351
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Faccio G, Salentinig S. Enzyme-Triggered Dissociation of a FRET-Based Protein Biosensor Monitored by Synchrotron SAXS. Biophys J 2017; 113:1731-1737. [PMID: 29045867 DOI: 10.1016/j.bpj.2017.08.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/19/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022] Open
Abstract
Protein biosensors are widely used for the monitoring of metabolite concentration and enzymatic activities inside living cells and in in vitro applications. Neutrophil elastase (NE) is a serine protease of relevance in inflammatory diseases whose activity can lead to pathological conditions if unregulated. This study focuses on the structural characterization of a biosensor for NE activity based on Förster resonance energy transfer (FRET). The cleavage by NE results in dissociation of the FRET fluorescent protein pair and alteration of the fluorescent emission spectrum. We have used small angle x-ray scattering at a high intensity synchrotron source, combined with model-free analysis of the scattering data, to demonstrate the structure of the biosensor and the effect of its exposure to NE on size and shape. These investigations, together with biochemical studies, established the nanostructure-activity relationship that may contribute to the detailed understanding of the FRET-based biosensor and guide the rational design of new biosensor constructs.
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Affiliation(s)
- Greta Faccio
- Laboratory for Biointerfaces, Department "Materials Meet Life", Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland.
| | - Stefan Salentinig
- Laboratory for Biointerfaces, Department "Materials Meet Life", Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland.
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352
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Yefremova Y, Danquah BD, Opuni KF, El-Kased R, Koy C, Glocker MO. Mass spectrometric characterization of protein structures and protein complexes in condensed and gas phase. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:445-459. [PMID: 29183193 DOI: 10.1177/1469066717722256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins are essential for almost all physiological processes of life. They serve a myriad of functions which are as varied as their unique amino acid sequences and their corresponding three-dimensional structures. To fulfill their tasks, most proteins depend on stable physical associations, in the form of protein complexes that evolved between themselves and other proteins. In solution (condensed phase), proteins and/or protein complexes are in constant energy exchange with the surrounding solvent. Albeit methods to describe in-solution thermodynamic properties of proteins and of protein complexes are well established and broadly applied, they do not provide a broad enough access to life-science experimentalists to study all their proteins' properties at leisure. This leaves great desire to add novel methods to the analytical biochemist's toolbox. The development of electrospray ionization created the opportunity to characterize protein higher order structures and protein complexes rather elegantly by simultaneously lessening the need of sophisticated sample preparation steps. Electrospray mass spectrometry enabled us to translate proteins and protein complexes very efficiently into the gas phase under mild conditions, retaining both, intact protein complexes, and gross protein structures upon phase transition. Moreover, in the environment of the mass spectrometer (gas phase, in vacuo), analyte molecules are free of interactions with surrounding solvent molecules and, therefore, the energy of inter- and intramolecular forces can be studied independently from interference of the solvating environment. Provided that gas phase methods can give information which is relevant for understanding in-solution processes, gas phase protein structure studies and/or investigations on the characterization of protein complexes has rapidly gained more and more attention from the bioanalytical scientific community. Recent reports have shown that electrospray mass spectrometry provides direct access to six prime protein complex properties: stabilities, compositions, binding surfaces (epitopes), disassembly processes, stoichiometries, and thermodynamic parameters.
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Affiliation(s)
- Yelena Yefremova
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
| | - Bright D Danquah
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
| | | | - Reham El-Kased
- 3 Microbiology and Immunology, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
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353
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Song J, Gomes GN, Shi T, Gradinaru CC, Chan HS. Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins. Biophys J 2017; 113:1012-1024. [PMID: 28877485 DOI: 10.1016/j.bpj.2017.07.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 12/28/2022] Open
Abstract
A mathematico-physically valid formulation is required to infer properties of disordered protein conformations from single-molecule Förster resonance energy transfer (smFRET). Conformational dimensions inferred by conventional approaches that presume a homogeneous conformational ensemble can be unphysical. When all possible-heterogeneous as well as homogeneous-conformational distributions are taken into account without prejudgment, a single value of average transfer efficiency 〈E〉 between dyes at two chain ends is generally consistent with highly diverse, multiple values of the average radius of gyration 〈Rg〉. Here we utilize unbiased conformational statistics from a coarse-grained explicit-chain model to establish a general logical framework to quantify this fundamental ambiguity in smFRET inference. As an application, we address the long-standing controversy regarding the denaturant dependence of 〈Rg〉 of unfolded proteins, focusing on Protein L as an example. Conventional smFRET inference concluded that 〈Rg〉 of unfolded Protein L is highly sensitive to [GuHCl], but data from SAXS suggested a near-constant 〈Rg〉 irrespective of [GuHCl]. Strikingly, our analysis indicates that although the reported 〈E〉 values for Protein L at [GuHCl] = 1 and 7 M are very different at 0.75 and 0.45, respectively, the Bayesian Rg2 distributions consistent with these two 〈E〉 values overlap by as much as 75%. Our findings suggest, in general, that the smFRET-SAXS discrepancy regarding unfolded protein dimensions likely arise from highly heterogeneous conformational ensembles at low or zero denaturant, and that additional experimental probes are needed to ascertain the nature of this heterogeneity.
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Affiliation(s)
- Jianhui Song
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, China; Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gregory-Neal Gomes
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada; Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Tongfei Shi
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Claudiu C Gradinaru
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada; Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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354
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Gong Z, Liu Z, Dong X, Ding YH, Dong MQ, Tang C. Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL. BIOPHYSICS REPORTS 2017; 3:100-108. [PMID: 29238747 PMCID: PMC5719800 DOI: 10.1007/s41048-017-0044-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/18/2017] [Indexed: 12/16/2022] Open
Abstract
Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigid-body refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein–protein complexes, and is freely available at www.tanglab.org/resources.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
| | - Zhu Liu
- Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou, 310057 China
| | - Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
| | - Yue-He Ding
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605 USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206 China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
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355
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Bernetti M, Masetti M, Pietrucci F, Blackledge M, Jensen MR, Recanatini M, Mollica L, Cavalli A. Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations. J Phys Chem B 2017; 121:9572-9582. [DOI: 10.1021/acs.jpcb.7b08925] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mattia Bernetti
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Matteo Masetti
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Fabio Pietrucci
- Institut
de Minéralogie,
de Physique des Matériaux et de Cosmochimie, Sorbonne Universités−Université
Pierre et Marie Curie Paris 6, CNRS UMR 7590, IRD UMR 206, Museum national d’Histoire naturelle, F-75005 Paris, France
| | - Martin Blackledge
- Protein
Dynamics and Flexibility by NMR Group, Institut de Biologie Structurale, 38044 Grenoble, France
| | - Malene Ringkjobing Jensen
- Protein
Dynamics and Flexibility by NMR Group, Institut de Biologie Structurale, 38044 Grenoble, France
| | - Maurizio Recanatini
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Luca Mollica
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Andrea Cavalli
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
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356
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Sønderby P, Rinnan Å, Madsen JJ, Harris P, Bukrinski JT, Peters GHJ. Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape. J Chem Inf Model 2017; 57:2463-2475. [DOI: 10.1021/acs.jcim.6b00789] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Pernille Sønderby
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Åsmund Rinnan
- Department
of Food Science, Faculty of Science, University of Copenhagen, DK-1958 Frederiksberg C, Denmark
| | - Jesper J. Madsen
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | | | - Günther H. J. Peters
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
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357
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Florenzano F, Veronica C, Ciasca G, Ciotti MT, Pittaluga A, Olivero G, Feligioni M, Iannuzzi F, Latina V, Maria Sciacca MF, Sinopoli A, Milardi D, Pappalardo G, Marco DS, Papi M, Atlante A, Bobba A, Borreca A, Calissano P, Amadoro G. Extracellular truncated tau causes early presynaptic dysfunction associated with Alzheimer's disease and other tauopathies. Oncotarget 2017; 8:64745-64778. [PMID: 29029390 PMCID: PMC5630290 DOI: 10.18632/oncotarget.17371] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/11/2017] [Indexed: 12/14/2022] Open
Abstract
The largest part of tau secreted from AD nerve terminals and released in cerebral spinal fluid (CSF) is C-terminally truncated, soluble and unaggregated supporting potential extracellular role(s) of NH2 -derived fragments of protein on synaptic dysfunction underlying neurodegenerative tauopathies, including Alzheimer's disease (AD). Here we show that sub-toxic doses of extracellular-applied human NH2 tau 26-44 (aka NH 2 htau) -which is the minimal active moiety of neurotoxic 20-22kDa peptide accumulating in vivo at AD synapses and secreted into parenchyma- acutely provokes presynaptic deficit in K+ -evoked glutamate release on hippocampal synaptosomes along with alteration in local Ca2+ dynamics. Neuritic dystrophy, microtubules breakdown, deregulation in presynaptic proteins and loss of mitochondria located at nerve endings are detected in hippocampal cultures only after prolonged exposure to NH 2 htau. The specificity of these biological effects is supported by the lack of any significant change, either on neuronal activity or on cellular integrity, shown by administration of its reverse sequence counterpart which behaves as an inactive control, likely due to a poor conformational flexibility which makes it unable to dynamically perturb biomembrane-like environments. Our results demonstrate that one of the AD-relevant, soluble and secreted N-terminally truncated tau forms can early contribute to pathology outside of neurons causing alterations in synaptic activity at presynaptic level, independently of overt neurodegeneration.
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Affiliation(s)
| | | | - Gabriele Ciasca
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Maria Teresa Ciotti
- Institute of Cellular Biology and Neuroscience, CNR, IRCSS Santa Lucia Foundation, Rome, Italy
| | - Anna Pittaluga
- Department of Pharmacy, Pharmacology and Toxicology Section, University of Genoa, Genoa, Viale Cembrano, Italy
| | - Gunedalina Olivero
- Department of Pharmacy, Pharmacology and Toxicology Section, University of Genoa, Genoa, Viale Cembrano, Italy
| | - Marco Feligioni
- European Brain Research Institute, Rome, Italy
- Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Milan, Italy
| | | | | | | | | | - Danilo Milardi
- Institute of Biostructures and Bioimaging, CNR, Catania, Italy
| | | | - De Spirito Marco
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Massimiliano Papi
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Anna Atlante
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa, Viale Benedetto XV, Italy
| | - Antonella Bobba
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa, Viale Benedetto XV, Italy
| | - Antonella Borreca
- Institute of Cellular Biology and Neuroscience, CNR, IRCSS Santa Lucia Foundation, Rome, Italy
| | | | - Giuseppina Amadoro
- European Brain Research Institute, Rome, Italy
- Institute of Translational Pharmacology, CNR, Rome, Italy
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358
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Golub M, Hejazi M, Kölsch A, Lokstein H, Wieland DCF, Zouni A, Pieper J. Solution structure of monomeric and trimeric photosystem I of Thermosynechococcus elongatus investigated by small-angle X-ray scattering. PHOTOSYNTHESIS RESEARCH 2017; 133:163-173. [PMID: 28258466 DOI: 10.1007/s11120-017-0342-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
The structure of monomeric and trimeric photosystem I (PS I) of Thermosynechococcus elongatus BP1 (T. elongatus) was investigated by small-angle X-ray scattering (SAXS). The scattering data reveal that the protein-detergent complexes possess radii of gyration of 58 and 78 Å in the cases of monomeric and trimeric PS I, respectively. The results also show that the samples are monodisperse, virtually free of aggregation, and contain empty detergent micelles. The shape of the protein-detergent complexes can be well approximated by elliptical cylinders with a height of 78 Å. Monomeric PS I in buffer solution exhibits minor and major radii of the elliptical cylinder of about 50 and 85 Å, respectively. In the case of trimeric PS I, both radii are equal to about 110 Å. The latter model can be shown to accommodate three elliptical cylinders equal to those describing monomeric PS I. A structure reconstitution also reveals that the protein-detergent complexes are larger than their respective crystal structures. The reconstituted structures are larger by about 20 Å mainly in the region of the hydrophobic surfaces of the monomeric and trimeric PS I complexes. This seeming contradiction can be resolved by the addition of a detergent belt constituted by a monolayer of dodecyl-β-D-maltoside molecules. Assuming a closest possible packing, a number of roughly 1024 and 1472 detergent molecules can be determined for monomeric and trimeric PS I, respectively. Taking the monolayer of detergent molecules into account, the solution structure can be almost perfectly modeled by the crystal structures of monomeric and trimeric PS I.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwaldi 1, 50411, Tartu, Estonia
| | - Mahdi Hejazi
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115, Berlin, Germany
| | - Adrian Kölsch
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115, Berlin, Germany
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague, Czech Republic
| | - D C Florian Wieland
- Department for Metalic Biomaterials, Institute for Materials Research, Helmholtz Zentrum Geesthacht, 21502, Geesthacht, Germany
| | - Athina Zouni
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115, Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwaldi 1, 50411, Tartu, Estonia.
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359
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Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017; 73:710-728. [PMID: 28876235 PMCID: PMC5586245 DOI: 10.1107/s2059798317011597] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/02/2022] Open
Abstract
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- ANSTO, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale (IBS), and Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A. Jacques
- University of Technology Sydney, ithree Institute, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Nigel M. Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP48, 91192 Gif-sur-Yvette CEDEX, France
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-2501, USA
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Nokestrasse 85, 22607 Hamburg, Germany
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - John A. Tainer
- Basic Science Research Division, Molecular and Cellular Oncology, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - John Westbrook
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 07102, USA
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360
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Morley DO, Malfois M, Kamonsutthipaijit N, Kondratuk DV, Anderson HL, Wilson M. A Coarse-Grained Model for Free and Template-Bound Porphyrin Nanorings. J Phys Chem A 2017; 121:5907-5920. [PMID: 28703593 DOI: 10.1021/acs.jpca.7b05279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coarse-grained simulation models are developed to study both template-bound and free porphyrin nanoring systems. Key interactions are modeled with relatively simple (and physically motivated) energy functions which allow for relatively facile transfer both between different ring sizes and between the template-bound and free nanoring systems. The effects of varying the model parameters on the respective radii of gyration are determined. The effects of including different templates on the ring structure are investigated both in terms of the detailed geometry of the template and the interaction strength between the template and the metal centers in the nanorings. The role of the template-nanoring interaction strength in controlling potential "caterpillar track" rotational motion is discussed. The relationship of the model to experimental small-angle X-ray, exchange spectroscopy, and electron spin resonance results is discussed.
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Affiliation(s)
- David Ormrod Morley
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Marc Malfois
- Diamond Light Source Ltd , Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Nuntaporn Kamonsutthipaijit
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory , Mansfield Road, Oxford OX1 3TA, U.K
| | - Dmitry V Kondratuk
- Diamond Light Source Ltd , Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory , Mansfield Road, Oxford OX1 3TA, U.K
| | - Mark Wilson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
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361
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Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M. Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Miriam Sonntag
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Bernd Simon
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ); Forschungszentrum Jülich GmbH; Lichtenbergstr. 1 85748 Garching Germany
| | - Arie Geerlof
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Ralf Stehle
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Frank Gabel
- Univ. Grenoble Alpes; CEA, CNRS, IBS; 38000 Grenoble France
- Institut Laue-Langevin (ILL); Avenue des Martyrs 38042 Grenoble France
| | - Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
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362
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Complementary uses of small angle X-ray scattering and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1623-1630. [PMID: 28743534 DOI: 10.1016/j.bbapap.2017.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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363
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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364
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Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M. Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201702904] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Miriam Sonntag
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Bernd Simon
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ); Forschungszentrum Jülich GmbH; Lichtenbergstr. 1 85748 Garching Germany
| | - Arie Geerlof
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Ralf Stehle
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Frank Gabel
- Univ. Grenoble Alpes; CEA, CNRS, IBS; 38000 Grenoble France
- Institut Laue-Langevin (ILL); Avenue des Martyrs 38042 Grenoble France
| | - Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
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365
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Dahal E, Choi M, Alam N, Bhirde AA, Beaucage SL, Badano A. Structural evaluation of an amyloid fibril model using small-angle x-ray scattering. Phys Biol 2017; 14:046001. [DOI: 10.1088/1478-3975/aa776a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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366
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Abstract
X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.
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Affiliation(s)
- Steve P Meisburger
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - William C Thomas
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Nozomi Ando
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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367
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Vangaveti S, D’Esposito RJ, Lippens JL, Fabris D, Ranganathan SV. A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry. Phys Chem Chem Phys 2017; 19:14937-14946. [PMID: 28374022 PMCID: PMC6958515 DOI: 10.1039/c7cp00717e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) is a rapidly emerging tool for the investigation of nucleic acid structure and dynamics. IMS-MS determinations can provide valuable information regarding alternative topologies, folding intermediates, and conformational heterogeneities, which are not readily accessible to other analytical techniques. The leading strategies for data interpretation rely on computational and experimental approaches to correctly assign experimental observations to putative structures. A very effective strategy involves the application of molecular dynamics (MD) simulations to predict the structure of the analyte molecule, calculate its collision cross section (CCS), and then compare this computational value with the corresponding experimental data. While this approach works well for small nucleic acid species, analyzing larger nucleic acids of biological interest is hampered by the computational cost associated with capturing their extensive structure and dynamics in all-atom detail. In this report, we describe the implementation of a coarse graining (CG) approach to reduce the cost of the computational methods employed in the data interpretation workflow. Our framework employs a five-bead model to accurately represent each nucleotide in the nucleic acid structure. The beads are appropriately parameterized to enable the direct calculation of CCS values from CG models, thus affording the ability to pursue the analysis of larger, highly dynamic constructs. The validity of this approach was successfully confirmed by the excellent correlation between the CCS values obtained in parallel by all-atom and CG workflows.
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Affiliation(s)
| | | | - J. L. Lippens
- Discovery Analytical Sciences, Amgen, Thousand Oaks, CA
| | - D. Fabris
- The RNA Institute, University at Albany, NY
- Department of Chemistry, University at Albany, NY
- Department of Biological Sciences, University at Albany, NY
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368
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Thompson MK, Ehlinger AC, Chazin WJ. Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR. Methods Enzymol 2017; 592:49-76. [PMID: 28668130 DOI: 10.1016/bs.mie.2017.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples.
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Affiliation(s)
- Matthew K Thompson
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Aaron C Ehlinger
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.
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369
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Abstract
Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.
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Affiliation(s)
- Hosung Ki
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Key Young Oang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, South Korea;
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
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370
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Laurin Y, Eyer J, Robert CH, Prevost C, Sacquin-Mora S. Mobility and Core-Protein Binding Patterns of Disordered C-Terminal Tails in β-Tubulin Isotypes. Biochemistry 2017; 56:1746-1756. [PMID: 28290671 DOI: 10.1021/acs.biochem.6b00988] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although they play a significant part in the regulation of microtubule structure, dynamics, and function, the disordered C-terminal tails of tubulin remain invisible to experimental structural methods and do not appear in the crystallographic structures that are currently available in the Protein Data Bank. Interestingly, these tails concentrate most of the sequence variability between tubulin isotypes and are the sites of the principal post-translational modifications undergone by this protein. Using homology modeling, we developed two complete models for the human αI/βI- and αI/βIII-tubulin isotypes that include their C-terminal tails. We then investigated the conformational variability of the two β-tails using long time-scale classical molecular dynamics simulations that revealed similar features, notably the unexpected presence of common anchoring regions on the surface of the tuulin dimer, but also distinctive mobility or interaction patterns, some of which could be related to the tail lengths and charge distributions. We also observed in our simulations that the C-terminal tail from the βI isotype, but not the βIII isotype, formed contacts in the putative binding site of a recently discovered peptide that disrupts microtubule formation in glioma cells. Hindering the binding site in the βI isotype would be consistent with this peptide's preferential disruption of microtubule formation in glioma, whose cells overexpress βIII, compared to normal glial cells. While these observations need to be confirmed with more intensive sampling, our study opens new perspectives for the development of isotype-specific chemotherapy drugs.
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Affiliation(s)
- Yoann Laurin
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Joel Eyer
- Laboratoire de Neurobiologie & Transgenèse, UPRES EA 3143, INSERM, Centre Hospitalier Universitaire , Angers, France
| | - Charles H Robert
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prevost
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
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371
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Prischi F, Pastore A. Hybrid Methods in Iron-Sulfur Cluster Biogenesis. Front Mol Biosci 2017; 4:12. [PMID: 28349052 PMCID: PMC5346568 DOI: 10.3389/fmolb.2017.00012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
Hybrid methods, which combine and integrate several biochemical and biophysical techniques, have rapidly caught up in the last twenty years to provide a way to obtain a fuller description of proteins and molecular complexes with sizes and complexity otherwise not easily affordable. Here, we review the use of a robust hybrid methodology based on a mixture of NMR, SAXS, site directed mutagenesis and molecular docking which we have developed to determine the structure of weakly interacting molecular complexes. We applied this technique to gain insights into the structure of complexes formed amongst proteins involved in the molecular machine, which produces the essential iron-sulfur cluster prosthetic groups. Our results were validated both by X-ray structures and by other groups who adopted the same approach. We discuss the advantages and the limitations of our methodology and propose new avenues, which could improve it.
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Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex Colchester, UK
| | - Annalisa Pastore
- Maurice Wohl Institute, King's College LondonLondon, UK; Molecular Medicine Department, University of PaviaPavia, Italy
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372
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Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin. J Biol Chem 2017; 292:6667-6679. [PMID: 28270505 DOI: 10.1074/jbc.m117.775858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/27/2017] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) can damage DNA, proteins, and lipids, so cells have antioxidant systems that regulate ROS. In many bacteria, a dedicated peroxiredoxin reductase, alkyl hydroperoxide reductase subunit F (AhpF), catalyzes the rapid reduction of the redox-active disulfide center of the antioxidant protein peroxiredoxin (AhpC) to detoxify ROS such as hydrogen peroxide, organic hydroperoxide, and peroxynitrite. AhpF is a flexible multidomain protein that enables a series of electron transfers among the redox centers by accepting reducing equivalents from NADH. A flexible linker connecting the N-terminal domain (NTD) and C-terminal domain (CTD) of AhpF suggests that the enzyme adopts a large-scale domain motion that alternates between the closed and open states to shuttle electrons from the CTD via the NTD to AhpC. Here, we conducted comprehensive mutational, biochemical, and biophysical analyses to gain insights into the role of the flexible linker and the residues critical for the domain motions of Escherichia coli AhpF (EcAhpF) during electron transfer. Small-angle X-ray scattering studies of linker mutants revealed that a group of charged residues, 200EKR202, is crucial for the swiveling motion of the NTD. Moreover, NADH binding significantly affected EcAhpF flexibility and the movement of the NTD relative to the CTD. The mutants also exhibited a decrease in H2O2 reduction by the AhpF-AhpC ensemble. We propose that a concerted movement involving the NTD, C-terminal NADH, and FAD domains, and the flexible linker between them is essential for optimal intra-domain cross-talk and for efficient electron transfer to the redox partner AhpC required for peroxidation.
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Affiliation(s)
- Neelagandan Kamariah
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671
| | - Birgit Eisenhaber
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671
| | - Frank Eisenhaber
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671.,the School of Computer Engineering, Nanyang Technological University, Singapore 637553, Republic of Singapore
| | - Gerhard Grüber
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, .,the School of Biological Sciences, Nanyang Technological University, Singapore 637551, and
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373
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Solution structure and excitation energy transfer in phycobiliproteins of Acaryochloris marina investigated by small angle scattering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:318-324. [PMID: 28131736 DOI: 10.1016/j.bbabio.2017.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/09/2017] [Accepted: 01/24/2017] [Indexed: 11/22/2022]
Abstract
The structure of phycobiliproteins of the cyanobacterium Acaryochloris marina was investigated in buffer solution at physiological temperatures, i.e. under the same conditions applied in spectroscopic experiments, using small angle neutron scattering. The scattering data of intact phycobiliproteins in buffer solution containing phosphate can be well described using a cylindrical shape with a length of about 225Å and a diameter of approximately 100Å. This finding is qualitatively consistent with earlier electron microscopy studies reporting a rod-like shape of the phycobiliproteins with a length of about 250 (M. Chen et al., FEBS Letters 583, 2009, 2535) or 300Å (J. Marquart et al., FEBS Letters 410, 1997, 428). In contrast, phycobiliproteins dissolved in buffer lacking phosphate revealed a splitting of the rods into cylindrical subunits with a height of 28Å only, but also a pronounced sample aggregation. Complementary small angle neutron and X-ray scattering experiments on phycocyanin suggest that the cylindrical subunits may represent either trimeric phycocyanin or trimeric allophycocyanin. Our findings are in agreement with the assumption that a phycobiliprotein rod with a total height of about 225Å can accommodate seven trimeric phycocyanin subunits and one trimeric allophycocyanin subunit, each of which having a height of about 28Å. The structural information obtained by small angle neutron and X-ray scattering can be used to interpret variations in the low-energy region of the 4.5K absorption spectra of phycobiliproteins dissolved in buffer solutions containing and lacking phosphate, respectively.
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374
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Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Solà M. DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p. Nucleic Acids Res 2017; 45:951-967. [PMID: 27899643 PMCID: PMC5314765 DOI: 10.1093/nar/gkw1147] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/16/2016] [Accepted: 11/01/2016] [Indexed: 12/16/2022] Open
Abstract
The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces cerevisiae), mtDNA is a ∼80 kbp linear molecule and Abf2p, a double HMG-box protein, packages and maintains it. The protein binds DNA in a non-sequence-specific manner, but displays a distinct 'phased-binding' at specific DNA sequences containing poly-adenine tracts (A-tracts). We present here two crystal structures of Abf2p in complex with mtDNA-derived fragments bearing A-tracts. Each HMG-box of Abf2p induces a 90° bend in the contacted DNA, causing an overall U-turn. Together with previous data, this suggests that U-turn formation is the universal mechanism underlying mtDNA compaction induced by HMG-box proteins. Combining this structural information with mutational, biophysical and computational analyses, we reveal a unique DNA binding mechanism for Abf2p where a characteristic N-terminal flag and helix are crucial for mtDNA maintenance. Additionally, we provide the molecular basis for A-tract mediated exclusion of Abf2p binding. Due to high prevalence of A-tracts in yeast mtDNA, this has critical relevance for nucleoid architecture. Therefore, an unprecedented A-tract mediated protein positioning mechanism regulates DNA packaging proteins in the mitochondria, and in combination with DNA-bending and U-turn formation, governs mtDNA compaction.
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Affiliation(s)
- Arka Chakraborty
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Giorgio Medici
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Rafel Prohens
- Unitat de Polimorfisme i Calorimetria, Centres Científics i Tecnològics, University of Barcelona, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
| | - Josep Vilardell
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain
- Molecular Genomics Department, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, 08028, Spain
| | - Maria Solà
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
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375
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Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK. Internal Structure and Preferential Protein Binding of Colloidal Aggregates. ACS Chem Biol 2017; 12:282-290. [PMID: 27983786 DOI: 10.1021/acschembio.6b00791] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Colloidal aggregates of small molecules are the most common artifact in early drug discovery, sequestering and inhibiting target proteins without specificity. Understanding their structure and mechanism has been crucial to developing tools to control for, and occasionally even exploit, these particles. Unfortunately, their polydispersity and transient stability have prevented exploration of certain elementary properties, such as how they pack. Dye-stabilized colloidal aggregates exhibit enhanced homogeneity and stability when compared to conventional colloidal aggregates, enabling investigation of some of these properties. By small-angle X-ray scattering and multiangle light scattering, pair distance distribution functions suggest that the dye-stabilized colloids are filled, not hollow, spheres. Stability of the coformulated colloids enabled investigation of their preference for binding DNA, peptides, or folded proteins, and their ability to purify one from the other. The coformulated colloids showed little ability to bind DNA. Correspondingly, the colloids preferentially sequestered protein from even a 1600-fold excess of peptides that are themselves the result of a digest of the same protein. This may reflect the avidity advantage that a protein has in a surface-to-surface interaction with the colloids. For the first time, colloids could be shown to have preferences of up to 90-fold for particular proteins over others. Loaded onto the colloids, bound enzyme could be spun down, resuspended, and released back into buffer, regaining most of its activity. Implications of these observations for colloid mechanisms and utility will be considered.
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Affiliation(s)
- Da Duan
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Hayarpi Torosyan
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Daniel Elnatan
- Howard
Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
| | - Christopher K. McLaughlin
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Jennifer Logie
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Molly S. Shoichet
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - David A. Agard
- Howard
Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
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376
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Brennich ME, Round AR, Hutin S. Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline. J Vis Exp 2017. [PMID: 28117806 PMCID: PMC5409194 DOI: 10.3791/54861] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biological small angle X-ray scattering (BioSAXS) is a powerful technique in molecular and structural biology used to determine solution structure, particle size and shape, and surface-to-volume ratio of macromolecules. The technique is applicable to a very wide variety of solution conditions spanning a broad range of concentrations, pH values, ionic strengths, temperatures, additives, etc., but the sample is required to be monodisperse. This caveat led to the implementation of liquid chromatography systems on SAXS beamlines. Here, we describe the upstream integration of size-exclusion (SEC) and ion-exchange chromatography (IEC) on a beamline, different methods for optimal background subtraction, and data reduction. As an example, we describe how we use SEC- and IEC-SAXS on a fragment of the essential vaccinia virus protein D5, consisting of a D5N helicase domain. We determine its overall shape and molecular weight, showing the hexameric structure of the protein.
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Affiliation(s)
| | - Adam R Round
- European Molecular Biology Laboratory; School of Chemical and Physical Sciences, Keele University
| | - Stephanie Hutin
- Groupe de Microscopie Electronique et Méthodes, Institut de Biologie Structurale;
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377
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Gorantla NV, Shkumatov AV, Chinnathambi S. Conformational Dynamics of Intracellular Tau Protein Revealed by CD and SAXS. Methods Mol Biol 2017; 1523:3-20. [PMID: 27975241 DOI: 10.1007/978-1-4939-6598-4_1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A native conformation of a protein is essential for its biological role. In certain conditions, some proteins show non-native conformations, leading to aggregation, which in turn may produce severe pathologies. Such physiological conditions are classified as protein misfolding diseases. Alzheimer's disease (AD) is the most common form of dementia. Extracellular senile plaques formed by Amyloid β and intracellular aggregates formed by microtubule-associated protein Tau (MAPT) are the hallmarks of AD. Physiological role of MAPT is to maintain the integrity and stability of microtubules, however it tends to self-aggregate forming intracellular paired helical filaments (PHFs) during AD. MAPT is also subjected to various post-translational modifications such as phosphorylation, glycosylation, truncation, and acetylation. Being natively unfolded, MAPT is prone to full characterization at atomic level. Small-angle X-ray scattering (SAXS) is often applied in combination with other biophysical methods, like nuclear magnetic resonance (NMR), circular dichroism (CD), fluorescence spectroscopy, analytical ultracentrifugation (AUC), or dynamic light scattering (DLS) to characterize natively unfolded systems. Here we describe the practical aspects of MAPT characterization by SAXS and CD in detail as well as outline the inferred structural and functional implications.
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Affiliation(s)
- Nalini Vijay Gorantla
- Neurobiology Group, Division of Biochemical Sciences, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, 411008, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), 10025, New Delhi, India
| | | | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, 411008, Pune, Maharashtra, India. .,Academy of Scientific and Innovative Research (AcSIR), 10025, New Delhi, India.
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378
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Abstract
Over the past decade, it has become evident that a large proportion of proteins contain intrinsically disordered regions, which play important roles in pivotal cellular functions. Many computational tools have been developed with the aim of identifying the level and location of disorder within a protein. In this chapter, we describe a neural network based technique called SPINE-D that employs a unique three-state design and can accurately capture disordered residues in both short and long disordered regions. SPINE-D was trained on a large database of 4229 non-redundant proteins, and yielded an AUC of 0.86 on a cross-validation test and 0.89 on an independent test. SPINE-D can also detect a semi-disordered state that is associated with induced folders and aggregation-prone regions in disordered proteins and weakly stable or locally unfolded regions in structured proteins. We implement an online web service and an offline stand-alone program for SPINE-D, they are freely available at http://sparks-lab.org/SPINE-D/ . We then walk you through how to use the online and offline SPINE-D in making disorder predictions, and examine the disorder and semi-disorder prediction in a case study on the p53 protein.
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Affiliation(s)
- Tuo Zhang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Eshel Faraggi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46032, USA
- Research and Information Systems, LLC, Indianapolis, IN, USA
| | - Zhixiu Li
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast Campus, Science 1 (G24) 2.10, Parklands Drive, Southport, QLD, 4222, Australia.
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379
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Hsieh A, Lu L, Chance MR, Yang S. A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:229-238. [PMID: 29218563 DOI: 10.1007/978-981-10-6038-0_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques. Here, we provide a practical protocol for implementing our integrated iSPOT platform by integrating three different biophysical techniques: small-angle X-ray scattering (SAXS), hydroxyl radical footprinting, and computational docking simulations. Specifically, individual techniques are described from experimental and/or computational perspectives, and complementary structural information from these different techniques are integrated for accurate characterization of the structures of large protein-protein complexes.
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Affiliation(s)
- An Hsieh
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106-4988, USA
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Mark R Chance
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106-4988, USA
| | - Sichun Yang
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106-4988, USA.
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380
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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381
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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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382
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Baldwin AG, Yang Y, Bridges NJ, Braley JC. Tributyl Phosphate Aggregation in the Presence of Metals: An Assessment Using Diffusion NMR Spectroscopy. J Phys Chem B 2016; 120:12184-12192. [PMID: 27805405 DOI: 10.1021/acs.jpcb.6b09154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diffusion nuclear magnetic resonance (NMR) spectroscopy was used to find the interaggregate interactions and sizes of tributyl phosphate (TBP) aggregates containing varying concentrations of uranium or zirconium and HNO3 in an n-dodecane diluent. The average diffusion coefficients of TBP species were measured using a pulsed-field gradient stimulated echo experiment with a longitudinal eddy-current delay (STE-LED). Interaggregate interactions were determined by measuring the diffusion coefficient of TBP in a sample after a series of dilutions with n-dodecane. The interaction-independent infinite dilution diffusion coefficient was also calculated from these measurements. The sizes of TBP aggregates were calculated from the infinite dilution diffusion coefficient using the Wilke-Chang equation. Interactions between TBP aggregates were observed to correspond to a hard sphere potential with a repulsive component. Aggregate sizes found by NMR were comparable to literature values found using small-angle neutron scattering. The diffusion of TBP in heavy organic third phases indicates that the third phase may be a bicontinuous structure like that found in traditional surfactant systems.
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Affiliation(s)
- Anna G Baldwin
- Department of Chemistry, Colorado School of Mines , Golden, Colorado 80401, United States
| | - Yuan Yang
- Department of Chemistry, Colorado School of Mines , Golden, Colorado 80401, United States
| | - Nicholas J Bridges
- Savannah River National Laboratory, Aiken, South Carolina 29808, United States
| | - Jenifer C Braley
- Department of Chemistry, Colorado School of Mines , Golden, Colorado 80401, United States
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383
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Keppel TR, Sarpong K, Murray EM, Monsey J, Zhu J, Bose R. Biophysical Evidence for Intrinsic Disorder in the C-terminal Tails of the Epidermal Growth Factor Receptor (EGFR) and HER3 Receptor Tyrosine Kinases. J Biol Chem 2016; 292:597-610. [PMID: 27872189 DOI: 10.1074/jbc.m116.747485] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/15/2016] [Indexed: 12/21/2022] Open
Abstract
The epidermal growth factor receptor (EGFR)/ErbB family of receptor tyrosine kinases includes oncogenes important in the progression of breast and other cancers, and they are targets for many drug development strategies. Each member of the ErbB family possesses a unique, structurally uncharacterized C-terminal tail that plays an important role in autophosphorylation and signal propagation. To determine whether these C-terminal tails are intrinsically disordered regions, we conducted a battery of biophysical experiments on the EGFR and HER3 tails. Using hydrogen/deuterium exchange mass spectrometry, we measured the conformational dynamics of intracellular half constructs and compared the tails with the ordered kinase domains. The C-terminal tails demonstrate more rapid deuterium exchange behavior when compared with the kinase domains. Next, we expressed and purified EGFR and HER3 tail-only constructs. Results from circular dichroism spectroscopy, size exclusion chromatography with multiangle light scattering, dynamic light scattering, analytical ultracentrifugation, and small angle X-ray scattering each provide evidence that the EGFR and HER3 C-terminal tails are intrinsically disordered with extended, non-globular structure in solution. The intrinsic disorder and extended conformation of these tails may be important for their function by increasing the capture radius and reducing the thermodynamic barriers for binding of downstream signaling proteins.
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Affiliation(s)
| | | | | | | | - Jian Zhu
- Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Ron Bose
- From the Divisions of Oncology and
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384
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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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385
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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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386
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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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387
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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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388
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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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389
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Yan M, Chakravarthy S, Tokuda JM, Pollack L, Bowman GD, Lee YS. Succinyl-5-aminoimidazole-4-carboxamide-1-ribose 5'-Phosphate (SAICAR) Activates Pyruvate Kinase Isoform M2 (PKM2) in Its Dimeric Form. Biochemistry 2016; 55:4731-6. [PMID: 27481063 DOI: 10.1021/acs.biochem.6b00658] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Human pyruvate kinase isoform M2 (PKM2) is a glycolytic enzyme isoform implicated in cancer. Malignant cancer cells have higher levels of dimeric PKM2, which is regarded as an inactive form of tetrameric pyruvate kinase. This perceived inactivity has fueled controversy about how the dimeric form of pyruvate kinase might contribute to cancer. Here we investigate enzymatic properties of PKM2(G415R), a variant derived from a cancer patient, which we show by size-exclusion chromatography and small-angle X-ray scattering to be a dimer that cannot form a tetramer in solution. Although PKM2(G415R) binds to fructose 1,6-bisphosphate (FBP), unlike the wild type this PKM2 variant shows no activation by FBP. In contrast, PKM2(G415R) is activated by succinyl-5-aminoimidazole-4-carboxamide-1-ribose 5'-phosphate (SAICAR), an endogenous metabolite that we previously showed correlates with an increased level of cell proliferation and promotes protein kinase activity of PKM2. Our results demonstrate an important and unexpected enzymatic activity of the PKM2 dimer that likely has a key role in cancer progression.
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Affiliation(s)
- Ming Yan
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States.,Department of Biology, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Joshua M Tokuda
- School of Applied and Engineering Physics, Cornell University , Ithaca, New York 14853, United States
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University , Ithaca, New York 14853, United States
| | - Gregory D Bowman
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Young-Sam Lee
- Department of Biology, Johns Hopkins University , Baltimore, Maryland 21218, United States
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390
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Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity. Int J Mol Sci 2016; 17:ijms17081305. [PMID: 27517921 PMCID: PMC5000702 DOI: 10.3390/ijms17081305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/13/2023] Open
Abstract
Spider aciniform (wrapping) silk is a remarkable fibrillar biomaterial with outstanding mechanical properties. It is a modular protein consisting, in Argiope trifasciata, of a core repetitive domain of 200 amino acid units (W units). In solution, the W units comprise a globular folded core, with five α-helices, and disordered tails that are linked to form a ~63-residue intrinsically disordered linker in concatemers. Herein, we present nuclear magnetic resonance (NMR) spectroscopy-based 15N spin relaxation analysis, allowing characterization of backbone dynamics as a function of residue on the ps–ns timescale in the context of the single W unit (W1) and the two unit concatemer (W2). Unambiguous mapping of backbone dynamics throughout W2 was made possible by segmental NMR active isotope-enrichment through split intein-mediated trans-splicing. Spectral density mapping for W1 and W2 reveals a striking disparity in dynamics between the folded core and the disordered linker and tail regions. These data are also consistent with rotational diffusion behaviour where each globular domain tumbles almost independently of its neighbour. At a localized level, helix 5 exhibits elevated high frequency dynamics relative to the proximal helix 4, supporting a model of fibrillogenesis where this helix unfolds as part of the transition to a mixed α-helix/β-sheet fibre.
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391
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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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392
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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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393
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Pérard J, Covès J, Castellan M, Solard C, Savard M, Miras R, Galop S, Signor L, Crouzy S, Michaud-Soret I, de Rosny E. Quaternary Structure of Fur Proteins, a New Subfamily of Tetrameric Proteins. Biochemistry 2016; 55:1503-15. [DOI: 10.1021/acs.biochem.5b01061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julien Pérard
- CNRS, Laboratoire de Chimie et Biologie
des Métaux
(LCBM), UMR 5249, CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38054 Grenoble, France
| | - Jacques Covès
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Mathieu Castellan
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Charles Solard
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Myriam Savard
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Roger Miras
- CNRS, Laboratoire de Chimie et Biologie
des Métaux
(LCBM), UMR 5249, CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38054 Grenoble, France
| | - Sandra Galop
- CNRS, Laboratoire de Chimie et Biologie
des Métaux
(LCBM), UMR 5249, CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38054 Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Serge Crouzy
- CNRS, Laboratoire de Chimie et Biologie
des Métaux
(LCBM), UMR 5249, CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38054 Grenoble, France
| | - Isabelle Michaud-Soret
- CNRS, Laboratoire de Chimie et Biologie
des Métaux
(LCBM), UMR 5249, CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38054 Grenoble, France
| | - Eve de Rosny
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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394
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Jeschke G. Ensemble models of proteins and protein domains based on distance distribution restraints. Proteins 2016; 84:544-60. [PMID: 26994550 DOI: 10.1002/prot.25000] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
Conformational ensembles of intrinsically disordered peptide chains are not fully determined by experimental observations. Uncertainty due to lack of experimental restraints and due to intrinsic disorder can be distinguished if distance distributions restraints are available. Such restraints can be obtained from pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy applied to pairs of spin labels. Here, we introduce a Monte Carlo approach for generating conformational ensembles that are consistent with a set of distance distribution restraints, backbone dihedral angle statistics in known protein structures, and optionally, secondary structure propensities or membrane immersion depths. The approach is tested with simulated restraints for a terminal and an internal loop and for a protein with 69 residues by using sets of sparse restraints for underlying well-defined conformations and for published ensembles of a premolten globule-like and a coil-like intrinsically disordered protein.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Zürich, 8093, Switzerland
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395
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Husain B, Mayo C, Cole JL. Role of the Interdomain Linker in RNA-Activated Protein Kinase Activation. Biochemistry 2015; 55:253-61. [PMID: 26678943 DOI: 10.1021/acs.biochem.5b01171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA-activated protein kinase (PKR) is a key component of the interferon-induced antiviral pathway in higher eukaryotes. Upon recognition of viral dsRNA, PKR is activated via dimerization and autophosphorylation. PKR contains two N-terminal dsRNA binding domains (dsRBD) and a C-terminal kinase domain. The dsRBDs and the kinase are separated by a long, unstructured ∼80-amino acid linker in the human enzyme. The length of the N-terminal portion of the linker varies among PKR sequences, and it is completely absent in one ortholog. Here, we characterize the effects of deleting the variable region from the human enzyme to produce PKRΔV. The linker deletion results in quantitative but not qualitative changes in catalytic activity, RNA binding, and conformation. PKRΔV is somewhat more active and exhibits more cooperative RNA binding. As we previously observed for the full-length enzyme, PKRΔV is flexible in solution and adopts a range of compact and extended conformations. The conformational ensemble is biased toward compact states that might be related to weak interactions between the dsRBD and kinase domains. PKR retains RNA-induced autophosphorylation upon complete removal of the linker, indicating that the C-terminal, basic region is also not required for activity.
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Affiliation(s)
- Bushra Husain
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Christopher Mayo
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - James L Cole
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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