201
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Gabel F. Small-Angle Neutron Scattering for Structural Biology of Protein–RNA Complexes. Methods Enzymol 2015; 558:391-415. [DOI: 10.1016/bs.mie.2015.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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202
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Watanabe-Matsui M, Matsumoto T, Matsui T, Ikeda-Saito M, Muto A, Murayama K, Igarashi K. Heme binds to an intrinsically disordered region of Bach2 and alters its conformation. Arch Biochem Biophys 2015; 565:25-31. [DOI: 10.1016/j.abb.2014.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/07/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022]
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203
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Resolving Individual Components in Protein–RNA Complexes Using Small-Angle X-ray Scattering Experiments. Methods Enzymol 2015; 558:363-390. [DOI: 10.1016/bs.mie.2015.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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204
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Grant TD, Luft JR, Carter LG, Matsui T, Weiss TM, Martel A, Snell EH. The accurate assessment of small-angle X-ray scattering data. ACTA ACUST UNITED AC 2015; 71:45-56. [PMID: 25615859 PMCID: PMC4304685 DOI: 10.1107/s1399004714010876] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/12/2014] [Indexed: 12/05/2022]
Abstract
A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins, showing that these techniques are more sensitive than manual assessment of data quality. Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.
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Affiliation(s)
- Thomas D Grant
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Joseph R Luft
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Lester G Carter
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Anne Martel
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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205
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Jeffries CM, Svergun DI. High-throughput studies of protein shapes and interactions by synchrotron small-angle X-ray scattering. Methods Mol Biol 2015; 1261:277-301. [PMID: 25502205 DOI: 10.1007/978-1-4939-2230-7_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solution-based small angle X-ray scattering (SAXS) affords the opportunity to extract accurate structural parameters and global shape information from diverse biological macromolecular systems. SAXS is an ideal complementary technique to other structural and biophysical methods but it can also be applied alone to access structural information that is otherwise unobtainable using high-resolution methods. Macromolecular structures ranging from kilodaltons to gigadaltons can be analyzed, which encompasses the size of most proteins and functional cellular complexes. The SAXS analysis is performed using only a few microliters of solution containing microgram quantities of purified material in sample environments that can be tailored to mimic physiological conditions or altered to suit a particular question. High-brilliance synchrotron X-ray sources and parallel advances in hardware and computing have reduced data acquisition times to the millisecond range and the application of automated methods have allowed data processing and low resolution shape modelling to be completed within minutes. These developments have paved the way for high-throughput studies that generate significant quantities of structural information over a short period of time. Here, we briefly consider the basics of SAXS and describe major methods and protocols employed in high-throughput SAXS studies.
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Affiliation(s)
- Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestraße 85, 22603, Hamburg, Germany
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206
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Abstract
This review covers a breakthrough in the structural biology of the gigantic modular polyketide synthases (PKS): the structural characterization of intact modules by single-particle cryo-electron microscopy and small-angle X-ray scattering.
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Affiliation(s)
- Kira J. Weissman
- Molecular and Structural Enzymology Group
- Université de Lorraine
- IMoPA
- UMR 7365
- Vandœuvre-lès-Nancy
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207
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Ryan TM, Kirby N, Mertens HDT, Roberts B, Barnham KJ, Cappai R, Pham CLL, Masters CL, Curtain CC. Small angle X-ray scattering analysis of Cu2+-induced oligomers of the Alzheimer's amyloid β peptide. Metallomics 2015; 7:536-43. [DOI: 10.1039/c4mt00323c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Research into causes of Alzheimer's disease and its treatment has produced a tantalising array of hypotheses about the role of transition metal dyshomeostasis, many of them on the interaction of these metals with the neurotoxic amyloid-β peptide (Aβ).
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Affiliation(s)
- Timothy M. Ryan
- University of Melbourne
- Florey Institute of Neuroscience and Mental Health
- Victoria 3010, Australia
| | - Nigel Kirby
- SAXS/WAXS Beamline
- The Australian Synchrotron
- Clayton, Australia
| | | | - Blaine Roberts
- University of Melbourne
- Florey Institute of Neuroscience and Mental Health
- Victoria 3010, Australia
| | - Kevin J. Barnham
- University of Melbourne
- Florey Institute of Neuroscience and Mental Health
- Victoria 3010, Australia
- Department of Pathology
- Bio21 Molecular Science and Technology Institute
| | - Roberto Cappai
- Department of Pathology
- Bio21 Molecular Science and Technology Institute
- The University of Melbourne
- Victoria, Australia
| | - Chi Le Lan Pham
- Department of Pathology
- Bio21 Molecular Science and Technology Institute
- The University of Melbourne
- Victoria, Australia
| | - Colin L. Masters
- University of Melbourne
- Florey Institute of Neuroscience and Mental Health
- Victoria 3010, Australia
| | - Cyril C. Curtain
- University of Melbourne
- Florey Institute of Neuroscience and Mental Health
- Victoria 3010, Australia
- Department of Pathology
- Bio21 Molecular Science and Technology Institute
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208
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Kim HS, Gabel F. Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:57-66. [PMID: 25615860 PMCID: PMC4304686 DOI: 10.1107/s1399004714013923] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 06/13/2014] [Indexed: 01/04/2023]
Abstract
Small-angle scattering (SAS) has witnessed a breathtaking renaissance and expansion over the past 15 years regarding the determination of biomacromolecular structures in solution. While important issues such as sample quality, good experimental practice and guidelines for data analysis, interpretation, presentation, publication and deposition are increasingly being recognized, crucial topics such as the uniqueness, precision and accuracy of the structural models obtained by SAS are still only poorly understood and addressed. The present article provides an overview of recent developments in these fields with a focus on the influence of complementary NMR restraints and of a hydration shell on the uniqueness of biomacromolecular models. As a first topic, the impact of incorporating NMR orientational restraints in addition to SAS distance restraints is discussed using a quantitative visual representation that illustrates how the possible conformational space of a two-body system is reduced as a function of the available data. As a second topic, the impact of a hydration shell on modelling parameters of a two-body system is illustrated, in particular on its inter-body distance. Finally, practical recommendations are provided to take both effects into account and promising future perspectives of SAS approaches are discussed.
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Affiliation(s)
- Henry S. Kim
- Université Grenoble Alpes, IBS, 71 avenue des Martyrs, 38044 Grenoble, France
- CNRS, IBS, 71 avenue des Martyrs, 38044 Grenoble, France
- CEA, IBS, 71 avenue des Martyrs, 38044 Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, IBS, 71 avenue des Martyrs, 38044 Grenoble, France
- CNRS, IBS, 71 avenue des Martyrs, 38044 Grenoble, France
- CEA, IBS, 71 avenue des Martyrs, 38044 Grenoble, France
- Institut Laue–Langevin, 38042 Grenoble CEDEX 9, France
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209
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Lamech LT, Mallam AL, Lambowitz AM. Evolution of RNA-protein interactions: non-specific binding led to RNA splicing activity of fungal mitochondrial tyrosyl-tRNA synthetases. PLoS Biol 2014; 12:e1002028. [PMID: 25536042 PMCID: PMC4275181 DOI: 10.1371/journal.pbio.1002028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/12/2014] [Indexed: 12/28/2022] Open
Abstract
Studies of tRNA synthetases that adapted to assist the splicing of group I introns provide insight into how proteins can evolve new RNA-binding functions. The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically active RNA structure. Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic domain and flexibly attached C-terminal anticodon-binding domain (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural adaptations that occurred during or after the divergence of Peziomycotina and Saccharomycotina. However, the function of the CTD and how it contributed to the evolution of splicing activity have been unclear. Here, small angle X-ray scattering analysis of CYT-18 shows that both CTDs of the homodimeric protein extend outward from the catalytic domain, but move inward to bind opposite ends of a group I intron RNA. Biochemical assays show that the isolated CTD of CYT-18 binds RNAs non-specifically, possibly contributing to its interaction with the structurally different ends of the intron RNA. Finally, we find that the yeast mtTyrRS, which diverged from Pezizomycotina fungal mtTyrRSs prior to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its CTD, but lacks further adaptations needed for group I intron splicing. Our results suggest a scenario of constructive neutral (i.e., pre-adaptive) evolution in which an initial non-specific interaction between the CTD of an ancestral fungal mtTyrRS and a self-splicing group I intron was “fixed” by an intron RNA mutation that resulted in protein-dependent splicing. Once fixed, this interaction could be elaborated by further adaptive mutations in both the catalytic domain and CTD that enabled specific binding of group I introns. Our results highlight a role for non-specific RNA binding in the evolution of RNA-binding proteins. The acquisition of new modes of post-transcriptional gene regulation played an important role in the evolution of eukaryotes and was achieved by an increase in the number of RNA-binding proteins with new functions. RNA-binding proteins bind directly to double- or single-stranded RNA and regulate many cellular processes. Here, we address how proteins evolve new RNA-binding functions by using as a model system a fungal mitochondrial tyrosyl-tRNA synthetase that evolved to acquire a novel function in splicing group I introns. Group I introns are RNA enzymes (or “ribozymes”) that catalyze their own removal from transcripts, but can become dependent upon proteins to stabilize their active structure. We show that the C-terminal domain of the synthetase is flexibly attached and has high non-specific RNA-binding activity that likely pre-dated the evolution of splicing activity. Our findings suggest an evolutionary scenario in which an initial non-specific interaction between an ancestral synthetase and a self-splicing group I intron was fixed by an intron RNA mutation, thereby making it dependent upon the protein for structural stabilization. The interaction then evolved by the acquisition of adaptive mutations throughout the protein and RNA that increased both the splicing efficiency and its protein-dependence. Our results suggest a general mechanism by which non-specific binding interactions can lead to the evolution of new RNA-binding functions and provide novel insights into splicing and synthetase mechanisms.
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Affiliation(s)
- Lilian T. Lamech
- The Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Anna L. Mallam
- The Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Alan M. Lambowitz
- The Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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210
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Cheguru P, Majumder A, Yadav R, Gopalakrishna KN, Gakhar L, Artemyev NO. The solution structure of the transducin-α-uncoordinated 119 protein complex suggests occlusion of the Gβ₁γ₁-binding sites. FEBS J 2014; 282:550-61. [PMID: 25425538 DOI: 10.1111/febs.13161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/17/2014] [Accepted: 11/24/2014] [Indexed: 11/28/2022]
Abstract
Uncoordinated 119 protein (UNC119) is a partner of transducin-α subunit (Gαt ) that is essential for transducin trafficking in rod photoreceptors. The interaction is known to involve binding of the acylated N terminus of Gαt to the hydrophobic pocket of UNC119. To gain insights into the mechanism of transducin trafficking, we isolated a highly pure protein complex between myristoylated chimeric Gαt (Gαt *) and UNC119₅₀₋₂₄₀, and examined the solution structure by small angle X-ray scattering and chemical crosslinking. The solution structure of the Gαt -UNC119₅₀₋₂₄₀ complex was derived with rigid body/ab initio modeling against the small angle X-ray scattering data by use of known atomic structures of Gαt and UNC119, and a distance constraint based on the protein crosslinking with p-phenyldimaleimide. The model of the Gαt -UNC119₅₀₋₂₄₀ complex indicates rotation and bending of the N-terminal α-helix of Gαt from its position in the structure of the heterotrimeric G-protein transducin (Gt ). This allows a considerably more compact complex conformation, which also suggests a novel interface involving the switch II/α3-β5 surface of Gαt . Supporting a novel interface, UNC119 was found to bind full-length Gαt * more strongly than the Gαt N-terminal peptide. Furthermore, UNC119 competed with the effector molecule phosphodiesterase-6 γ-subunit, which is known to bind to the same surface of Gαt . The solution structure of the Gαt -UNC119 complex suggests that the ability of UNC119 to dissociate Gt subunits and release Gαt from the membrane is attributable to disruption and sterical occlusion of the Gβ₁γ₁-binding sites on Gαt .
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Affiliation(s)
- Pallavi Cheguru
- Department of Molecular Physiology and Biophysics, University of Iowa, IA, USA
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211
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Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH. Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data. Structure 2014; 22:1862-1874. [PMID: 25456817 PMCID: PMC5046226 DOI: 10.1016/j.str.2014.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 01/09/2023]
Abstract
Multidomain proteins in which individual domains are connected by linkers often possess inherent interdomain flexibility that significantly complicates their structural characterization in solution using either nuclear magnetic resonance (NMR) spectroscopy or small-angle X-ray scattering (SAXS) alone. Here, we report a protocol for joint refinement of flexible multidomain protein structures against NMR distance and angular restraints, residual dipolar couplings, and SAXS data. The protocol is based on the ensemble optimization method principle (Bernadó et al., 2007) and is compared with different refinement strategies for the structural characterization of the flexible two-domain protein sf3636 from Shigella flexneri 2a. The results of our refinement suggest the existence of a dominant population of configurational states in solution possessing an overall elongated shape and restricted relative twisting of the two domains.
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Affiliation(s)
- Alexander Lemak
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Bin Wu
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Adelinda Yee
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Aleksandras Gutmanas
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - Maite Garcia
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Anthony Semesi
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
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212
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A model-free method for extracting interaction potential between protein molecules using small-angle X-ray scattering. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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213
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White SJ, Johnson SD, Sellick MA, Bronowska A, Stockley PG, Wälti C. The Influence of Two-Dimensional Organization on Peptide Conformation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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214
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White SJ, Johnson SD, Sellick MA, Bronowska A, Stockley PG, Wälti C. The influence of two-dimensional organization on peptide conformation. Angew Chem Int Ed Engl 2014; 54:974-8. [PMID: 25413024 PMCID: PMC4506555 DOI: 10.1002/anie.201408971] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/13/2014] [Indexed: 11/08/2022]
Abstract
Molecular crowding plays a significant role in regulating molecular conformation in cellular environments. It is also likely to be important wherever high molecular densities are required, for example in surface-phase studies, in which molecular densities generally far exceed those observed in solution. Using on-surface circular dichroism (CD) spectroscopy, we have investigated the structure of a synthetic peptide assembled into a highly packed monolayer. The immobilized peptide undergoes a structural transition between α-helical and random coil conformation upon changes in pH and ionic concentration, but critically the threshold for conformational change is altered dramatically by molecular crowding within the peptide monolayer. This study highlights the often overlooked role molecular crowding plays in regulating molecular structure and function in surface-phase studies of biological molecules.
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Affiliation(s)
- Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT (UK)
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215
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Goldenberg DP, Argyle B. Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study. Biophys J 2014; 106:905-14. [PMID: 24559993 DOI: 10.1016/j.bpj.2013.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 01/04/2023] Open
Abstract
Small-angle neutron scattering was used to study the effects of macromolecular crowding by two globular proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an intrinsically disordered protein, the N protein of bacteriophage λ. The λ N protein was uniformly labeled with (2)H, and the concentrations of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples containing up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded protein was estimated to be 30 Å and was found to be remarkably insensitive to the presence of crowders, varying by <2 Å for the highest crowder concentrations. The scattering profiles were also used to estimate the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examined. These results are contrary to the predictions of theoretical treatments and previous experimental studies demonstrating compaction of unfolded proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective volumes of disordered proteins and the variation of these volumes within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding proteins, which may compensate for the effects of steric exclusion.
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Affiliation(s)
| | - Brian Argyle
- Department of Biology, University of Utah, Salt Lake City, Utah
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216
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An16-resilin: an advanced multi-stimuli-responsive resilin-mimetic protein polymer. Acta Biomater 2014; 10:4768-4777. [PMID: 25107894 DOI: 10.1016/j.actbio.2014.07.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 07/21/2014] [Accepted: 07/29/2014] [Indexed: 11/21/2022]
Abstract
Engineered protein polymers that display responsiveness to multiple stimuli are emerging as a promising class of soft material with unprecedented functionality. The remarkable advancement in genetic engineering and biosynthesis has created the opportunity for precise control over the amino acid sequence, size, structure and resulting functions of such biomimetic proteins. Herein, we describe the multi-stimuli-responsive characteristics of a resilin-mimetic protein, An16-resilin (An16), derived from the consensus sequence of resilin gene in the mosquito Anopheles gambiae. We demonstrate that An16 is an intrinsically disordered protein that displays unusual dual-phase thermal transition behavior along with responsiveness to pH, ion, light and humidity. Identifying the molecular mechanisms that allow An16 to sense and switch in response to varying environments furthers the ability to design intelligent biomacromolecules.
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217
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Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering. Methods Mol Biol 2014; 1240:165-89. [PMID: 25352145 DOI: 10.1007/978-1-4939-1896-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
We used small-angle X-ray scattering (SAXS) to evaluate the solution structure of a double-stranded RNA with 32 base pairs. We wanted to compare the solution structure to the crystal structure to assess the impact of the crystal lattice on the overall conformation of the RNA. The RNA was designed to self-anneal and form a head-to-head fusion of two identical mRNA/oligo(U) tail domains (the U-helix) from a trypanosome RNA editing substrate formed by the annealing of a guide RNA to a pre-edited mRNA. This substrate is from the U insertion/deletion RNA editing system of trypanosomes. Each strand in the fusion RNA had 16 purines from the pre-mRNA followed by 16 uracils (Us) from the U-tail at the 3' end of the guide RNA. The strands were designed to form a double helix with blunt ends, but each strand had the potential to form hairpins and single-stranded RNA helices. Hairpins could form by the 3' oligouridylate tract folding back to hybridize with the 5' oligopurine tract and forming an intervening loop. Single-stranded helices could form by the stacking of bases in the polypurine tract. Some of the 16 Us 3' to the polypurine tract may have been unstacked and in random coils. Our SAXS studies showed that the RNA formed a mix of single-stranded structures in the absence of MgCl2. In the presence of MgCl2 at concentrations similar to those in the crystal, the solution structure was consistent with the double-stranded, blunt-ended structure, in agreement with the crystal structure. Here we describe the preparation of RNA samples, data collection with an in-house SAXS instrument designed for biological samples, and the processing and modeling of the scattering data.
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218
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Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI. SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res 2014; 43:D357-63. [PMID: 25352555 PMCID: PMC4383894 DOI: 10.1093/nar/gku1047] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Small-angle X-ray and neutron scattering (SAXS and SANS) are fundamental tools used to study the global shapes of proteins, nucleic acids, macromolecular complexes and assemblies in solution. Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically. The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf). The small-angle scattering biological data bank (SASBDB) www.sasbdb.org has been designed in accordance with the plans of the SAStf as part of a future federated system of databases for biological SAXS and SANS. SASBDB is a comprehensive repository of freely accessible and fully searchable SAS experimental data and models that are deposited together with the relevant experimental conditions, sample details and instrument characteristics. At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.
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Affiliation(s)
- Erica Valentini
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Gianpietro Previtali
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
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219
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Solanki AK, Rathore YS, Badmalia MD, Dhoke RR, Nath SK, Nihalani D, Ashish. Global shape and ligand binding efficiency of the HIV-1-neutralizing antibodies differ from those of antibodies that cannot neutralize HIV-1. J Biol Chem 2014; 289:34780-800. [PMID: 25331945 DOI: 10.1074/jbc.m114.563486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asymmetric disposition of Fab arms in the structures solved for the broadly neutralizing monoclonal antibody (nmAb) IgG1 b12 raised the question of whether the unusual shape observed for b12 is common for all IgG1 mAbs or if there is a difference in the overall shape of nmAbs versus non-nmAbs. We compared small angle x-ray scattering (SAXS) data-based models and limited proteolysis profiles of some IgG1 mAbs known to be having and lacking HIV-1 neutralizing potency. In non-nmAbs, the Fab arms were found to be symmetrically disposed in space relative to central Fc, but in most nmAbs, the Fab arms were asymmetrically disposed, as seen for IgG1 b12. The only exceptions were 2G12 and 4E10, where both Fab arms were closed above Fc, suggesting some Fab-Fc and/or Fab-Fab interaction in the nmAbs that constrained extension of the Fab-Fc linker. Interestingly, these observations were correlated with differential proteolysis profiles of the mAbs by papain. Under conditions when papain could cut both Fab arms of non-nmAbs, only one Fab arm could be removed from neutralizing ones (except for 2G12 and 4E10). Chromatography and small angle x-ray scattering results of papain-digested products revealed that 1) the Fab-Fc or Fab-Fab interactions in unliganded mAbs are retained in digested products, and 2) whereas anti-gp120 non-nmAbs could bind two gp120 molecules, nmAbs could bind only one gp120. Additional experiments showed that except for 2G12 and 4E10, unopen shapes of nmAbs remain uninfluenced by ionic strength but can be reversibly opened by low pH of buffer accompanied by loss of ligand binding ability.
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Affiliation(s)
- Ashish K Solanki
- From the CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India and
| | - Yogendra S Rathore
- From the CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India and
| | - Maulik D Badmalia
- From the CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India and
| | - Reema R Dhoke
- From the CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India and
| | - Samir K Nath
- From the CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India and
| | - Deepak Nihalani
- the Renal Electrolyte Division, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ashish
- From the CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India and
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220
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Vance TR, Olijve LC, Campbell R, Voets I, Davies P, Guo S. Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice. Biosci Rep 2014; 34:e00121. [PMID: 24892750 PMCID: PMC4083281 DOI: 10.1042/bsr20140083] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 01/12/2023] Open
Abstract
The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches.
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Key Words
- bacterial ig-like fold
- ca2+-binding
- crystal structure
- extender domain
- ice-binding adhesin
- solution structure
- aa, amino acid
- afp, antifreeze protein
- auc, analytical ultracentrifugation
- big, bacterial immunoglobulin
- mpafp, marinomonas primoryensis antifreeze protein
- orf, open reading frame
- rdf, radial distribution function
- rii, region ii
- rii tetra-tandemer, four tandem rii
- riv, repetitive region iv
- rtx, repeats-in-toxin
- saxs, small-angle x-ray scattering
- tiss, type i secretion system
- wlc, worm-like chain
- xrd, x-ray diffraction
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Affiliation(s)
- Tyler D. R. Vance
- *Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Luuk L. C. Olijve
- †Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Robert L. Campbell
- *Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Ilja K. Voets
- †Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Peter L. Davies
- *Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Shuaiqi Guo
- *Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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221
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Abstract
With recent advances in data analysis algorithms, X-ray detectors and synchrotron sources, small-angle X-ray scattering (SAXS) has become much more accessible to the structural biology community. Although limited to ∼10 Å resolution, SAXS can provide a wealth of structural information on biomolecules in solution and is compatible with a wide range of experimental conditions. SAXS is thus an attractive alternative when crystallography is not possible. Moreover, advanced use of SAXS can provide unique insight into biomolecular behavior that can only be observed in solution, such as large conformational changes and transient protein-protein interactions. Unlike crystal diffraction data, however, solution scattering data are subtle in appearance, highly sensitive to sample quality and experimental errors and easily misinterpreted. In addition, synchrotron beamlines that are dedicated to SAXS are often unfamiliar to the nonspecialist. Here we present a series of procedures that can be used for SAXS data collection and basic cross-checks designed to detect and avoid aggregation, concentration effects, radiation damage, buffer mismatch and other common problems. Human serum albumin (HSA) serves as a convenient and easily replicated example of just how subtle these problems can sometimes be, but also of how proper technique can yield pristine data even in problematic cases. Because typical data collection times at a synchrotron are only one to several days, we recommend that the sample purity, homogeneity and solubility be extensively optimized before the experiment.
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Affiliation(s)
- Soren Skou
- Niels Bohr Institute, Copenhagen University, Copenhagen, Denmark
| | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, Ithaca, NY, USA
| | - Nozomi Ando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA, Tel: (617) 571-0411, Fax: (617) 258-7847
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222
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Clark NJ, Raththagala M, Wright NT, Buenger EA, Schildbach JF, Krueger S, Curtis JE. Structures of TraI in solution. J Mol Model 2014; 20:2308. [PMID: 24898939 DOI: 10.1007/s00894-014-2308-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Bacterial conjugation, a DNA transfer mechanism involving transport of one plasmid strand from donor to recipient, is driven by plasmid-encoded proteins. The F TraI protein nicks one F plasmid strand, separates cut and uncut strands, and pilots the cut strand through a secretion pore into the recipient. TraI is a modular protein with identifiable nickase, ssDNA-binding, helicase and protein-protein interaction domains. While domain structures corresponding to roughly 1/3 of TraI have been determined, there has been no comprehensive structural study of the entire TraI molecule, nor an examination of structural changes to TraI upon binding DNA. Here, we combine solution studies using small-angle scattering and circular dichroism spectroscopy with molecular Monte Carlo and molecular dynamics simulations to assess solution behavior of individual and groups of domains. Despite having several long (>100 residues) apparently disordered or highly dynamic regions, TraI folds into a compact molecule. Based on the biophysical characterization, we have generated models of intact TraI. These data and the resulting models have provided clues to the regulation of TraI function.
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Affiliation(s)
- Nicholas J Clark
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD, 20899, USA
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223
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Pandey K, Dhoke RR, Rathore YS, Nath SK, Verma N, Bawa S, Ashish. Low pH Overrides the Need of Calcium Ions for the Shape–Function Relationship of Calmodulin: Resolving Prevailing Debates. J Phys Chem B 2014; 118:5059-74. [DOI: 10.1021/jp501641r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kalpana Pandey
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Reema R. Dhoke
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | | | - Samir K. Nath
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Neha Verma
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Simranjot Bawa
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Ashish
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
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224
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Le RK, Harris BJ, Iwuchukwu IJ, Bruce BD, Cheng X, Qian S, Heller WT, O’Neill H, Frymier PD. Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-β-d-maltoside using small-angle neutron scattering and molecular dynamics simulation. Arch Biochem Biophys 2014; 550-551:50-7. [DOI: 10.1016/j.abb.2014.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/15/2014] [Indexed: 10/25/2022]
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225
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Hennig J, Sattler M. The dynamic duo: combining NMR and small angle scattering in structural biology. Protein Sci 2014; 23:669-82. [PMID: 24687405 DOI: 10.1002/pro.2467] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 12/12/2022]
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of complementary aspects provided by different structural biology techniques. Although X-ray crystallography remains the method of choice for structural analysis of large complexes, crystallization of flexible systems is often difficult and does typically not provide insights into conformational dynamics present in solution. Nuclear magnetic resonance spectroscopy (NMR) is well-suited to study dynamics at picosecond to second time scales, and to map binding interfaces even of large systems at residue resolution but suffers from poor sensitivity with increasing molecular weight. Small angle scattering (SAS) methods provide low resolution information in solution and can characterize dynamics and conformational equilibria complementary to crystallography and NMR. The combination of NMR, crystallography, and SAS is, thus, very useful for analysis of the structure and conformational dynamics of (large) protein complexes in solution. In high molecular weight systems, where NMR data are often sparse, SAS provides additional structural information and can differentiate between NMR-derived models. Scattering data can also validate the solution conformation of a crystal structure and indicate the presence of conformational equilibria. Here, we review current state-of-the-art approaches for combining NMR, crystallography, and SAS data to characterize protein complexes in solution.
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Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr.1, D-85764, Neuherberg, Germany; Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747, Garching, Germany
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226
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Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J 2014; 105:962-74. [PMID: 23972848 DOI: 10.1016/j.bpj.2013.07.020] [Citation(s) in RCA: 406] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 07/03/2013] [Accepted: 07/11/2013] [Indexed: 12/29/2022] Open
Abstract
A major challenge in structural biology is to characterize structures of proteins and their assemblies in solution. At low resolution, such a characterization may be achieved by small angle x-ray scattering (SAXS). Because SAXS analyses often require comparing profiles calculated from many atomic models against those determined by experiment, rapid and accurate profile computation from molecular structures is needed. We developed fast open-source x-ray scattering (FoXS) for profile computation. To match the experimental profile within the experimental noise, FoXS explicitly computes all interatomic distances and implicitly models the first hydration layer of the molecule. For assessing the accuracy of the modeled hydration layer, we performed contrast variation experiments for glucose isomerase and lysozyme, and found that FoXS can accurately represent density changes of this layer. The hydration layer model was also compared with a SAXS profile calculated for the explicit water molecules in the high-resolution structures of glucose isomerase and lysozyme. We tested FoXS on eleven protein, one DNA, and two RNA structures, revealing superior accuracy and speed versus CRYSOL, AquaSAXS, the Zernike polynomials-based method, and Fast-SAXS-pro. In addition, we demonstrated a significant correlation of the SAXS score with the accuracy of a structural model. Moreover, FoXS utility for analyzing heterogeneous samples was demonstrated for intrinsically flexible XLF-XRCC4 filaments and Ligase III-DNA complex. FoXS is extensively used as a standalone web server as a component of integrative structure determination by programs IMP, Chimera, and BILBOMD, as well as in other applications that require rapidly and accurately calculated SAXS profiles.
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Affiliation(s)
- Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
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227
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Tian X, Langkilde AE, Thorolfsson M, Rasmussen HB, Vestergaard B. Small-angle x-ray scattering screening complements conventional biophysical analysis: comparative structural and biophysical analysis of monoclonal antibodies IgG1, IgG2, and IgG4. J Pharm Sci 2014; 103:1701-10. [PMID: 24700358 PMCID: PMC4298811 DOI: 10.1002/jps.23964] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/25/2014] [Accepted: 03/13/2014] [Indexed: 12/21/2022]
Abstract
A crucial step in the development of therapeutic monoclonal antibodies is the selection of robust pharmaceutical candidates and screening of efficacious protein formulations to increase the resistance toward physicochemical degradation and aggregation during processing and storage. Here, we introduce small-angle X-ray scattering (SAXS) to characterize antibody solution behavior, which strongly complements conventional biophysical analysis. First, we apply a variety of conventional biophysical techniques for the evaluation of structural, conformational, and colloidal stability and report a systematic comparison between designed humanized IgG1, IgG2, and IgG4 with identical variable regions. Then, the high information content of SAXS data enables sensitive detection of structural differences between three IgG subclasses at neutral pH and rapid formation of dimers of IgG2 and IgG4 at low pH. We reveal subclass-specific variation in intermolecular repulsion already at low and medium protein concentrations, which explains the observed improved stability of IgG1 with respect to aggregation. We show how excipients dramatically influence such repulsive effects, hence demonstrating the potential application of extensive SAXS screening in antibody selection, eventual engineering, and formulation development.
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Affiliation(s)
- Xinsheng Tian
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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228
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Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K, Gabius HJ. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta Gen Subj 2014; 1850:186-235. [PMID: 24685397 DOI: 10.1016/j.bbagen.2014.03.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts. SCOPE OF REVIEW This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching. MAJOR CONCLUSIONS The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids. GENERAL SIGNIFICANCE Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.
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Affiliation(s)
- Dolores Solís
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 07110 Bunyola, Mallorca, Illes Baleares, Spain.
| | - Nicolai V Bovin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, 117871 GSP-7, V-437, Moscow, Russian Federation.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - Antonio Romero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
| | - Karel Smetana
- Charles University, 1st Faculty of Medicine, Institute of Anatomy, U nemocnice 3, 128 00 Prague 2, Czech Republic.
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany.
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229
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Kathuria SV, Kayatekin C, Barrea R, Kondrashkina E, Graceffa R, Guo L, Nobrega RP, Chakravarthy S, Matthews CR, Irving TC, Bilsel O. Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS. J Mol Biol 2014; 426:1980-94. [PMID: 24607691 DOI: 10.1016/j.jmb.2014.02.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 02/14/2014] [Accepted: 02/24/2014] [Indexed: 01/08/2023]
Abstract
It is generally held that random-coil polypeptide chains undergo a barrier-less continuous collapse when the solvent conditions are changed to favor the fully folded native conformation. We test this hypothesis by probing intramolecular distance distributions during folding in one of the paradigms of folding reactions, that of cytochrome c. The Trp59-to-heme distance was probed by time-resolved Förster resonance energy transfer in the microsecond time range of refolding. Contrary to expectation, a state with a Trp59-heme distance close to that of the guanidinium hydrochloride (GdnHCl) denatured state is present after ~27 μs of folding. A concomitant decrease in the population of this state and an increase in the population of a compact high-FRET (Förster resonance energy transfer) state (efficiency>90%) show that the collapse is barrier limited. Small-angle X-ray scattering (SAXS) measurements over a similar time range show that the radius of gyration under native favoring conditions is comparable to that of the GdnHCl denatured unfolded state. An independent comprehensive global thermodynamic analysis reveals that marginally stable partially folded structures are also present in the nominally unfolded GdnHCl denatured state. These observations suggest that specifically collapsed intermediate structures with low stability in rapid equilibrium with the unfolded state may contribute to the apparent chain contraction observed in previous fluorescence studies using steady-state detection. In the absence of significant dynamic averaging of marginally stable partially folded states and with the use of probes sensitive to distance distributions, barrier-limited chain contraction is observed upon transfer of the GdnHCl denatured state ensemble to native-like conditions.
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Affiliation(s)
- Sagar V Kathuria
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Can Kayatekin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Raul Barrea
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | | | - Rita Graceffa
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Liang Guo
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - R Paul Nobrega
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - C Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Thomas C Irving
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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230
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Disease causing mutants of TDP-43 nucleic acid binding domains are resistant to aggregation and have increased stability and half-life. Proc Natl Acad Sci U S A 2014; 111:4309-14. [PMID: 24591609 DOI: 10.1073/pnas.1317317111] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the last two decades many secrets of the age-related human neural proteinopathies have been revealed. A common feature of these diseases is abnormal, and possibly pathogenic, aggregation of specific proteins in the effected tissue often resulting from inherent or decreased structural stability. An archetype example of this is superoxide dismutase-1, the first genetic factor to be linked with amyotrophic lateral sclerosis (ALS). Mutant or posttranslationally modified TAR DNA binding protein-32 (TDP-43) is also strongly associated with ALS and an increasingly large number of other neurodegenerative diseases, including frontotemporal lobar degeneration (FTLD). Cytoplasmic mislocalization and elevated half-life is a characteristic of mutant TDP-43. Furthermore, patient age at the onset of disease symptoms shows a good inverse correlation with mutant TDP-43 half-life. Here we show that ALS and FTLD-associated TDP-43 mutations in the central nucleic acid binding domains lead to elevated half-life and this is commensurate with increased thermal stability and inhibition of aggregation. It is achieved without impact on secondary, tertiary, or quaternary structure. We propose that tighter structural cohesion contributes to reduced protein turnover, increasingly abnormal proteostasis and, ultimately, faster onset of disease symptoms. These results contrast our perception of neurodegenerative diseases as misfolded proteinopathies and delineate a novel path from the molecular characteristics of mutant TDP-43 to aberrant cellular effects and patient phenotype.
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231
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Maric S, Skar-Gislinge N, Midtgaard S, Thygesen MB, Schiller J, Frielinghaus H, Moulin M, Haertlein M, Forsyth VT, Pomorski TG, Arleth L. Stealth carriers for low-resolution structure determination of membrane proteins in solution. ACTA ACUST UNITED AC 2014; 70:317-28. [PMID: 24531466 DOI: 10.1107/s1399004713027466] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/07/2013] [Indexed: 02/07/2023]
Abstract
Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial nanoscale bilayer disc carriers that mimic the native bilayer environment allows the handling of membrane proteins in solution. This enables the use of small-angle scattering techniques for fast and reliable structural analysis. The difficulty with this approach is that the carrier discs contribute to the measured scattering intensity in a highly nontrivial fashion, making subsequent data analysis challenging. Here, an elegant solution to circumvent the intrinsic complexity brought about by the presence of the carrier disc is presented. In combination with small-angle neutron scattering (SANS) and the D2O/H2O-based solvent contrast-variation method, it is demonstrated that it is possible to prepare specifically deuterated carriers that become invisible to neutrons in 100% D2O at the length scales relevant to SANS. These `stealth' carrier discs may be used as a general platform for low-resolution structural studies of membrane proteins using well established data-analysis tools originally developed for soluble proteins.
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Affiliation(s)
- Selma Maric
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nicholas Skar-Gislinge
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Søren Midtgaard
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Mikkel B Thygesen
- CARB Centre, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jürgen Schiller
- Institut für Medizinische Physik und Biophysik, Medizinische Fakultät, Universität Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Henrich Frielinghaus
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Scattering, TUM FRM-2, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Martine Moulin
- Life Sciences Group, Institut Laue-Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue-Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Thomas Günther Pomorski
- Center for Membrane Pumps in Cells and Disease, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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232
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Rath EM, Duff AP, Håkansson AP, Knott RB, Church WB. Small-angle X-ray scattering of BAMLET at pH 12: a complex of α-lactalbumin and oleic acid. Proteins 2014; 82:1400-8. [PMID: 24408789 DOI: 10.1002/prot.24508] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/04/2013] [Accepted: 12/26/2013] [Indexed: 11/11/2022]
Abstract
BAMLET (Bovine Alpha-lactalbumin Made LEthal to Tumors) is a member of the family of the HAMLET-like complexes, a novel class of protein-based anti-cancer complexes that incorporate oleic acid and deliver it to cancer cells. Small angle X-ray scattering (SAXS) was performed on the complex at pH 12, examining the high pH structure as a function of oleic acid added. The SAXS data for BAMLET species prepared with a range of oleic acid concentrations indicate extended, irregular, partially unfolded protein conformations that vary with the oleic acid concentration. Increases in oleic acid concentration correlate with increasing radius of gyration without an increase in maximum particle dimension, indicating decreasing protein density. The models for the highest oleic acid content BAMLET indicate an unusual coiled elongated structure that contrasts with apo-α-lactalbumin at pH 12, which is an elongated globular molecule, suggesting that oleic acid inhibits the folding or collapse of the protein component of BAMLET to the globular form. Circular dichroism of BAMLET and apo-α-lactalbumin was performed and the results suggest that α-lactalbumin and BAMLET unfold in a continuum of increasing degree of unfolded states. Taken together, these results support a model in which BAMLET retains oleic acid by non-specific association in the core of partially unfolded protein, and represent a new type of lipoprotein structure.
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Affiliation(s)
- Emma M Rath
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, 2006, Australia
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233
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Dickson CF, Kumar KK, Jacques DA, Malmirchegini GR, Spirig T, Mackay JP, Clubb RT, Guss JM, Gell DA. Structure of the hemoglobin-IsdH complex reveals the molecular basis of iron capture by Staphylococcus aureus. J Biol Chem 2014; 289:6728-6738. [PMID: 24425866 DOI: 10.1074/jbc.m113.545566] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins.
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Affiliation(s)
- Claire F Dickson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Kaavya Krishna Kumar
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David A Jacques
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Thomas Spirig
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Joel P Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - J Mitchell Guss
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David A Gell
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia.
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234
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Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure 2014; 21:875-81. [PMID: 23747111 DOI: 10.1016/j.str.2013.04.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/24/2013] [Accepted: 04/18/2013] [Indexed: 12/13/2022]
Abstract
This report presents the conclusions of the July 12-13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, New Jersey. The task force includes experts in small-angle scattering (SAS), crystallography, data archiving, and molecular modeling who met to consider questions regarding the contributions of SAS to modern structural biology. Recognizing there is a rapidly growing community of structural biology researchers acquiring and interpreting SAS data in terms of increasingly sophisticated molecular models, the task force recommends that (1) a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download; (2) a standard dictionary is required for definitions of terms for data collection and for managing the SAS data repository; (3) options should be provided for including in the repository SAS-derived shape and atomistic models based on rigid-body refinement against SAS data along with specific information regarding the uniqueness and uncertainty of the model, and the protocol used to obtain it; (4) criteria need to be agreed upon for assessment of the quality of deposited SAS data and the accuracy of SAS-derived models, and the extent to which a given model fits the SAS data; (5) with the increasing diversity of structural biology data and models being generated, archiving options for models derived from diverse data will be required; and (6) thought leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding.
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Affiliation(s)
- Jill Trewhella
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia.
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235
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Casey LW, Mark AE, Kobe B. Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer. Aust J Chem 2014. [DOI: 10.1071/ch14396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The role of small-angle X-ray scattering (SAXS) in structural biology is now well established, and its usefulness in combination with macromolecular crystallography is clear. However, the highly averaged SAXS data present a significant risk of over-interpretation to the unwary practitioner, and it can be challenging to frame SAXS results in a manner that maximises the reliability of the conclusions drawn. In this review, a series of recent examples are used to illustrate both the challenges for interpretation and approaches through which these can be overcome.
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236
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Lukman S, Verma CS, Fuentes G. Exploiting Protein Intrinsic Flexibility in Drug Design. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:245-69. [DOI: 10.1007/978-3-319-02970-2_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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237
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Baird NJ, Ferré-D'Amaré AR. Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol 2014; 1103:211-25. [PMID: 24318897 PMCID: PMC4049135 DOI: 10.1007/978-1-62703-730-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a powerful tool for examining the global conformation of riboswitches in solution, and how this is modulated by binding of divalent cations and small molecule ligands. SAXS experiments, which typically require only minutes per sample, directly yield two quantities describing the size and shape of the RNA: the radius of gyration (Rg) and the maximum linear dimension (Dmax). Examination of these quantities can reveal if a riboswitch undergoes cation-induced compaction. Comparison of the Rg and Dmax values between samples containing different concentrations of ligand reveals the overall structural response of the riboswitch to ligand. The Kratky plot (a graphical representation that emphasizes the higher-resolution SAXS data) and the P(r) plot or pair-probability distribution (an indirect Fourier transform, or power spectrum of the data) can provide additional evidence of riboswitch conformational changes. Simulation methods have been developed for generating three-dimensional reconstructions consistent with the one-dimensional SAXS data. These low-resolution molecular envelopes can aid in deciphering the relative helical arrangement within the RNA.
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Affiliation(s)
- Nathan J. Baird
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R. Ferré-D'Amaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
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238
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Exploring RNA oligomerization and ligand binding by fluorescence correlation spectroscopy and small angle X-ray scattering. Methods Mol Biol 2014; 1086:321-34. [PMID: 24136613 DOI: 10.1007/978-1-62703-667-2_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA forms defined structures and binds specifically to target molecules. The combination of data which results from fluorescence correlation spectroscopy (FCS) and small angle X-ray scattering (SAXS) measurements can be used to determine intermolecular interactions between RNA and its binding partners. To define oligomerization states of free RNA and its complexes with bound target molecules, hydrodynamic radii, radii of gyration as well as the maximum sizes of the components have to be determined and compared. Furthermore, the program OLIGOMER allows calculating the portions of monomeric and dimeric RNA, for instance, within a mixture.
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239
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Kaieda S, Plivelic TS, Halle B. Structure and kinetics of chemically cross-linked protein gels from small-angle X-ray scattering. Phys Chem Chem Phys 2014; 16:4002-11. [DOI: 10.1039/c3cp54219j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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240
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Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M. SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:203-8. [PMID: 24365937 PMCID: PMC3874021 DOI: 10.1107/s1600577513030117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 11/03/2013] [Indexed: 05/03/2023]
Abstract
Small-angle X-ray scattering (SAXS) is an experimental technique that allows structural information on biomolecules in solution to be gathered. High-quality SAXS profiles have typically been obtained by manual merging of scattering profiles from different concentrations and exposure times. This procedure is very subjective and results vary from user to user. Up to now, no robust automatic procedure has been published to perform this step, preventing the application of SAXS to high-throughput projects. Here, SAXS Merge, a fully automated statistical method for merging SAXS profiles using Gaussian processes, is presented. This method requires only the buffer-subtracted SAXS profiles in a specific order. At the heart of its formulation is non-linear interpolation using Gaussian processes, which provides a statement of the problem that accounts for correlation in the data.
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Affiliation(s)
- Yannick G Spill
- Unité de Bioinformatique Structurale, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503 B, University of California San Francisco, San Francisco, CA 94158, USA
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503 B, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel Russel
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503 B, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ben Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503 B, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503 B, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael Nilges
- Unité de Bioinformatique Structurale, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
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241
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Hyland LL, Taraban MB, Yu YB. Using Small-Angle Scattering Techniques to Understand Mechanical Properties of Biopolymer-Based Biomaterials. SOFT MATTER 2013; 9:10.1039/C3SM51209F. [PMID: 24273590 PMCID: PMC3835338 DOI: 10.1039/c3sm51209f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The design and engineering of innovative biopolymer-based biomaterials for a variety of biomedical applications should be based on the understanding of the relationship between their nanoscale structure and mechanical properties. Down the road, such understanding could be fundamental to tune the properties of engineered tissues, extracellular matrices for cell delivery and proliferation/differentiation, etc. In this tutorial review, we attempt to show in what way biomaterial structural data can help to understand the bulk material properties. We begin with some background on common types of biopolymers used in biomaterials research, discuss some typical mechanical testing techniques and then review how others in the field of biomaterials have utilized small-angle scattering for material characterization. Detailed examples are then used to show the full range of possible characterization techniques available for biopolymer-based biomaterials. Future developments in the area of material characterization by small-angle scattering will undoubtedly facilitate the use of structural data to control the kinetics of assembly and final properties of prospective biomaterials.
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Affiliation(s)
| | - Marc B. Taraban
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA. Fax: 301-315-9953; Tel: 301-405-2829
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA. Fax: 410-706-5017; Tel: 410-706-7514
| | - Y. Bruce Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA. Fax: 410-706-5017; Tel: 410-706-7514
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242
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Guttman M, Lee KK. A functional interaction between gp41 and gp120 is observed for monomeric but not oligomeric, uncleaved HIV-1 Env gp140. J Virol 2013; 87:11462-75. [PMID: 23966389 PMCID: PMC3807357 DOI: 10.1128/jvi.01681-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/09/2013] [Indexed: 11/20/2022] Open
Abstract
The envelope glycoprotein (Env) is the sole antigenic feature on the surface of HIV and the target for the humoral immune system. Soluble, uncleaved gp140 Env constructs truncated at the transmembrane domain are being investigated intensively as potential vaccine immunogens by many groups, and understanding their structural properties is essential. We used hydrogen/deuterium-exchange mass spectrometry and small-angle X-ray scattering to probe structural order in a panel of commonly used gp140 constructs and matched gp120 monomers. We observed that oligomeric forms of uncleaved gp140, generally presumed to be trimeric, contain a protease-resistant form of gp41 akin to the postfusion, helical bundle conformation and appear to lack specific interactions between gp120 and gp41. In contrast, the monomeric form of gp140 shows significant stabilization of the gp120 inner domain imparted by the gp41 region, demonstrating excellent agreement with past mutagenesis studies. Moreover, the gp140 monomers respond to CD4 binding in manner that is consistent with the initial stages of Env activation: CD4 binding induces structural ordering throughout gp120 while loosening its association with gp41. The results indicate that uncleaved gp140 oligomers do not represent an authentic prefusion form of Env, whereas gp140 monomers isolated from the same glycoprotein preparations in many ways exhibit function and internal structural order that are consistent with expectations for certain aspects of native Env. gp140 monomers may thus be a useful reagent for advancing structural and functional studies.
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Affiliation(s)
- Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
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243
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Holding AN, Lamers MH, Stephens E, Skehel JM. Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples. J Proteome Res 2013; 12:5923-33. [PMID: 24010795 PMCID: PMC3859183 DOI: 10.1021/pr4003867] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Chemical cross-linking
of proteins combined with mass spectrometry
provides an attractive and novel method for the analysis of native
protein structures and protein complexes. Analysis of the data however
is complex. Only a small number of cross-linked peptides are produced
during sample preparation and must be identified against a background
of more abundant native peptides. To facilitate the search and identification
of cross-linked peptides, we have developed a novel software suite,
named Hekate. Hekate is a suite of tools that address the challenges
involved in analyzing protein cross-linking experiments when combined
with mass spectrometry. The software is an integrated pipeline for
the automation of the data analysis workflow and provides a novel
scoring system based on principles of linear peptide analysis. In
addition, it provides a tool for the visualization of identified cross-links
using three-dimensional models, which is particularly useful when
combining chemical cross-linking with other structural techniques.
Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural
elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight
into the previously uncharacterized C-terminal domain of the protein.
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Affiliation(s)
- Andrew N Holding
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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244
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Petoukhov MV, Billas IML, Takacs M, Graewert MA, Moras D, Svergun DI. Reconstruction of quaternary structure from X-ray scattering by equilibrium mixtures of biological macromolecules. Biochemistry 2013; 52:6844-55. [PMID: 24000896 DOI: 10.1021/bi400731u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recent renaissance in small-angle X-ray scattering (SAXS) made this technique a major tool for the low-resolution structural characterization of biological macromolecules in solution. The major limitation of existing methods for reconstructing 3D models from SAXS is imposed by the requirement of solute monodispersity. We present a novel approach that couples low-resolution 3D SAXS reconstruction with composition analysis of mixtures. The approach is applicable to polydisperse and difficult to purify systems, including weakly associated oligomers and transient complexes. Ab initio shape analysis is possible for symmetric homo-oligomers, whereas rigid body modeling is applied also to dissociating complexes when atomic structures of the individual subunits are available. In both approaches, the sample is considered as an equilibrium mixture of intact complexes/oligomers with their dissociation products or free subunits. The algorithms provide the 3D low-resolution model (for ab initio modeling, also the shape of the monomer) and the volume fractions of the bound and free state(s). The simultaneous fitting of multiple scattering data sets collected under different conditions allows one to restrain the modeling further. The possibilities of the approach are illustrated in simulated and experimental SAXS data from protein oligomers and multisubunit complexes including nucleoproteins. Using this approach, new structural insights are provided in the association behavior and conformations of estrogen-related receptors ERRα and ERRγ. The possibility of 3D modeling from the scattering by mixtures significantly widens the range of applicability of SAXS and opens novel avenues in the analysis of oligomeric mixtures and assembly/dissociation processes.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation , Notkestrasse 85, Hamburg 22607, Germany
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245
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Lee V, Hawa T. Investigation of the effect of bilayer membrane structures and fluctuation amplitudes on SANS/SAXS profile for short membrane wavelength. J Chem Phys 2013; 139:124905. [DOI: 10.1063/1.4821816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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246
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Round A, Brown E, Marcellin R, Kapp U, Westfall CS, Jez JM, Zubieta C. Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2072-80. [PMID: 24100325 DOI: 10.1107/s0907444913019276] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/11/2013] [Indexed: 01/06/2023]
Abstract
The combination of protein crystallography and small-angle X-ray scattering (SAXS) provides a powerful method to investigate changes in protein conformation. These complementary structural techniques were used to probe the solution structure of the apo and the ligand-bound forms of the Arabidopsis thaliana acyl acid-amido synthetase GH3.12. This enzyme is part of the extensive GH3 family and plays a critical role in the regulation of plant hormones through the formation of amino-acid-conjugated hormone products via an ATP-dependent reaction mechanism. The enzyme adopts two distinct C-terminal domain orientations with `open' and `closed' active sites. Previous studies suggested that ATP only binds in the open orientation. Here, the X-ray crystal structure of GH3.12 is presented in the closed conformation in complex with the nonhydrolysable ATP analogue AMPCPP and the substrate salicylate. Using on-line HPLC purification combined with SAXS measurements, the most likely apo and ATP-bound protein conformations in solution were determined. These studies demonstrate that the C-terminal domain is flexible in the apo form and favours the closed conformation upon ATP binding. In addition, these data illustrate the efficacy of on-line HPLC purification integrated into the SAXS sample-handling environment to reliably monitor small changes in protein conformation through the collection of aggregate-free and highly redundant data.
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Affiliation(s)
- Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
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247
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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.
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Affiliation(s)
- R Jain
- Structural Dynamics of (Bio)chemical Systems, MPI-BPC, Am Fassberg 11, 37077, Goettingen, Germany
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248
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Borfecchia E, Garino C, Salassa L, Lamberti C. Synchrotron ultrafast techniques for photoactive transition metal complexes. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120132. [PMID: 23776294 DOI: 10.1098/rsta.2012.0132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In the last decade, the use of time-resolved X-ray techniques has revealed the structure of light-generated transient species for a wide range of samples, from small organic molecules to proteins. Time resolutions of the order of 100 ps are typically reached, allowing one to monitor thermally equilibrated excited states and capture their structure as a function of time. This review aims at providing a general overview of the application of time-resolved X-ray solution scattering (TR-XSS) and time-resolved X-ray absorption spectroscopy (TR-XAS), the two techniques prevalently employed in the investigation of light-triggered structural changes of transition metal complexes. In particular, we herein describe the fundamental physical principles for static XSS and XAS and illustrate the theory of time-resolved XSS and XAS together with data acquisition and analysis strategies. Selected pioneering examples of photoactive transition metal complexes studied by TR-XSS and TR-XAS are discussed in depth.
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Affiliation(s)
- Elisa Borfecchia
- Department of Chemistry, NIS Centre of Excellence, University of Turin, via P. Giuria 7, 10125 Turin, Italy
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249
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Suits MD, Boraston AB. Structure of the Streptococcus pneumoniae surface protein and adhesin PfbA. PLoS One 2013; 8:e67190. [PMID: 23894284 PMCID: PMC3718772 DOI: 10.1371/journal.pone.0067190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/16/2013] [Indexed: 12/29/2022] Open
Abstract
PfbA (plasmin- and fibronectin-binding protein A) is an extracellular Streptococcus pneumoniae cell-wall attached surface protein that binds to fibronectin, plasmin, and plasminogen. Here we present a structural analysis of the surface exposed domains of PfbA using a combined approach of X-ray crystallography and small-angle X-ray scattering (SAXS). The crystal structure of the PfbA core domain, here called PfbAβ, determined to 2.28 Å resolution revealed an elongated 12-stranded parallel β-helix fold, which structure-based comparisons reveal is most similar to proteins with carbohydrate modifying activity. A notable feature of the PfbAβ is an extensive cleft on one face of the protein with electrochemical and spatial features that are analogous to structurally similar carbohydrate-active enzymes utilizing this feature for substrate accommodation. Though this cleft displays a combination of basic amino acid residues and solvent exposed aromatic amino acids that are distinct features for recognition of carbohydrates, no obvious arrangement of amino acid side chains that would constitute catalytic machinery is evident. The pseudo-atomic SAXS model of a larger fragment of PfbA suggests that it has a relatively well-ordered structure with the N-terminal and core domains of PfbA adopting an extend organization and reveals a novel structural class of surface exposed pneumococcal matrix molecule adhesins.
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Affiliation(s)
- Michael D. Suits
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
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Bolduc D, Rahdar M, Tu-Sekine B, Sivakumaren SC, Raben D, Amzel LM, Devreotes P, Gabelli SB, Cole P. Phosphorylation-mediated PTEN conformational closure and deactivation revealed with protein semisynthesis. eLife 2013; 2:e00691. [PMID: 23853711 PMCID: PMC3707082 DOI: 10.7554/elife.00691] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/07/2013] [Indexed: 12/23/2022] Open
Abstract
The tumor suppressor PIP3 phosphatase PTEN is phosphorylated on four clustered Ser/Thr on its C-terminal tail (aa 380–385) and these phosphorylations are proposed to induce a reduction in PTEN’s plasma membrane recruitment. How these phosphorylations affect the structure and enzymatic function of PTEN is poorly understood. To gain insight into the mechanistic basis of PTEN regulation by phosphorylation, we generated semisynthetic site-specifically tetra-phosphorylated PTEN using expressed protein ligation. By employing a combination of biophysical and enzymatic approaches, we have found that purified tail-phosphorylated PTEN relative to its unphosphorylated counterpart shows reduced catalytic activity and membrane affinity and undergoes conformational compaction likely involving an intramolecular interaction between its C-tail and the C2 domain. Our results suggest that there is a competition between membrane phospholipids and PTEN phospho-tail for binding to the C2 domain. These findings reveal a key aspect of PTEN’s regulation and suggest pharmacologic approaches for direct PTEN activation. DOI:http://dx.doi.org/10.7554/eLife.00691.001 PTEN is an enzyme that is found in almost every tissue in the body, and its job is to stop cells dividing. If it fails to perform this job, the uncontrolled proliferation of cells can lead to the growth of tumors. PTEN stops cells dividing by localizing at the plasma membrane of a cell and removing a phosphate group from a lipid called PIP3: this sends a signal, via the PI3K pathway, that suppresses the replication and survival of cells. Three regions of PTEN are thought to be central to its biological functions: one of these regions, the phosphatase domain, is directly responsible for removing a phosphate group from the lipid PIP3; a second region, called the C2 domain, is known to be critical for PTEN binding to the cell membrane; however, the role of third region, called the C-terminal domain, is poorly understood. Many proteins are regulated by the addition and removal of phosphate groups, and PTEN is no exception. In particular, it seems as if the addition of phosphate groups to four amino acid residues in the C-terminal domain can switch off the activity of PTEN, but the details of this process have been elusive. Now, Bolduc et al. have employed a variety of biochemical and biophysical techniques to explore this process, finding that the addition of the phosphate groups reduced PTEN’s affinity for the plasma membrane. At the same time, interactions between the C-terminal and C2 domains of the PTEN cause the shape of the enzyme to change in a way that ‘buries’ the residues to which the phosphate groups have been added. In addition to offering new insights into PTEN, the work of Bolduc et al. could help efforts to identify compounds with clinical anti-cancer potential. DOI:http://dx.doi.org/10.7554/eLife.00691.002
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Affiliation(s)
- David Bolduc
- Department of Pharmacology and Molecular Sciences , Johns Hopkins University School of Medicine , Baltimore , United States
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