box size, however, many of these procedures have not been systematically evaluated. Methods In this study, we investigate how the docking accuracy of AutoDock Vina is affected by the selection of a search space. We propose a new procedure for calculating the optimal docking box size that maximizes the accuracy of binding pose prediction against a non-redundant and representative dataset of 3,659 protein-ligand complexes selected from the Protein Data Bank. Subsequently, we use the Directory of Useful Decoys, Enhanced to demonstrate that the optimized docking box size also yields an improved ranking in virtual screening. Binding pockets in both datasets are derived from the experimental complex structures and, additionally, predicted by eFindSite. Results A systematic analysis of ligand binding poses generated by AutoDock Vina shows that the highest accuracy is achieved when the dimensions of the search space are 2.9 times larger than the radius of gyration of a docking compound. Subsequent virtual screening benchmarks demonstrate that this optimized docking box size also improves compound ranking. For instance, using predicted ligand binding sites, the average enrichment factor calculated for the top 1 % (10 %) of the screening library is 8.20 (3.28) for the optimized protocol, compared to 7.67 (3.19) for the default procedure. Depending on the evaluation metric, the optimal docking box size gives better ranking in virtual screening for about two-thirds of target proteins. Conclusions This fully automated procedure can be used to optimize docking protocols in order to improve the ranking accuracy in production virtual screening simulations. Importantly, the optimized search space systematically yields better results than the default method not only for experimental pockets, but also for those predicted from protein structures. A script for calculating the optimal docking box size is freely available at www.brylinski.org/content/docking-box-size. We developed a procedure to optimize the box size in molecular docking calculations. Left panel shows the predicted binding pose of NADP (green sticks) compared to the experimental complex structure of human aldose reductase (blue sticks) using a default protocol. Right panel shows the docking accuracy using an optimized box size. ![]()
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Affiliation(s)
- Wei P Feinstein
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA ; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA ; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803 USA
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193
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Stefanovic AND, Lindhoud S, Semerdzhiev SA, Claessens MMAE, Subramaniam V. Oligomers of Parkinson’s Disease-Related α-Synuclein Mutants Have Similar Structures but Distinctive Membrane Permeabilization Properties. Biochemistry 2015; 54:3142-50. [DOI: 10.1021/bi501369k] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anja N. D. Stefanovic
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Saskia Lindhoud
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Slav A. Semerdzhiev
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Mireille M. A. E. Claessens
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
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194
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Rathore YS, Dhoke RR, Badmalia M, Sagar A, Ashish. SAXS data based global shape analysis of trigger factor (TF) proteins from E. coli, V. cholerae, and P. frigidicola: resolving the debate on the nature of monomeric and dimeric forms. J Phys Chem B 2015; 119:6101-12. [PMID: 25950744 DOI: 10.1021/acs.jpcb.5b00759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dimerization of bacterial chaperone trigger factor (TF) is an inherent protein concentration based property which available biophysical characterization and crystal structures have kept debatable. We acquired small-angle X-ray scattering (SAXS) intensity data from different TF homologues from Escherichia coli (ECTF), Vibrio cholerae (VCTF), and Psychrobacter frigidicola (PFTF) while varying each protein concentration. We found that ECTF and VCTF adopt a compact dimeric shape at higher concentrations which did not resemble the "back-to-back" conformation reported earlier for ECTF from crystallography (PDB ID: 1W26 ). In contrast, PFTF remained monomeric throughout the concentration range 2-90 μM displaying a multimodal open extended conformation. OLIGOMER analysis showed that both the ECTF and VCTF remained completely monomeric at lower concentrations (2-11 μM), while, at higher concentrations (60-90 μM), they adopted a dimeric form. Interestingly, the equilibrium existed in the medium concentration range (>11 and <60 μM), which correlates with the physiological concentration (40-50 μM) of TF in cell cytoplasm. Additionally, circular dichroism data revealed that solution structures of ECTF and VCTF contain predominantly α-helical content, while PFTF contains 310-helical content.
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Affiliation(s)
| | - Reema R Dhoke
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Amin Sagar
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ashish
- CSIR-Institute of Microbial Technology, Chandigarh, India
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195
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Hynson RMG, Duff AP, Kirby N, Mudie S, Lee LK. Differential ultracentrifugation coupled to small-angle X-ray scattering on macromolecular complexes. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715005051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) can provide accurate structural information and low-resolution shapes of macromolecules in solution. The technique is particularly amenable to large protein assemblies, which produce a strong scattering signal. Hence, SAXS can be a powerful tool to elucidate quaternary structure, especially when used in combination with high-resolution structural techniques such as X-ray crystallography and NMR. Sample requirements for SAXS experiments are stringent and only monodispersed samples can be satisfactorily analysed. Often, it is not possible to obtain a stable monodispersed sample of the protein of interest, in particular for multi-subunit protein complexes. In these circumstances, when the complex is less than approximately 1 MDa, size exclusion chromatography (SEC) coupled with SAXS (SEC-SAXS) can facilitate the separation of monodispersed protein from a polydispersed sample for a sufficient amount of time to collect useful SAXS data. However, many very large multi-subunit macromolecular assemblies have not been successfully purified with SEC, and hence despite being well suited to SAXS there is often no way to produce sample of sufficient quality. Rather than SEC, differential ultracentrifugation (DU) is the method of choice for the final step in the purification of large macromolecular protein complexes. Here, a new method is described for collecting SAXS data on samples directly from the fractionated elution of ultracentrifuge tubes after DU. It is demonstrated using apoferritin as a model protein that, like SEC-SAXS, DU-coupled SAXS can facilitate simultaneous purification and data collection. It is envisaged that this new method will enable high-quality SAXS data to be collected on a host of large macromolecular protein complex assemblies for the first time.
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196
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Petoukhov MV, Svergun DI. Ambiguity assessment of small-angle scattering curves from monodisperse systems. ACTA ACUST UNITED AC 2015; 71:1051-8. [PMID: 25945570 DOI: 10.1107/s1399004715002576] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/06/2015] [Indexed: 01/09/2023]
Abstract
A novel approach is presented for an a priori assessment of the ambiguity associated with spherically averaged single-particle scattering. The approach is of broad interest to the structural biology community, allowing the rapid and model-independent assessment of the inherent non-uniqueness of three-dimensional shape reconstruction from scattering experiments on solutions of biological macromolecules. One-dimensional scattering curves recorded from monodisperse systems are nowadays routinely utilized to generate low-resolution particle shapes, but the potential ambiguity of such reconstructions remains a major issue. At present, the (non)uniqueness can only be assessed by a posteriori comparison and averaging of repetitive Monte Carlo-based shape-determination runs. The new a priori ambiguity measure is based on the number of distinct shape categories compatible with a given data set. For this purpose, a comprehensive library of over 14,000 shape topologies has been generated containing up to seven beads closely packed on a hexagonal grid. The computed scattering curves rescaled to keep only the shape topology rather than the overall size information provide a `scattering map' of this set of shapes. For a given scattering data set, one rapidly obtains the number of neighbours in the map and the associated shape topologies such that in addition to providing a quantitative ambiguity measure the algorithm may also serve as an alternative shape-analysis tool. The approach has been validated in model calculations on geometrical bodies and its usefulness is further demonstrated on a number of experimental X-ray scattering data sets from proteins in solution. A quantitative ambiguity score (a-score) is introduced to provide immediate and convenient guidance to the user on the uniqueness of the ab initio shape reconstruction from the given data set.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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197
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Wen B, Peng J, Zuo X, Gong Q, Zhang Z. Characterization of protein flexibility using small-angle x-ray scattering and amplified collective motion simulations. Biophys J 2015; 107:956-64. [PMID: 25140431 DOI: 10.1016/j.bpj.2014.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/08/2014] [Accepted: 07/01/2014] [Indexed: 01/12/2023] Open
Abstract
Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations.
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Affiliation(s)
- Bin Wen
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Junhui Peng
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Xiaobing Zuo
- Advanced Photon Source, Argonne National Laboratory, Chicago, Illinois
| | - Qingguo Gong
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
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198
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Jiménez-García B, Pons C, Svergun DI, Bernadó P, Fernández-Recio J. pyDockSAXS: protein-protein complex structure by SAXS and computational docking. Nucleic Acids Res 2015; 43:W356-61. [PMID: 25897115 PMCID: PMC4489248 DOI: 10.1093/nar/gkv368] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/02/2015] [Indexed: 11/13/2022] Open
Abstract
Structural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein–protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein–protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction.
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Affiliation(s)
- Brian Jiménez-García
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, F-34090 Montpellier, France
| | - Juan Fernández-Recio
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain
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199
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Bacterial killing via a type IV secretion system. Nat Commun 2015; 6:6453. [PMID: 25743609 DOI: 10.1038/ncomms7453] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/29/2015] [Indexed: 12/24/2022] Open
Abstract
Type IV secretion systems (T4SSs) are multiprotein complexes that transport effector proteins and protein-DNA complexes through bacterial membranes to the extracellular milieu or directly into the cytoplasm of other cells. Many bacteria of the family Xanthomonadaceae, which occupy diverse environmental niches, carry a T4SS with unknown function but with several characteristics that distinguishes it from other T4SSs. Here we show that the Xanthomonas citri T4SS provides these cells the capacity to kill other Gram-negative bacterial species in a contact-dependent manner. The secretion of one type IV bacterial effector protein is shown to require a conserved C-terminal domain and its bacteriolytic activity is neutralized by a cognate immunity protein whose 3D structure is similar to peptidoglycan hydrolase inhibitors. This is the first demonstration of the involvement of a T4SS in bacterial killing and points to this special class of T4SS as a mediator of both antagonistic and cooperative interbacterial interactions.
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200
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Jeffries CM, Graewert MA, Svergun DI, Blanchet CE. Limiting radiation damage for high-brilliance biological solution scattering: practical experience at the EMBL P12 beamline PETRAIII. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:273-279. [PMID: 25723929 DOI: 10.1107/s1600577515000375] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 01/08/2015] [Indexed: 06/04/2023]
Abstract
Radiation damage is the general curse of structural biologists who use synchrotron small-angle X-ray scattering (SAXS) to investigate biological macromolecules in solution. The EMBL-P12 biological SAXS beamline located at the PETRAIII storage ring (DESY, Hamburg, Germany) caters to an extensive user community who integrate SAXS into their diverse structural biology programs. The high brilliance of the beamline [5.1 × 10(12) photons s(-1), 10 keV, 500 (H) µm × 250 (V) µm beam size at the sample position], combined with automated sample handling and data acquisition protocols, enable the high-throughput structural characterization of macromolecules in solution. However, considering the often-significant resources users invest to prepare samples, it is crucial that simple and effective protocols are in place to limit the effects of radiation damage once it has been detected. Here various practical approaches are evaluated that users can implement to limit radiation damage at the P12 beamline to maximize the chances of collecting quality data from radiation sensitive samples.
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Affiliation(s)
- Cy M Jeffries
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
| | - Melissa A Graewert
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
| | - Clément E Blanchet
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
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