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Abstract
Ab initio modeling methods have proven to be powerful means of interpreting solution scattering data. In the absence of atomic models, or complementary to them, ab initio modeling approaches can be used for generating low-resolution particle envelopes using only solution scattering profiles. Recently, a new ab initio reconstruction algorithm has been introduced to the scientific community, called DENSS. DENSS is unique among ab initio modeling algorithms in that it solves the inverse scattering problem, i.e., the 1D scattering intensities are directly used to determine the 3D particle density. The reconstruction of particle density has several advantages over conventional uniform density modeling approaches, including the ability to reconstruct a much wider range of particle types and the ability to visualize low-resolution density fluctuations inside the particle envelope. In this chapter we will discuss the theory behind this new approach, how to use DENSS, and how to interpret the results. Several examples with experimental and simulated data will be provided.
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Affiliation(s)
- Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, United States.
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2
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Comparative study of the interaction of some meso-substituted anionic cyanine dyes with human serum albumin. Biophys Chem 2020; 261:106378. [DOI: 10.1016/j.bpc.2020.106378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/19/2020] [Accepted: 04/09/2020] [Indexed: 11/17/2022]
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3
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Carusone TM, Cardiero G, Cerreta M, Mandrich L, Moran O, Porzio E, Catara G, Lacerra G, Manco G. WTAP and BIRC3 are involved in the posttranscriptional mechanisms that impact on the expression and activity of the human lactonase PON2. Cell Death Dis 2020; 11:324. [PMID: 32382056 PMCID: PMC7206036 DOI: 10.1038/s41419-020-2504-2] [Citation(s) in RCA: 11] [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: 12/31/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022]
Abstract
The activity of human paraoxonase 2 (PON2) is rapidly reduced in cells incubated with the bacterial quorormone 3-Oxo-dodecanoyl Homoserine Lactone (3OC12HSL), an observation that led to hypothesize a fast PON2 post-translational modification (PTM). Recently, we detected a 3OC12HSL-induced PTM in a cell-free system in which a crude extract from 3OC12HSL-treated HeLa cells was able to inactivate and ubiquitinate at position 144 a recombinant PON2. Here we show the occurrence of this and new PTMs on PON2 in HeLa cells. PTMs were found to gather nearby the two SNPs, A148G, and S311C, that are related to type-2 diabetes and its complications. Furthermore, we detected a PTM nearby a 12 amino acids region that is deleted in PON2 Isoform 2. An in vitro mutation analysis showed that the SNPs and the deletion are involved in PON2 activity and suggested a role of PTMs on its modulation, while a SAXS analysis pointed to Isoform 2 as being largely unstructured, compared to the wild type. Besides, we discovered a control of PON2 expression via a putative mRNA operon involving the Wilms tumor 1 associated protein (WTAP) and the E3 ubiquitin ligase (E3UbL) baculoviral IAP repeat-containing 3 (BIRC3).
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Affiliation(s)
- Teresa Maria Carusone
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Giovanna Cardiero
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", (IGB-ABT, CNR), National Research Council, Naples, Italy
| | - Mariangela Cerreta
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Luigi Mandrich
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Oscar Moran
- Institute of Biophysics (IBF, CNR), National Research Council, Genoa, Italy
| | - Elena Porzio
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Giuseppina Lacerra
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", (IGB-ABT, CNR), National Research Council, Naples, Italy.
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy.
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Lapinaite A, Carlomagno T, Gabel F. Small-Angle Neutron Scattering of RNA-Protein Complexes. Methods Mol Biol 2020; 2113:165-188. [PMID: 32006315 DOI: 10.1007/978-1-0716-0278-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Small-angle neutron scattering (SANS) provides structural information on biomacromolecules and their complexes in dilute solutions at the nanometer length scale. The overall dimensions, shapes, and interactions can be probed and compared to information obtained by complementary structural biology techniques such as crystallography, NMR, and EM. SANS, in combination with solvent H2O/D2O exchange and/or deuteration, is particularly well suited to probe the internal structure of RNA-protein (RNP) complexes since neutrons are more sensitive than X-rays to the difference in scattering length densities of proteins and RNA, with respect to an aqueous solvent. In this book chapter we provide a practical guide on how to carry out SANS experiments on RNP complexes, as well as possibilities of data analysis and interpretation.
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Affiliation(s)
- Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research, Leibniz University Hannover, Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Braunschweig, Germany
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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Wang C, Lin Y, Bougie D, Gillilan RE. Predicting data quality in biological X-ray solution scattering. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:727-738. [PMID: 30082508 DOI: 10.1107/s2059798318005004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/27/2018] [Indexed: 11/10/2022]
Abstract
Biological small-angle X-ray solution scattering (BioSAXS) is now widely used to gain information on biomolecules in the solution state. Often, however, it is not obvious in advance whether a particular sample will scatter strongly enough to give useful data to draw conclusions under practically achievable solution conditions. Conformational changes that appear to be large may not always produce scattering curves that are distinguishable from each other at realistic concentrations and exposure times. Emerging technologies such as time-resolved SAXS (TR-SAXS) pose additional challenges owing to small beams and short sample path lengths. Beamline optics vary in brilliance and degree of background scatter, and major upgrades and improvements to sources promise to expand the reach of these methods. Computations are developed to estimate BioSAXS sample intensity at a more detailed level than previous approaches, taking into account flux, energy, sample thickness, window material, instrumental background, detector efficiency, solution conditions and other parameters. The results are validated with calibrated experiments using standard proteins on four different beamlines with various fluxes, energies and configurations. The ability of BioSAXS to statistically distinguish a variety of conformational movements under continuous-flow time-resolved conditions is then computed on a set of matched structure pairs drawn from the Database of Macromolecular Motions (http://molmovdb.org). The feasibility of experiments is ranked according to sample consumption, a quantity that varies by over two orders of magnitude for the set of structures. In addition to photon flux, the calculations suggest that window scattering and choice of wavelength are also important factors given the short sample path lengths common in such setups.
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Affiliation(s)
- Chenzheng Wang
- DellEMC Shanghai COE, Shanghai 200433, People's Republic of China
| | - Yuexia Lin
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Devin Bougie
- CLASSE (Cornell Laboratory for Accelerator-based ScienceS and Education), Cornell University, Ithaca, NY 14853, USA
| | - Richard E Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, Ithaca, NY 14853, USA
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Single-alkyl and multi-alkyl chain-containing amphiphilic oligomers with several sugar side chains: solution properties and nanostructural analysis of aggregates by SANS. Colloid Polym Sci 2017. [DOI: 10.1007/s00396-017-4063-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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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Pronkin PG, Sorokina ON, Bychkova AV, Kolganova MN, Kovarskii AL, Rozenfel’d MA, Tatikolov AS. Electronic excitation energy transfer between molecules of cyanine dyes in a complex with protein and in systems of magnetic nanoparticles with protein coatings. HIGH ENERGY CHEMISTRY 2014. [DOI: 10.1134/s0018143915010105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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A simple procedure to evaluate the efficiency of bio-macromolecular rigid-body refinement by small-angle scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:1-11. [DOI: 10.1007/s00249-011-0751-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/06/2011] [Indexed: 02/02/2023]
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10
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Galantini L, Leggio C, Konarev PV, Pavel NV. Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea. Biophys Chem 2010; 147:111-22. [DOI: 10.1016/j.bpc.2010.01.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/08/2010] [Accepted: 01/10/2010] [Indexed: 11/28/2022]
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Leggio C, Galantini L, Konarev PV, Pavel NV. Urea-Induced Denaturation Process on Defatted Human Serum Albumin and in the Presence of Palmitic Acid. J Phys Chem B 2009; 113:12590-602. [DOI: 10.1021/jp904330v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Claudia Leggio
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
| | - Luciano Galantini
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
| | - Peter V. Konarev
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
| | - Nicolae V. Pavel
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
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12
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Galantini L, Leggio C, Pavel NV. Human Serum Albumin Unfolding: A Small-Angle X-ray Scattering and Light Scattering Study. J Phys Chem B 2008; 112:15460-9. [DOI: 10.1021/jp806821e] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luciano Galantini
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34−Roma 62, Pzz.le A. Moro 5, I-00185 Roma, Italy, and INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy
| | - Claudia Leggio
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34−Roma 62, Pzz.le A. Moro 5, I-00185 Roma, Italy, and INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy
| | - Nicolae Viorel Pavel
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34−Roma 62, Pzz.le A. Moro 5, I-00185 Roma, Italy, and INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy
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Moran O, Roessle MW, Mariuzza RA, Dimasi N. Structural features of the full-length adaptor protein GADS in solution determined using small-angle X-ray scattering. Biophys J 2008; 94:1766-72. [PMID: 17993503 PMCID: PMC2242750 DOI: 10.1529/biophysj.107.116590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 10/18/2007] [Indexed: 11/18/2022] Open
Abstract
The Grb2-related adaptor protein GADS plays a central role during the initial phases of signal transduction in T lymphocytes. GADS possesses N- and C-terminal Src homology 3 (SH3) domains flanking a central Src homology 2 (SH2) domain and a 126-residue region rich in glutamine and proline residues, presumed to be largely unstructured. The SH2 domain of GADS binds the adaptor protein LAT; the C-terminal SH3 domain pairs GADS to the adaptor protein SLP-76, whereas the function of the central region is unknown. High-resolution three-dimensional models are available for the isolated SH2 and C-terminal SH3 domains in complex with their respective binding partners, LAT and SLP-76. However, in part because of its intrinsic instability, there is no structural information for the entire GADS molecule. Here, we report the low-resolution structure of full-length GADS in solution using small-angle x-ray scattering (SAXS). Based on the SAXS data, complemented by gel filtration experiments, we show that full-length GADS is monomeric in solution and that its overall structural parameters are smaller than those expected for a protein with a long unstructured region. Ab initio and rigid body modeling of the SAXS data reveal that full-length GADS is a relatively compact molecule and that the potentially unstructured region retains a significant degree of structural order. The biological function of GADS is discussed based on its overall structure.
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Affiliation(s)
- Oscar Moran
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy
| | - Manfred W. Roessle
- European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany
| | - Roy A. Mariuzza
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, 20870 Rockville, Maryland
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Faunce CA, Paradies HH. Observations of liquidlike order of charged rodlike lipid A diphosphate assemblies at pH 8.5. J Chem Phys 2008; 128:065105. [DOI: 10.1063/1.2834206] [Citation(s) in RCA: 8] [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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Leggio C, Galantini L, Pavel NV. About the albumin structure in solution: cigar Expanded form versus heart Normal shape. Phys Chem Chem Phys 2008; 10:6741-50. [DOI: 10.1039/b808938h] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Khorramian BA, Stivala SS, Patel A. The upper limit of particle size as a function of slit combinations on the Kratky camera. J MACROMOL SCI B 2006. [DOI: 10.1080/00222348708248055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- B. A. Khorramian
- a Department of Chemistry , Long Island University , Brooklyn, New York, 11201
- c Bell Laboratories , 2000 Northeast Expressway, Norcross, Georgia, 30071
| | - S. S. Stivala
- b Department of Chemistry and Chemical , Engineering Stevens Institute of Technology , Hoboken, New Jersey, 07030
| | - A. Patel
- b Department of Chemistry and Chemical , Engineering Stevens Institute of Technology , Hoboken, New Jersey, 07030
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Affiliation(s)
- Jacques Rault
- a Laboratoire de Physique des Solides Université Paris-Sud , Centre d'Orsay, 91405, Orsay, France
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Bonicontro A, Risuleo G. Structural studies of E. coli ribosomes by spectroscopic techniques: a specialized review. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 62:1070-80. [PMID: 15950526 DOI: 10.1016/j.saa.2005.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Accepted: 04/15/2005] [Indexed: 05/02/2023]
Abstract
We present a review on our interdisciplinary line of research based on strategies of molecular biology and biophysics. These have been applied to the study of the prokaryotic ribosome of the bacterium Escherichia coli. Our investigations on this organelle have continued for more than a decade and we have adopted different spectroscopic biophysical techniques such as: dielectric and fluorescence spectroscopy as well as light scattering (photon correlation spectroscopy). Here we report studies on the whole 70S ribosomes and on the separated subunits 30S and 50S. Our results evidence intrinsic structural features of the subunits: the small shows a more "floppy" structure, while the large one appears to be more rigid. Also, an inner "kernel" formed by the RNA/protein association is found within the ribosome. This kernel is surrounded by a ribonucleoprotein complex more exposed to the solvent. Initial analyses were done on the so called Kaldtschmit-Wittmann ribosome: more recently we have extended the studies to the "tight couple" ribosome known for its better functional performance in vitro. Data evidence a phenomenological correlation between the differential biological activity and the intrinsic structural properties of the two-ribosome species. Finally, investigations were also conducted on particles treated at sub-denaturing temperatures and on ribosomes partially deproteinized by salt treatment (ribosomal cores). Results suggest that the thermal treatment and the selective removal of proteins cause analogous structural alterations.
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Affiliation(s)
- Adalberto Bonicontro
- INFM-CRS SOFT, Dipartimento di Fisica, Università di Roma La Sapienza, P.le A. Moro 2, I-00185 Roma, Italy
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Fang X, Littrell K, Yang XJ, Henderson SJ, Siefert S, Thiyagarajan P, Pan T, Sosnick TR. Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 2000; 39:11107-13. [PMID: 10998249 DOI: 10.1021/bi000724n] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We apply synchrotron-based small-angle X-ray scattering to investigate the relationship between compaction, metal binding, and structure formation of two RNAs at 37 degrees C: the 76 nucleotide yeast tRNA(Phe) and the 255 nucleotide catalytic domain of the Bacillus subtilis RNase P RNA. For both RNAs, this method provides direct evidence for the population of a distinct folding intermediate. The relative compaction between the intermediate and the native state does not correlate with the size of the RNA but does correlate well with the amount of surface burial as quantified previously by the urea-dependent m-value. The total compaction process can be described in two major stages. Starting from a completely unfolded state (4-8 M urea, no Mg(2+)), the major amount of compaction occurs upon the dilution of the denaturant and the addition of micromolar amounts of Mg(2+) to form the intermediate. The native state forms in a single transition from the intermediate state upon cooperative binding of three to four Mg(2+) ions. The characterization of this intermediate by small-angle X-ray scattering lends strong support for the cooperative Mg(2+)-binding model to describe the stability of a tertiary RNA.
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Affiliation(s)
- X Fang
- Department of Biochemistry & Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
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Henderson SJ. Monte Carlo modeling of small-angle scattering data from non-interacting homogeneous and heterogeneous particles in solution. Biophys J 1996; 70:1618-27. [PMID: 8785321 PMCID: PMC1225131 DOI: 10.1016/s0006-3495(96)79725-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A Monte Carlo algorithm that rapidly generates the scattered intensity function for complex heterogeneous particles is described. The heterogeneous particles are built from any number and orientation of simple building blocks, which include ellipsoidal shells, hollow ellipsoidal cylinders, ellipsoidal helices, triangular prisms, rectangular prisms, and semi-ellipsoidal shells. Applications are discussed such as real proteins and their complexes, polysaccharides, void effects on I(q), Guinier range estimation, and calculation of Stuhrmann plots.
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Tuzikov FV, Zinoviev VV, Vavilin VI, Malygin EG. Application of the small-angle X-ray scattering technique for the study of two-step equilibrium enzyme-substrate interactions. Biopolymers 1996; 38:131-9. [PMID: 8589248 DOI: 10.1002/(sici)1097-0282(199602)38:2<131::aid-bip1>3.0.co;2-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The small-angle x-ray scattering (SAXS) technique is used for the investigation of two-stage equilibrium macromolecular interactions of the enzyme-substrate type in solution. Experimental procedures and methods of analyzing the data obtained from SAXS have been elaborated. The algorithm for the data analysis allows one to determine the stoichiometric, equilibrium, and structural parameters of the enzyme-substrate complexes obtained. The thermodynamic characteristics for the formation of complexes of double-stranded oligonucleotide with Eco dam methyltransferase (MTase) have been determined and demonstrate a high cooperativity of MTase binding when the ternary complex containing the dimeric enzyme is formed. The structural parameters (Rg, Rc, semiaxes) have been determined for free enzyme and polynucleotides and of enzyme-substrate complexes, indicating structural rearrangements of the enzyme in the interaction with substrates.
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Affiliation(s)
- F V Tuzikov
- Institute of Molecular Biology, Koltsovo, Novosibirsk Region, Russia
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Hirai M, Kawai-Hirai R, Hirai T, Ueki T. Structural change of jack bean urease induced by addition of surfactants studied with synchrotron-radiation small-angle X-ray scattering. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 215:55-61. [PMID: 8344285 DOI: 10.1111/j.1432-1033.1993.tb18006.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Both the quaternary and subunit structures of jack bean urease in solutions with ionic and nonionic surfactants have been studied by small-angle X-ray scattering using a synchrotron-radiation source. The effects of those surfactants on the enzyme activity of urease have also been investigated in the same kind of solvent systems as those used for the scattering experiments. The present results show that the quaternary structure of urease in solution is fairly elongate and that by the relatively minor binding of SDS (SDS/protein = 0.23/1) the native urease molecule is dissociated into six identical subunits with nearly spherical structures. In addition the enzyme activity of urease was mostly retained under every solvent condition investigated, indicating that the subunit found in the present scattering experiments is the fundamental monomeric unit for both the quaternary-structure formation and enzyme function of urease.
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Affiliation(s)
- M Hirai
- Department of Physics, Faculty of General Studies, Gunma University, Maebashi-shi, Japan
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Hjelm RP, Alkan MH, Thiyagarajan P. Small-Angle Neutron Scattering Studies of Mixed Bile Salt-Lecithin Colloids. ACTA ACUST UNITED AC 1990. [DOI: 10.1080/00268949008025796] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Sinev MA, Razgulyaev OI, Vas M, Timchenko AA, Ptitsyn OB. Correlation between enzyme activity and hinge-bending domain displacement in 3-phosphoglycerate kinase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 180:61-6. [PMID: 2707265 DOI: 10.1111/j.1432-1033.1989.tb14615.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Diffuse X-ray-scattering data give evidence for large-scale structural change in pig muscle 3-phosphoglycerate kinase upon substrate binding. Simultaneous binding of 3-phosphoglycerate and MgATP either to the unmodified enzyme or to its active methylated derivative leads to about an 0.1-nm decrease in radius of gyration. These data coincide well with the previous data for yeast 3-phosphoglycerate kinase. When, instead of methylation, the two reactive thiol groups of pig muscle 3-phosphoglycerate kinase are carboxamidomethylated, the enzyme becomes inactive and the radii of gyration of its 'apo' and 'holo' forms do not differ within limits of experimental error. Thus, a correlation exists between the activity of 3-phosphoglycerate kinase and its substrate-induced large-scale conformational change. This correlation is a strong argument in favor of the functional importance of domain locking in the reaction catalyzed by 3-phosphoglycerate kinase.
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Affiliation(s)
- M A Sinev
- Institute of Protein Research, Academy of Sciences of the USSR, Pushchino, Moscow Region
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26
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Hayter J, Rivera M, McGroarty E. Neutron scattering analysis of bacterial lipopolysaccharide phase structure. Changes at high pH. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61159-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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27
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Sinev MA, Timchenko AA, Ptitsyn OB. A study of apo- and holo-forms of horse liver alcohol dehydrogenase in solution by diffuse x-ray scattering. Biopolymers 1986; 25:1385-97. [PMID: 2943325 DOI: 10.1002/bip.360250803] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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28
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Carlson RD. Neutron scattering studies of the H2a-H2b and (H3-H4)2 histone complexes. BASIC LIFE SCIENCES 1984; 27:47-72. [PMID: 6712573 DOI: 10.1007/978-1-4899-0375-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Neutron scattering experiments have shown that both the (H3-H4)2 and H2a-H2b histone complexes are quite asymmetric in solution. The (H3-H4)2 tetramer is an oblate or flattened structure, with a radius of gyration almost as large as that of the core octamer. If the tetramer is primarily globular, it must have an axial ratio of about 1:5. It is more likely, however, that this asymmetry results in part from N-terminal arms that extend outward approximately within the major plane of the particle. If this is the case, less asymmetric models for the globular part of the tetramer, including a dislocated disk of the type proposed by Klug et al. (23), can be made consistent with the scattering data. The H2a-H2b dimer, on the other hand, is an elongated structure. The low resolution data are in good agreement with those calculated for a cylindrical model 64 X 27 A, but other elongated models fit those data almost as well, including one that approximates free N-terminal arms at each end. Free arms are not necessary, but they must extend from the ends if they exist. A contrast matching experiment done with 50% deuterated H2b and undeuterated H2a in the reconstituted dimer showed that these two histones must each be rather elongated within the complex and are not just confined to one end. The amount of scattering contrast between the undeuterated and 50% deuterated histones was sufficient to suggest further experiments using complexes reconstituted from mixtures of undeuterated and partially deuterated histones which will help elucidate their arrangement within the histone complexes and within the octamer core of the nucleosome core particle.
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29
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Rontó G, Agamalyan MM, Drabkin GM, Feigin LA, Lvov YM. Structure of bacteriophage T7. Small-angle X-ray and neutron scattering study. Biophys J 1983; 43:309-14. [PMID: 6354291 PMCID: PMC1329299 DOI: 10.1016/s0006-3495(83)84354-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Small-angle x-ray and neutron scattering techniques were applied to bacteriophage T7 solutions at different scattering densities. Scattering curves determined under a variety of experimental conditions were used to derive a set of parameters characterizing the shape, size, and weight of the whole phage particle and of its DNA and protein components. The T7 head has an icosahedral shape with an edge of 37.7 +/- 0.5 nm, a volume of (12.0 +/- 1.0) x 10(4) nm3, and a small tail amounting to 6--7% of the head volume. The intraphage DNA region is most probably a hollow sphere. The best fit to the data was obtained with a model in which the hollow sphere filled with a protein core with a diameter of 24 nm. The average degree of swelling (i.e., the ratio of the hydrated to the dry volume) of the particle is 2.3; the degree of swelling of the DNA component is higher, 3.2, and that of the protein part is lower, 1.2.
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30
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Miake-Lye RC, Doniach S, Hodgson KO. Anomalous x-ray scattering from terbium-labeled parvalbumin in solution. Biophys J 1983; 41:287-92. [PMID: 6838970 PMCID: PMC1329182 DOI: 10.1016/s0006-3495(83)84440-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We have used anomalous small-angle x-ray scattering as a structural probe for solutions of rabbit parvalbumin labeled with terbium. This technique makes use of the large changes in the terbium scattering factor that occur when the x-ray energy is tuned around an L3 absorption edge of this heavy-atom label. These changes in scattering result in changes in the small-angle scattering curve of the labeled protein as a whole, which can then be analyzed to derive structural information concerning the distribution of labels in the protein. Based on a Gaussian model for the protein electron density, the mean distance from the terbiums to the protein center of mass is determined to be 13.2 A and is consistent with crystallographic results. Our results demonstrate the usefulness of terbium as an anomalous scattering label and provide criteria to help establish anomalous scattering as a reliable structural technique for proteins in solution.
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31
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32
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Tsukruk V, Shilov V, Lipatov Y. Studies on one-dimensional order in smectic polymers. Analysis of small-angle x-ray scattering and correlation functions. Eur Polym J 1983. [DOI: 10.1016/0014-3057(83)90127-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Gray DM, Gray CW, Carlson RD. Neutron scattering data on reconstituted complexes of fd deoxyribonucleic acid and gene 5 protein show that the deoxyribonucleic acid is near the center. Biochemistry 1982; 21:2702-13. [PMID: 7046792 DOI: 10.1021/bi00540a020] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We have performed low-angle neutron scattering studies on reconstituted complexes of fd DNA and the gene 5 protein that is produced during infection of Escherichia coli by filamentous fd phage. Essentially identical helical complexes have been made with normal protonated DNA or DNA in which at least 87% of the nonexchangeable protons are replaced by deuterium. From neutron scattering profiles of both complexes over a range of D2O/H2O solvent mixtures, the DNA deuteration is shown to have a dramatic influence on the measured cross-sectional radius of gyration. Most importantly, data for the complex containing deuterated DNA lead to a more negative slope in a plot of the square of the cross-sectional radius of gyration vs. the inverse of the solute-solvent contrast, compared with the slope of a plot of data for the complex containing protonated DNA. This means that, in a cross-sectional view of the complex, the DNA is near the center of the structure. By our analysis, the DNA has a cross-sectional radius of gyration of 17.6 +/- 3 A, while the protein has a cross-sectional radius of gyration of about 33.5 A. Therefore, the model for the structure of the helical complex that has been proposed from X-ray diffraction studies on gene 5 protein crystallized with oligodeoxynucleotides [McPherson, A., Jurnak, F., Wang, A., Kolpak, F., Rich, A., Molineux, I., & Fitzgerald, P. (1980) Biophys. J. 32, 155-170] is not valid for the complex in solution. From our neutron diffraction data we have also obtained values for the solvent-excluded volume and mass per unit length. The relation of our findings to the solution structure of the complex is discussed.
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34
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Moore PB. 8. Small-Angle Scattering Techniques for the Study of Biological Macromolecules and Macromolecular Aggregates. METHODS IN EXPERIMENTAL PHYSICS 1982. [DOI: 10.1016/s0076-695x(08)60157-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Gilmour S, Randall J, Torbet J, Dwek RA, Wain-Hobson S, Dower SK, van Schravendijk MR. Small-angle neutron scattering studies of the conformation of myeloma protein MOPC315 and its Fab fragment, and the interaction with a monovalent dinitrophenyl hapten. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON. SERIES B, BIOLOGICAL SCIENCES 1981; 211:433-53. [PMID: 6112756 DOI: 10.1098/rspb.1981.0016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The first small-angle scattering study of an immunoglobulin A is reported. Neutron measurements have been made to determine conformational parameters of the mouse myeloma protein MOPC315 and to relate these to previous immunoglobulin G results. Use of the contrast method shows that the MOPC315 IgA molecule is not simply globular, that it has a dry volume of 220.0 +/- 4.5 nm3 corresponding to a mass density of 1.275 +/- 0.025 g cm-3 and that its full and cross-sectional radii of gyration, corrected for concentration dependence, are 7.97 +/- 0.07 nm, 2.40 +/- 0.08 nm and 1.33 +/- 0.07 nm respectively. Similar study of its Fab fragment gives a dry molecular volume of 69.0 +/- 0.7 nm3, a mass density of 1.285 +/- 0.015 g cm-3 and uncorrected radii of gyration that are consistent with those of the parent and support an overall "T" or "Y" conformation in solution. Addition to saturation of a small monovalent dinitrophenyl hapten leaves the dry volume of the whole molecule unaltered, but may slightly lower one or more of its radii of gyration. The significance of this finding is discussed. Comparative studies with rabbit anti-dinitrophenyl immunoglobulin G antibody suggest a different initial conformation but similar consequences of hapten binding, which, if real, are probably unrelated to classical complement fixation.
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36
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Fedorov BA. On the determination of globular protein volume in solution by small-angle X-Ray scattering. Biopolymers 1981. [DOI: 10.1002/bip.1981.360200312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Oostergetel G, Krijgsman P, Mellema J, Cusack S, Miller A. Evidence for the absence of swelling of alfalfa mosaic virions. Virology 1981; 109:206-10. [DOI: 10.1016/0042-6822(81)90489-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/1980] [Indexed: 10/26/2022]
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38
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Zipper P, Durchschlag H. Small-angle X-ray scattering studies on the X-ray induced aggregation of malate synthase. RADIATION AND ENVIRONMENTAL BIOPHYSICS 1980; 18:99-121. [PMID: 7454971 DOI: 10.1007/bf01326049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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39
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R�ntgenkleinwinkeluntersuchungen der strahleninduzierten Aggregation von Ribonuclease, Lactat-Dehydrogenase, Glycerinaldehyd-3-phosphat-Dehydrogenase und Serumalbumin. Ein Vergleich mit Malatsynthase. MONATSHEFTE FUR CHEMIE 1980. [DOI: 10.1007/bf00899265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Small-angle X-ray scattering studies on the X-ray induced aggregation of malate synthase I. Structural and kinetic studies. MONATSHEFTE FUR CHEMIE 1980. [DOI: 10.1007/bf00903664] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Labischinski H, Subramanian AR. Protein S1 from Escherichia coli ribosomes: an improved isolation procedure and shape determination by small-angle X-ray scattering. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 95:359-66. [PMID: 378663 DOI: 10.1111/j.1432-1033.1979.tb12973.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ribosomal protein S1 from Escherichia coli was studied in solution by small-angle X-ray scattering and the following parameters were obtained. The radius of gyration R = 8.0 +/- 0.2 nm; largest diameter D = 28 nm; molecular weight = (8--9) x 10(4). The data also yielded (with the assumption of a rigid particle with almost constant electron density) two radii of gyration of cross-section Rq1 = 2.5 +/- 0.1 nm and Rq2 = 1.05 +/- 0.05 nm and molecular volume = 140 nm3. The experimental scattering curve of S1 was compared with the theoretical scattering curves for several rigid triaxial homogeneous bodies and the closest fit was given by that of a flat elliptical cylinder with the dimensions of 4.5 nm and 0.88 nm for the two semiaxes and 26.5 nm for height. The results from the present X-ray scattering studies and those from limited proteolytic digestion of protein S1 [J. Mol. Biol. 127, 41--54, (1979)] support the notion that the structure of protein S1 is organized into two distinct subdomains within its elongated overall shape. Protein S1 was purified for this study by an efficient procedure which yielded 12 mg S1/g ribosomes. The isolated protein was fully active in functional tests both before and after X-ray irradiation.
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42
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Damaschun G, Müller JJ, Bielka H. Scattering studies of ribosomes and ribosomal components. Methods Enzymol 1979; 59:706-50. [PMID: 374959 DOI: 10.1016/0076-6879(79)59122-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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43
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44
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45
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Kretzschmar KM, Mendelson RA, Morales MF. Investigation of the shape and size of myosin subfragment 1 using small-angle X-ray scattering. Biochemistry 1978; 17:2314-8. [PMID: 678510 DOI: 10.1021/bi00605a009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Measurement of x-ray scattering at very small angles by solutions of myosin subfragment 1 (S1) yields a radius of gyration of 3.24 nm (mean) +/- 0.03 nm (standard error for N = 9). If S1 is assumed to be ellipsoid of revolution, of uniform electron density, with a molecular weight of 1.15 X 10(5) and a partial specific volume of 0.73 cm3 g-1, then the axial ratio of the ellipsoid is 2.89 +/- 0.06 (prolate) or 0.26 +/- 0.01 (oblate), and the major axis is 13.0 +/- 0.2 nm (prolate) or 10.1 +/- 0.1 nm (oblate). Measurements at larger angles allow models of S1 morphology to be tested; theoretical scattering curves for various ellipsoids of revolution were calculated. The observed scatterina can be approximated by the scattering from ellipsoids with axial ratio 2.0 to 3.0 (prolate), or 0.25 to 0.4 (oblate). Models that fit the data over the range of scattering angles from 0 to 30 mrad are: prolate ellipsoid with axial ratio 2.3, major axis 12 nm; and oblate ellipsoid with axial ratio 0.4 and major axis 10 nm. Thus analyses of two parts of the scattering curve, by different methods, indicate that S1 is fae from spherical, and that its morphology may be approximated by ellipsoids of the aforesaid dimensions.
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46
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Zipper P, Durchschlag H. Small-angle X-ray scattering on malate synthase from baker's yeast. The native substrate-free enzyme and enzyme-substrate complexes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 87:85-99. [PMID: 352692 DOI: 10.1111/j.1432-1033.1978.tb12354.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Malate synthase from baker's yeast has been investigated in solution by the small-angle X-ray scattering technique. Size, shape and structure of the native substrate-free enzyme and of various enzyme-substrate complexes have been determined. As the enzyme was found to be rather unstable against X-rays, several precautions as well as sophisticated evaluation procedures had to be adopted to make sure that the results were not influenced by radiation damage. These included use of low primary intensity, short time of measurement, the presence of high concentrations of dithiothreitol, combined use of the conventional slit-collimation system and the new cone-collimation system. 1. For the native substrate-free enzyme the following molecular parameters could be established: radius of gyration R = 3.96 +/- 0.02 nm, maximum particle diameter D = 11.2 +/- 0.6 nm, radius of gyration of the thickness Rt = 1.04 +/- 0.04 nm, molecular weight Mr = 187000 +/- 3000, correlation volume Vc = 338 +/- 5 nm3, hydration x = 0.35 +/- 0.02 g/g, mean intersection length - l = 5.0 +/- 0.2 nm. Comparison of the experimental scattering curve with theoretical curves for various models showed that the enzyme is equivalent in scattering to an oblate ellipsoid of revolution rather than to a circular cylinder. The semiaxes of this ellipsoid are a = b = 6.06 nm and c = 2.21 nm. Thus with an axial ratio of about 1:0.36 the enzyme is of very anisometric shape. 2. Binding of the substrates (acetyl-CoA, glyoxylate) or the substrate analogue pyruvate causes slight structural changes of the enzyme. These changes are reflected mainly by a slight decrease of the radius of gyration (0.3--1.3%, as established both with the slit-smeared and the desmeared curves). Concomitantly there occurs a decrease of the maximum particle diameter and an increase of the radius of gyration of the thickness. These changes imply an increase of the axial ratio by 2.2--6.9%, i.e. substrate binding induces a decrease of anisometry. While the particle volume appears to be unchanged on binding glyoxylate or its analogue pyruvate, binding of acetyl-CoA causes slight changes of this parameter. In a similar manner the binding of acetyl-CoA leads to a slight enhancement of the molecular weight; this increase corresponds to the binding of 2.7 +/- 1 molecules of acetyl-CoA.
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47
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Müller K, Laggner P, Glatter O, Kostner G. The structure of human-plasma low-density lipoprotein B. An X-ray small-angle scattering study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 82:73-90. [PMID: 202466 DOI: 10.1111/j.1432-1033.1978.tb11998.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
1. X-ray small-angle scattering of human plasma lipoprotein B of the low-density fraction (rho = 1.016--1.060 g.cm-3) has been recorded to high precision at different electron density contrasts. 2. The overall structure of the particles is characterized by a quasi-spherical shape and radial symmetry. A maximum diameter of 23 nm and a molecular weight of 2.4 X 10(6) have been determined. 3. The internal structure is described in terms of a model consisting of spherical layers with different electron densities indicating that the neutral lipids are arranged in the core of the molecule up to a radius of about 8 nm surrounded by a monolayer of free cholesterol, phospholipids and protein. The neural lipids are shown to be in an ordered, liquid crystalline state at 4 degrees C and to undergo a thermotropic transition into a disordered state at higher temperatures.
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48
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Hamada F, Ishimuro Y, Hayashi T, Nakajima A. Conformation study on poly (L-tyrosine in dimethyl formamide by small-angle X-ray scattering. Biopolymers 1977; 16:2351-61. [PMID: 912005 DOI: 10.1002/bip.1977.360161102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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49
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Kneale GG, Baldwin JP, Bradbury EM. Neutron scattering studies of biological macromolecules in solution. Q Rev Biophys 1977; 10:485-527. [PMID: 343153 DOI: 10.1017/s0033583500003206] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Small-angle neutron scattering studies of biological macromolecules have developed rapidly in recent years due to the advent of high neutron-flux reactors,† efficient position-sensitive area detectors for neutrons (Allemand et al. 1975) and novel design of instruments (Ibel, 1976). At the same time position-sensitive detectors for X-rays (Gabriel & Dupont, 1972) have revitalized the small-angle X-ray scattering field (Kratky & Pilz, 1972; Luzzati et al. 1976) and it is now becoming clear that neutrons and X-rays can provide complementary structural information on biological complexes.
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50
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Furugren B, Andersson LO, Einarsson R. Small-angle x-ray scattering studies on human antithrombin III and its complex with heparin. Arch Biochem Biophys 1977; 178:419-24. [PMID: 836042 DOI: 10.1016/0003-9861(77)90211-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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