251
|
Leyrat C, Renner M, Harlos K, Huiskonen JT, Grimes JM. Drastic changes in conformational dynamics of the antiterminator M2-1 regulate transcription efficiency in Pneumovirinae. eLife 2014; 3:e02674. [PMID: 24842877 PMCID: PMC4051120 DOI: 10.7554/elife.02674] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/15/2014] [Indexed: 12/24/2022] Open
Abstract
The M2-1 protein of human metapneumovirus (HMPV) is a zinc-binding transcription antiterminator which is highly conserved among pneumoviruses. We report the structure of tetrameric HMPV M2-1. Each protomer features a N-terminal zinc finger domain and an α-helical tetramerization motif forming a rigid unit, followed by a flexible linker and an α-helical core domain. The tetramer is asymmetric, three of the protomers exhibiting a closed conformation, and one an open conformation. Molecular dynamics simulations and SAXS demonstrate a dynamic equilibrium between open and closed conformations in solution. Structures of adenosine monophosphate- and DNA- bound M2-1 establish the role of the zinc finger domain in base-specific recognition of RNA. Binding to 'gene end' RNA sequences stabilized the closed conformation of M2-1 leading to a drastic shift in the conformational landscape of M2-1. We propose a model for recognition of gene end signals and discuss the implications of these findings for transcriptional regulation in pneumoviruses.DOI: http://dx.doi.org/10.7554/eLife.02674.001.
Collapse
Affiliation(s)
- Cedric Leyrat
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Max Renner
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom Diamond Light Source Ltd, Didcot, United Kingdom
| |
Collapse
|
252
|
Abstract
Intrinsically disordered proteins (IDPs) and IDP regions fail to form a stable structure, yet they exhibit biological activities. Their mobile flexibility and structural instability are encoded by their amino acid sequences. They recognize proteins, nucleic acids, and other types of partners; they accelerate interactions and chemical reactions between bound partners; and they help accommodate posttranslational modifications, alternative splicing, protein fusions, and insertions or deletions. Overall, IDP-associated biological activities complement those of structured proteins. Recently, there has been an explosion of studies on IDP regions and their functions, yet the discovery and investigation of these proteins have a long, mostly ignored history. Along with recent discoveries, we present several early examples and the mechanisms by which IDPs contribute to function, which we hope will encourage comprehensive discussion of IDPs and IDP regions in biochemistry textbooks. Finally, we propose future directions for IDP research.
Collapse
Affiliation(s)
- Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202; ,
| | | |
Collapse
|
253
|
Lee SJC, Lee JW, Choi TS, Jin KS, Lee S, Ban C, Kim HI. Probing Conformational Change of Intrinsically Disordered α-Synuclein to Helical Structures by Distinctive Regional Interactions with Lipid Membranes. Anal Chem 2014; 86:1909-16. [DOI: 10.1021/ac404132g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shin Jung C. Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Jong Wha Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Tae Su Choi
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Kyeong Sik Jin
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Seonghwan Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Changill Ban
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Hugh I. Kim
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| |
Collapse
|
254
|
Methods for Using New Conceptual Tools and Parameters to Assess RNA Structure by Small-Angle X-Ray Scattering. Methods Enzymol 2014; 549:235-63. [DOI: 10.1016/b978-0-12-801122-5.00011-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
255
|
Szambowska A, Tessmer I, Kursula P, Usskilat C, Prus P, Pospiech H, Grosse F. DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding. Nucleic Acids Res 2013; 42:2308-19. [PMID: 24293646 PMCID: PMC3936751 DOI: 10.1093/nar/gkt1217] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The cell division cycle protein 45 (Cdc45) represents an essential replication factor that, together with the Mcm2-7 complex and the four subunits of GINS, forms the replicative DNA helicase in eukaryotes. Recombinant human Cdc45 (hCdc45) was structurally characterized and its DNA-binding properties were determined. Synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering and atomic force microscopy revealed that hCdc45 exists as an alpha-helical monomer and possesses a structure similar to its bacterial homolog RecJ. hCdc45 bound long (113-mer or 80-mer) single-stranded DNA fragments with a higher affinity than shorter ones (34-mer). hCdc45 displayed a preference for 3′ protruding strands and bound tightly to single-strand/double-strand DNA junctions, such as those presented by Y-shaped DNA, bubbles and displacement loops, all of which appear transiently during the initiation of DNA replication. Collectively, our findings suggest that hCdc45 not only binds to but also slides on DNA with a 3′–5′ polarity and, thereby acts as a molecular ‘wedge’ to initiate DNA strand displacement.
Collapse
Affiliation(s)
- Anna Szambowska
- Research Group Biochemistry, Leibniz Institute for Age Research -Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany, Laboratory of Molecular Biology IBB PAS, Affiliated with University of Gdansk, Wita Stwosza 59 Gdansk, Poland, Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, Josef Schneider Strasse 2, 7080 Wurzburg, Germany, Department of Biochemistry, Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland, Department of Chemistry, University of Hamburg/DESY, Notkestrasse 85, 22607 Hamburg, Germany, Biocenter Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland and Center for Molecular Biomedicine, Friedrich-Schiller University, Biochemistry Department, Jena, Germany
| | | | | | | | | | | | | |
Collapse
|
256
|
Roblin P, Lebrun P, Rucktooa P, Dewitte F, Lens Z, Receveur-Brechot V, Raussens V, Villeret V, Bompard C. The structural organization of the N-terminus domain of SopB, a virulence factor of Salmonella, depends on the nature of its protein partners. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2564-72. [PMID: 24075929 DOI: 10.1016/j.bbapap.2013.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 09/03/2013] [Accepted: 09/18/2013] [Indexed: 01/17/2023]
Abstract
The TTSS is used by Salmonella and many bacterial pathogens to inject virulence factors directly into the cytoplasm of target eukaryotic cells. Once translocated these so-called effector proteins hijack a vast array of crucial cellular functions to the benefit of the bacteria. In the bacterial cytoplasm, some effectors are stabilized and maintained in a secretion competent state by interaction with specific type III chaperones. In this work we studied the conformation of the Chaperone Binding Domain of the effector named Salmonella Outer protein B (SopB) alone and in complex with its cognate chaperone SigE by a combination of biochemical, biophysical and structural approaches. Our results show that the N-terminus part of SopB is mainly composed by α-helices and unfolded regions whose organization/stabilization depends on their interaction with the different partners. This suggests that the partially unfolded state of this N-terminal region, which confers the adaptability of the effector to bind very different partners during the infection cycle, allows the bacteria to modulate numerous host cells functions limiting the number of translocated effectors.
Collapse
Affiliation(s)
- Pierre Roblin
- INRA Biopolymères, Interactions et Assemblages, Rue de la Geraudière, 44316 Nantes, France; Synchrotron SOLEIL, L'orme des Merisiers, Saint Aubin, BP 48, 91192 Gif sur Yvette Cedex, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
257
|
Jain R, Petri M, Kirschbaum S, Feindt H, Steltenkamp S, Sonnenkalb S, Becker S, Griesinger C, Menzel A, Burg TP, Techert S. X-ray scattering experiments with high-flux X-ray source coupled rapid mixing microchannel device and their potential for high-flux neutron scattering investigations. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:109. [PMID: 24092048 DOI: 10.1140/epje/i2013-13109-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 12/13/2012] [Accepted: 07/26/2013] [Indexed: 06/02/2023]
Abstract
Small-angle X-ray scattering provides global, shape-sensitive structural information about macromolecules in solution. Its extension to time dimension in the form of time-resolved SAXS investigations and combination with other time-resolved biophysical methods contributes immensely to the study of protein dynamics. TR-SAXS can also provide unique information about the global structures of transient intermediates during protein dynamics. An experimental set-up with low protein consumption is essential for an extensive use of TR-SAXS experiments on protein dynamics. In this direction, a newly developed 20-microchannel microfluidic continuous-flow mixer was combined with SAXS. With this set-up, we demonstrate ubiquitin unfolding dynamics after rapid mixing with the chaotropic agent Guanidinium-HCl within milliseconds using only ∼ 40 nanoliters of the protein sample per scattering image. It is suggested that, in the future, this new TR-SAXS platform will help to increase the use of time-resolved small-angle X-ray scattering, wide-angle X-ray scattering and neutron scattering experiments for studying protein dynamics in the early millisecond regime. The potential research field for this set-up includes protein folding, protein misfolding, aggregation in amyloidogenic diseases, function of intrinsically disordered proteins and various protein-ligand interactions.
Collapse
Affiliation(s)
- R Jain
- Structural Dynamics of (Bio)chemical Systems, MPI-BPC, Am Fassberg 11, 37077, Goettingen, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
258
|
Dias J, Renault L, Pérez J, Mirande M. Small-angle X-ray solution scattering study of the multi-aminoacyl-tRNA synthetase complex reveals an elongated and multi-armed particle. J Biol Chem 2013; 288:23979-89. [PMID: 23836901 PMCID: PMC3745343 DOI: 10.1074/jbc.m113.489922] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/01/2013] [Indexed: 02/01/2023] Open
Abstract
In animal cells, nine aminoacyl-tRNA synthetases are associated with the three auxiliary proteins p18, p38, and p43 to form a stable and conserved large multi-aminoacyl-tRNA synthetase complex (MARS), whose molecular mass has been proposed to be between 1.0 and 1.5 MDa. The complex acts as a molecular hub for coordinating protein synthesis and diverse regulatory signal pathways. Electron microscopy studies defined its low resolution molecular envelope as an overall rather compact, asymmetric triangular shape. Here, we have analyzed the composition and homogeneity of the native mammalian MARS isolated from rabbit liver and characterized its overall internal structure, size, and shape at low resolution by hydrodynamic methods and small-angle x-ray scattering in solution. Our data reveal that the MARS exhibits a much more elongated and multi-armed shape than expected from previous reports. The hydrodynamic and structural features of the MARS are large compared with other supramolecular assemblies involved in translation, including ribosome. The large dimensions and non-compact structural organization of MARS favor a large protein surface accessibility for all its components. This may be essential to allow structural rearrangements between the catalytic and cis-acting tRNA binding domains of the synthetases required for binding the bulky tRNA substrates. This non-compact architecture may also contribute to the spatiotemporal controlled release of some of its components, which participate in non-canonical functions after dissociation from the complex.
Collapse
Affiliation(s)
- José Dias
- From the Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France and
| | - Louis Renault
- From the Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France and
| | - Javier Pérez
- SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, France
| | - Marc Mirande
- From the Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France and
| |
Collapse
|
259
|
Sotomayor-Pérez AC, Subrini O, Hessel A, Ladant D, Chenal A. Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State and the Folded Calcium-Bound State of a Repeat in Toxin (RTX) Protein. J Am Chem Soc 2013; 135:11929-34. [DOI: 10.1021/ja404790f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana-Cristina Sotomayor-Pérez
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Orso Subrini
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Audrey Hessel
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Daniel Ladant
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Alexandre Chenal
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| |
Collapse
|
260
|
Graewert MA, Svergun DI. Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS). Curr Opin Struct Biol 2013; 23:748-54. [PMID: 23835228 DOI: 10.1016/j.sbi.2013.06.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
Abstract
The advances made in small and wide angle X-ray scattering over the past decades have had a large impact on structural biology. Many new insights into challenging biological probes including large and transient complexes, flexible macromolecules as well as other exciting objects of various sizes were gained with this low resolution technique. Here, we review the recent developments in the experimental setups and in software for data collection and analysis, specifically for hybrid approaches. These progresses have allowed scientists to address a number of intriguing questions which could not be answered with other structural methods alone.
Collapse
Affiliation(s)
- Melissa A Graewert
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestraße 85, Hamburg 22603, Germany
| | | |
Collapse
|
261
|
Ravikumar KM, Huang W, Yang S. Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes. J Chem Phys 2013; 138:024112. [PMID: 23320673 DOI: 10.1063/1.4774148] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A generalized method, termed Fast-SAXS-pro, for computing small angle x-ray scattering (SAXS) profiles of proteins, nucleic acids, and their complexes is presented. First, effective coarse-grained structure factors of DNA nucleotides are derived using a simplified two-particle-per-nucleotide representation. Second, SAXS data of a 18-bp double-stranded DNA are measured and used for the calibration of the scattering contribution from excess electron density in the DNA solvation layer. Additional test on a 25-bp DNA duplex validates this SAXS computational method and suggests that DNA has a different contribution from its hydration surface to the total scattering compared to RNA and protein. To account for such a difference, a sigmoidal function is implemented for the treatment of non-uniform electron density across the surface of a protein/nucleic-acid complex. This treatment allows differential scattering from the solvation layer surrounding protein/nucleic-acid complexes. Finally, the applications of this Fast-SAXS-pro method are demonstrated for protein/DNA and protein/RNA complexes.
Collapse
Affiliation(s)
- Krishnakumar M Ravikumar
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-4988, USA
| | | | | |
Collapse
|
262
|
Sanchez-Sanchez A, Akbari S, Etxeberria A, Arbe A, Gasser U, Moreno AJ, Colmenero J, Pomposo JA. "Michael" Nanocarriers Mimicking Transient-Binding Disordered Proteins. ACS Macro Lett 2013; 2:491-495. [PMID: 35581804 DOI: 10.1021/mz400173c] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report herein a very efficient synthesis strategy for the construction of artificial transient-binding protein-mimic nano-objects. Michael addition-mediated multidirectional self-assembly of individual polymeric chains at r.t. leads to "Michael" nanocarriers that in solution resemble disordered multidomain proteins, as revealed by a combination of small angle neutron scattering measurements and coarse-grained molecular dynamics simulation results, whereas in the dry state adopt a collapsed, globular morphology, as observed by transmission electron microscopy. This extended-to-compact morphology transition taking place upon solvent removal is of paramount importance, among other applications, for the construction of efficient biosensors based on immobilized protein-mimic nano-objects and for the development of transient vitamin-binding systems. As a proof of concept, we show the controlled delivery of vitamin B9 from these novel transient-binding nanocarriers.
Collapse
Affiliation(s)
- Ana Sanchez-Sanchez
- Centro de Física de Materiales (CSIC, UPV/EHU)-Materials Physics Center, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Somayeh Akbari
- Laboratory for Tribology and Surface Nanotechnology, Bogišičeva
8, 1000 Ljubljana, Slovenia
| | - Agustín Etxeberria
- Departamento de Ciencia
y Tecnología de Polímeros, Universidad del País Vasco (UPV/EHU), Paseo
Manuel de Lardizabal 3, 20018 San Sebastián, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CSIC, UPV/EHU)-Materials Physics Center, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Urs Gasser
- Laboratory for Neutron
Scattering, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Angel J. Moreno
- Centro de Física de Materiales (CSIC, UPV/EHU)-Materials Physics Center, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Juan Colmenero
- Centro de Física de Materiales (CSIC, UPV/EHU)-Materials Physics Center, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Departamento de
Física de Materiales, Universidad del País Vasco (UPV/EHU), Apartado 1072, 20800
San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4,
20018 San Sebastián, Spain
| | - José A. Pomposo
- Centro de Física de Materiales (CSIC, UPV/EHU)-Materials Physics Center, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Departamento de
Física de Materiales, Universidad del País Vasco (UPV/EHU), Apartado 1072, 20800
San Sebastián, Spain
- IKERBASQUE - Basque Foundation for Science, Alameda Urquijo 36, 48011 Bilbao,
Spain
| |
Collapse
|
263
|
Beckham SA, Brouwer J, Roth A, Wang D, Sadler AJ, John M, Jahn-Hofmann K, Williams BRG, Wilce JA, Wilce MCJ. Conformational rearrangements of RIG-I receptor on formation of a multiprotein:dsRNA assembly. Nucleic Acids Res 2013; 41:3436-45. [PMID: 23325848 PMCID: PMC3597671 DOI: 10.1093/nar/gks1477] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 11/22/2022] Open
Abstract
The retinoic acid inducible gene-I (RIG-I)-like family of receptors is positioned at the front line of our innate cellular defence system. RIG-I detects and binds to foreign duplex RNA in the cytoplasm of both immune and non-immune cells, and initiates the induction of type I interferons and pro-inflammatory cytokines. The mechanism of RIG-I activation by double-stranded RNA (dsRNA) involves a molecular rearrangement proposed to expose the N-terminal pair of caspase activation recruitment domains, enabling an interaction with interferon-beta promoter stimulator 1 (IPS-1) and thereby initiating downstream signalling. dsRNA is particularly stimulatory when longer than 20 bp, potentially through allowing binding of more than one RIG-I molecule. Here, we characterize full-length RIG-I and RIG-I subdomains combined with a stimulatory 29mer dsRNA using multi-angle light scattering and size-exclusion chromatography-coupled small-angle X-ray scattering, to build up a molecular model of RIG-I before and after the formation of a 2:1 protein:dsRNA assembly. We report the small-angle X-ray scattering-derived solution structure of the human apo-RIG-I and observe that on binding of RIG-I to dsRNA in a 2:1 ratio, the complex becomes highly extended and flexible. Hence, here we present the first model of the fully activated oligomeric RIG-I.
Collapse
Affiliation(s)
- Simone A. Beckham
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Jason Brouwer
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Anna Roth
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Die Wang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Anthony J. Sadler
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Matthias John
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Kerstin Jahn-Hofmann
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Bryan R. G. Williams
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Jacqueline A. Wilce
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| | - Matthew C. J. Wilce
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia, Roche Kulmbach GmbH, 95326 Kulmbach, Germany and Sanofi Deutschland GmbH, 65926 Frankfurt, Germany
| |
Collapse
|
264
|
Perry JJP, Tainer JA. Developing advanced X-ray scattering methods combined with crystallography and computation. Methods 2013; 59:363-71. [PMID: 23376408 PMCID: PMC3684416 DOI: 10.1016/j.ymeth.2013.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/15/2013] [Accepted: 01/18/2013] [Indexed: 01/09/2023] Open
Abstract
The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one's repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions.
Collapse
Affiliation(s)
- J. Jefferson P. Perry
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA USA
- School of Biotechnology, Amrita University at Amritapuri, Kollam, Kerala, India
| | - John A. Tainer
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| |
Collapse
|
265
|
Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS. Biochem Soc Trans 2013; 40:955-62. [PMID: 22988847 DOI: 10.1042/bst20120149] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In recent years, IDPs (intrinsically disordered proteins) have emerged as pivotal actors in biology. Despite IDPs being present in all kingdoms of life, they are more abundant in eukaryotes where they are involved in the vast majority of regulation and signalling processes. The realization that, in some cases, functional states of proteins were partly or fully disordered was in contradiction to the traditional view where a well defined three-dimensional structure was required for activity. Several experimental evidences indicate, however, that structural features in IDPs such as transient secondary-structural elements and overall dimensions are crucial to their function. NMR has been the main tool to study IDP structure by probing conformational preferences at residue level. Additionally, SAXS (small-angle X-ray scattering) has the capacity to report on the three-dimensional space sampled by disordered states and therefore complements the local information provided by NMR. The present review describes how the synergy between NMR and SAXS can be exploited to obtain more detailed structural and dynamic models of IDPs in solution. These combined strategies, embedded into computational approaches, promise the elucidation of the structure-function properties of this important, but elusive, family of biomolecules.
Collapse
|
266
|
Abstract
Though lacking a well-defined three-dimensional structure, intrinsically unstructured proteins are ubiquitous in nature. These molecules play crucial roles in many cellular processes, especially signaling and regulation. Surprisingly, even enzyme catalysis can tolerate substantial disorder. This observation contravenes conventional wisdom but is relevant to an understanding of how protein dynamics modulates enzyme function. This chapter reviews properties and characteristics of disordered proteins, emphasizing examples of enzymes that lack defined structures, and considers implications of structural disorder for catalytic efficiency and evolution.
Collapse
|
267
|
Pérez J, Nishino Y. Advances in X-ray scattering: from solution SAXS to achievements with coherent beams. Curr Opin Struct Biol 2012; 22:670-8. [DOI: 10.1016/j.sbi.2012.07.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/15/2022]
|
268
|
Forrey C, Douglas JF, Gilson MK. The Fundamental Role of Flexibility on the Strength of Molecular Binding. SOFT MATTER 2012; 8:6385-6392. [PMID: 22707976 PMCID: PMC3374587 DOI: 10.1039/c2sm25160d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Non-covalent molecular association underlies a diverse set of biologically and technologically relevant phenomena, including the action of drugs on their biomolecular targets and self- and supra-molecular assembly processes. Computer models employed to model binding frequently use interaction potentials with atomistic detail while neglecting the thermal molecular motions of the binding species. However, errors introduced by this simplification and, more broadly, the thermodynamic consequences of molecular flexibility on binding, are little understood. Here, we isolate the fundamental relationship of molecular flexibility to binding thermodynamics via simulations of simplified molecules with a wide range of flexibilities but the same interaction potential. Disregarding molecular motion is found to generate large errors in binding entropy, enthalpy and free energy, even for molecules that are nearly rigid. Indeed, small decreases in rigidity markedly reduce affinity for highly rigid molecules. Remarkably, precisely the opposite occurs for more flexible molecules, for which increasing flexibility leads to stronger binding affinity. We also find that differences in flexibility suffice to generate binding specificity: for example, a planar surface selectively binds rigid over flexible molecules. Intriguingly, varying molecular flexibility while keeping interaction potentials constant leads to near-linear enthalpy-entropy compensation over a wide range of flexibilities, with the unexpected twist that increasing flexibility produces opposite changes in entropy and enthalpy for molecules in the flexible versus the rigid regime. Molecular flexibility is thus a crucial determinant of binding affinity and specificity and variations in flexibility can lead to strong yet non-intuitive consequences.
Collapse
Affiliation(s)
- Christopher Forrey
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Jack F. Douglas
- Polymers Division, National Institute of Standards and Technology, 1 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0736, USA
| |
Collapse
|
269
|
|