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Smith KP, Chakravarthy S, Rahi A, Chakraborty M, Vosberg KM, Tonelli M, Plach MG, Grigorescu AA, Curtis JE, Varma D. SAXS/MC studies of the mixed-folded protein Cdt1 reveal monomeric, folded over conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573975. [PMID: 38260441 PMCID: PMC10802334 DOI: 10.1101/2024.01.03.573975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cdt1 is a protein critical for DNA replication licensing and is well-established to be a binding partner of the minichromosome maintenance (MCM) complex. Cdt1 has also been demonstrated to have an emerging, "moonlighting" role at the kinetochore via direct binding to microtubules and to the Ndc80 complex. However, it is not known how the structure and conformations of Cdt1 could allow for these multiple, completely unique sets of protein complexes. And while there exist multiple robust methods to study entirely folded or entirely unfolded proteins, structure-function studies of combined, mixed folded/disordered proteins remain challenging. It this work, we employ multiple orthogonal biophysical and computational techniques to provide a detailed structural characterization of human Cdt1 92-546. DSF and DSCD show both folded winged helix (WH) domains of Cdt1 are relatively unstable. CD and NMR show the N-terminal and the linker regions are intrinsically disordered. Using DLS and SEC-MALS, we show that Cdt1 is polydisperse, monomeric at high concentrations, and without any apparent inter-molecular self-association. SEC-SAXS of the monomer in solution enabled computational modeling of the protein in silico. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble. Using experimental SAXS data, we filtered for conformations which did and did not fit our data. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with our SAXS data. The best fit models have the N-terminal and linker regions extended into solution and the two folded domains close to each other in apparent "folded over" conformations. The best fit Cdt1 conformations are consistent with a function as a scaffold protein which may be sterically blocked without the presence of binding partners. Our studies also provide a template for combining experimental and computational biophysical techniques to study mixed-folded proteins.
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Affiliation(s)
- Kyle P Smith
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Present Address, Xylia Therapeutics, Waltham, MA, 02451, USA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Amit Rahi
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Manas Chakraborty
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kristen M Vosberg
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Arabela A Grigorescu
- Keck Biophysics Facility, Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60201, USA
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD, 20899, United States
| | - Dileep Varma
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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2
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Hutin S, Tully MD, Brennich M. Small-Angle X-Ray Scattering for Macromolecular Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:163-172. [PMID: 38507206 DOI: 10.1007/978-3-031-52193-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography. We include practical advice on experimental design and point out common pitfalls of the technique.
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Affiliation(s)
- Stephanie Hutin
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Mark D Tully
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble, Grenoble, France.
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3
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Bolinsson H, Söderberg C, Herranz-Trillo F, Wahlgren M, Nilsson L. Realizing the AF4-UV-SAXS on-line coupling on protein and antibodies using high flux synchrotron radiation at the CoSAXS beamline, MAX IV. Anal Bioanal Chem 2023; 415:6237-6246. [PMID: 37572213 PMCID: PMC10558385 DOI: 10.1007/s00216-023-04900-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
In this paper, we demonstrate the coupling of synchrotron small angle X-ray scattering (SAXS) to asymmetrical flow-field flow fractionation (AF4) for protein characterization. To the best of our knowledge, this is the first time AF4 is successfully coupled to a synchrotron for on-line measurements on proteins. This coupling has potentially high impact, as it opens the possibility to characterize individual constituents of sensitive and/or complex samples, not suited for separation using other techniques, and for low electron density samples where high X-ray flux is required, e.g., biomolecules and biologics. AF4 fractionates complex samples in native or close to native environment, with low shear forces and system surface area. Many orders of magnitude in size can be fractionated in one measurement, without having to reconfigure the experimental setup. We report AF4 fractionations with correlated UV and statistically adequate SAXS data of bovine serum albumin and a monoclonal antibody and evaluate SAXS data recorded for the two protein systems.
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Affiliation(s)
- Hans Bolinsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden.
| | - Christopher Söderberg
- RISE Research Institutes of Sweden, Division Bioeconomy and Health, Chemical Process and Pharmaceutical Development, Lund, Sweden
| | | | - Marie Wahlgren
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Lars Nilsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
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4
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Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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5
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Fernandez-Martinez D, Tully MD, Leonard G, Mathieu M, Kandiah E. Structural insights into the bi-specific cross-over dual variable antibody architecture by cryo-EM. Sci Rep 2023; 13:8694. [PMID: 37248285 DOI: 10.1038/s41598-023-35678-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023] Open
Abstract
Multi-specific antibodies (msAbs) are being developed as next generation antibody-based therapeutics. Knowledge of the three-dimensional structures, in the full antibody context, of their fragment antigen-binding (Fab) moieties with or without bound antigens is key to elucidating their therapeutic efficiency and stability. However, the flexibility of msAbs, a feature essential for their multi specificity, has hindered efforts in this direction. Cross-Over Dual Variable immunoglobulin (CODVIg) is a promising bispecific antibody format, designed to simultaneously target the interleukins IL4 and IL13. In this work we present the biophysical and structural characterisation of a CODVFab:IL13 complex in the full antibody context, using cryo-electron microscopy at an overall resolution of 4.2 Å. Unlike the 1:2 stoichiometry previously observed for CODVIg:IL4, CODVIg:IL13 shows a 1:1 stoichiometry. As well as providing details of the IL13-CODV binding interface, including the residues involved in the epitope-paratope region, the structure of CODVFab:IL13 also validates the use of labelling antibody as a new strategy for the single particle cryo-EM study of msAbs in complex with one, or more, antigens. This strategy reduced the inherent flexibility of the IL13 binding domain of CODV without inducing either structural changes at the epitope level or steric hindrance between the IL4 and IL13 binding regions of CODVIg. The work presented here thus also contributes to the development of methodology for the structural study of msAbs, a promising platform for cancer immunotherapy.
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Affiliation(s)
- David Fernandez-Martinez
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042, Grenoble, France
- Sanofi R&D, Bio Structure and Biophysics, Centre de Recherche Vitry-Sur-Seine, 94403, Vitry-Sur-Seine Cedex, France
- Pathogenesis of Vascular Infections, Department of Cell Biology and Infection, Institut Pasteur, INSERM, 75015, Paris, France
| | - Mark D Tully
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Gordon Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Magali Mathieu
- Sanofi R&D, Bio Structure and Biophysics, Centre de Recherche Vitry-Sur-Seine, 94403, Vitry-Sur-Seine Cedex, France.
| | - Eaazhisai Kandiah
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042, Grenoble, France.
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6
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Liu S, Jiang Y, Xu B, Jiang S. Analysis of the effect of rolling speed on the texture properties of noodle dough from water-solid interaction, development of gluten network, and bubble distribution. Food Chem 2022; 404:134359. [DOI: 10.1016/j.foodchem.2022.134359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/27/2022] [Accepted: 09/18/2022] [Indexed: 10/14/2022]
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7
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A comparative study of unpasteurized and pasteurized frozen whole hen eggs using size-exclusion chromatography and small-angle X-ray scattering. Sci Rep 2022; 12:9218. [PMID: 35654960 PMCID: PMC9163139 DOI: 10.1038/s41598-022-12885-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Hen eggs are rich in proteins and are an important source of protein for humans. Pasteurized frozen whole hen eggs are widely used in cooking and confectionery and can be stored for long periods. However, processed eggs differ from raw eggs in properties such as viscosity, foaming ability, and thermal aggregation. To develop pasteurized frozen whole egg products with properties similar to those of unpasteurized whole eggs, it is necessary to establish a method that can differentiate between the two egg types with respect to the structures of their proteins. In this study, size-exclusion chromatography (SEC) and SEC coupled with small-angle X-ray scattering (SEC-SAXS) were successfully used to differentiate between the proteins in unpasteurized and pasteurized frozen whole eggs. We found that proteins in the plasma fraction of egg yolk, especially apovitellenins I and II, formed large aggregates in the pasteurized eggs, indicating that their structures are sensitive to temperature changes during pasteurization, freezing, and thawing. The results suggest that SEC and SEC-SAXS can be used to differentiate between unpasteurized and pasteurized frozen whole eggs. Additionally, they may be useful in determining molecular sizes and shapes of multiple components in various complex biological systems such as whole eggs.
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8
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Barclay A, Tidemand Johansen N, Tidemand FG, Arleth L, Pedersen MC. Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:483-493. [PMID: 35362471 PMCID: PMC8972807 DOI: 10.1107/s2059798322001838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022]
Abstract
The combination of online size-exclusion chromatography and small-angle X-ray scattering (SEC–SAXS) is rapidly becoming a key technique for structural investigations of elaborate biophysical samples in solution. Here, a novel model-refinement strategy centred around the technique is outlined and its utility is demonstrated by analysing data series from several SEC–SAXS experiments on phospholipid bilayer nanodiscs. Using this method, a single model was globally refined against many frames from the same data series, thereby capturing the frame-to-frame tendencies of the irradiated sample. These are compared with models refined in the traditional manner, in which refinement is based on the average profile of a set of consecutive frames from the same data series without an in-depth comparison of individual frames. This is considered to be an attractive model-refinement scheme as it considerably lowers the total number of parameters refined from the data series, produces tendencies that are automatically consistent between frames, and utilizes a considerably larger portion of the recorded data than is often performed in such experiments. Additionally, a method is outlined for correcting a measured UV absorption signal by accounting for potential peak broadening by the experimental setup.
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9
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Yamaguchi T, Akao K, Koutsioubas A, Frielinghaus H, Kohzuma T. Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c' Revealed by Small Angle Neutron Scattering. Biomolecules 2022; 12:95. [PMID: 35053243 PMCID: PMC8774185 DOI: 10.3390/biom12010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 11/27/2022] Open
Abstract
The dynamic structure changes, including the unfolding, dimerization, and transition from the compact to the open-bundle unfolding intermediate structure of Cyt c', were detected by a small-angle neutron scattering experiment (SANS). The structure of Cyt c' was changed into an unstructured random coil at pD = 1.7 (Rg = 25 Å for the Cyt c' monomer). The four-α-helix bundle structure of Cyt c' at neutral pH was transitioned to an open-bundle structure (at pD ~13), which is given by a numerical partial scattering function analysis as a joint-clubs model consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c' (radius of gyration, Rg = 18 Å for the Cyt c' dimer) at neutral or mildly alkaline pD transited to a remarkably larger open-bundle structure at pD ~13 (Rg = 25 Å for the Cyt c' monomer). The open-bundle structure was also supported by ab initio modeling.
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Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan; (T.Y.); (K.A.)
- Frontier Research Center of Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai 319-1106, Ibaraki, Japan
| | - Kouhei Akao
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan; (T.Y.); (K.A.)
| | - Alexandros Koutsioubas
- Jülich Centre for Neutron Science JCNS-4 at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, D-85747 Garching, Germany; (A.K.); (H.F.)
| | - Henrich Frielinghaus
- Jülich Centre for Neutron Science JCNS-4 at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, D-85747 Garching, Germany; (A.K.); (H.F.)
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan; (T.Y.); (K.A.)
- Frontier Research Center of Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai 319-1106, Ibaraki, Japan
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10
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Rosenberg DJ, Hura GL, Hammel M. Size exclusion chromatography coupled small angle X-ray scattering with tandem multiangle light scattering at the SIBYLS beamline. Methods Enzymol 2022; 677:191-219. [DOI: 10.1016/bs.mie.2022.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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11
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SEC-SAXS: Experimental set-up and software developments build up a powerful tool. Methods Enzymol 2022; 677:221-249. [DOI: 10.1016/bs.mie.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Graewert MA, Svergun DI. Advanced sample environments and sample requirements for biological SAXS. Methods Enzymol 2022; 677:1-39. [DOI: 10.1016/bs.mie.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Size and shape of cycloamylose estimated using column chromatography coupled with small-angle X-ray scattering. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.105948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data. CRYSTALS 2020. [DOI: 10.3390/cryst10110975] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We describe the updated size-exclusion chromatography small angle X-ray scattering (SEC-SAXS) set-up used at the P12 bioSAXS beam line of the European Molecular Biology Laboratory (EMBL) at the PETRAIII synchrotron, DESY Hamburg (Germany). The addition of size exclusion chromatography (SEC) directly on-line to the SAXS capillary has become a well-established approach to reduce the effects of the sample heterogeneity on the SAXS measurements. The additional use of multi-angle laser light scattering (MALLS), UV absorption spectroscopy, refractive index (RI), and quasi-elastic light scattering (QELS) in parallel to the SAXS measurements enables independent molecular weight validation and hydrodynamic radius estimates. This allows one to address sample monodispersity as well as conformational heterogeneity. The benefits of the current SEC-SAXS set-up are demonstrated on a set of selected standard proteins. The processed SEC-SAXS data and models are provided in the Small Angle Scattering Biological Data Bank (SASBDB) and are labeled as “bench-marked” datasets that include the unsubtracted data frames spanning the respective SEC elution profiles and corresponding MALLS-UV-RI-QELS data. These entries provide method developers with datasets suitable for testing purposes, in addition to an educational resource for SAS data analysis and modeling.
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15
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Domain Organization in Plant Blue-Light Receptor Phototropin2 of Arabidopsis thaliana Studied by Small-Angle X-ray Scattering. Int J Mol Sci 2020; 21:ijms21186638. [PMID: 32927860 PMCID: PMC7555306 DOI: 10.3390/ijms21186638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 01/10/2023] Open
Abstract
Phototropin2 (phot2) is a blue-light (BL) receptor protein that regulates the BL-dependent activities of plants for efficient photosynthesis. Phot2 is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) to absorb BL, and a kinase domain. Photo-activated LOV domains, especially LOV2, play a major role in photo-dependent increase in the phosphorylation activity of the kinase domain. The atomic details of the overall structure of phot2 and the intramolecular mechanism to convert BL energy to a phosphorylation signal remain unknown. We performed structural studies on the LOV fragments LOV1, LOV2, LOV2-linker, and LOV2-kinase, and full-length phot2, using small-angle X-ray scattering (SAXS). The aim of the study was to understand structural changes under BL irradiation and discuss the molecular mechanism that enhance the phosphorylation activity under BL. SAXS is a suitable technique for visualizing molecular structures of proteins in solution at low resolution and is advantageous for monitoring their structural changes in the presence of external physical and/or chemical stimuli. Structural parameters and molecular models of the recombinant specimens were obtained from SAXS profiles in the dark, under BL irradiation, and after dark reversion. LOV1, LOV2, and LOV2-linker fragments displayed minimal structural changes. However, BL-induced rearrangements of functional domains were noted for LOV2-kinase and full-length phot2. Based on the molecular model together with the absorption measurements and biochemical assays, we discuss the intramolecular interactions and domain motions necessary for BL-enhanced phosphorylation activity of phot2.
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Delhommel F, Gabel F, Sattler M. Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes. J Mol Biol 2020; 432:2890-2912. [DOI: 10.1016/j.jmb.2020.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 01/24/2023]
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17
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Théobald-Dietrich A, de Wijn R, Rollet K, Bluhm A, Rudinger-Thirion J, Paulus C, Lorber B, Thureau A, Frugier M, Sauter C. Structural Analysis of RNA by Small-Angle X-ray Scattering. Methods Mol Biol 2020; 2113:189-215. [PMID: 32006316 DOI: 10.1007/978-1-0716-0278-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.
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Affiliation(s)
- Anne Théobald-Dietrich
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Raphaël de Wijn
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Kévin Rollet
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alexandra Bluhm
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Joëlle Rudinger-Thirion
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Caroline Paulus
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Bernard Lorber
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | | | - Magali Frugier
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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18
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Oide M, Hikima T, Oroguchi T, Kato T, Yamaguchi Y, Yoshihara S, Yamamoto M, Nakasako M, Okajima K. Molecular shape under far-red light and red light-induced association of Arabidopsis phytochrome B. FEBS J 2019; 287:1612-1625. [PMID: 31621187 DOI: 10.1111/febs.15095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/17/2019] [Accepted: 10/14/2019] [Indexed: 11/29/2022]
Abstract
Phytochrome B (phyB) is a plant photoreceptor protein that regulates various photomorphogenic responses to optimize plant growth and development. PhyB exists in two photoconvertible forms: a red light-absorbing (Pr) and a far-red light-absorbing (Pfr) form. Therefore, to understand the mechanism of phototransformation, the structural characterization of full-length phyB in these two forms is necessary. Here, we report the molecular structure of Arabidopsis thaliana phyB in Pr form and the molecular properties of the Pfr form determined by small-angle X-ray scattering coupled with size-exclusion chromatography. In solution, the Pr form associated as a dimer with a radius of gyration of 50 Å. The molecular shape was a crossed shape, in which the orientation of the photosensory modules differed from that in the crystal structure of dimeric photosensory module. PhyB exhibited structural reversibility in the Pfr-to-Pr phototransformation and thermal reversion from Pfr to Pr in the dark. In addition, Pfr only exhibited nonspecific association, which distinguished molecular properties of Pfr form from those of the inactive Pr form.
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Affiliation(s)
- Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | | | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yuhki Yamaguchi
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Shizue Yoshihara
- Department of Biological Science, Osaka Prefecture University, Sakai, Japan
| | | | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
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19
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Watanabe Y. Size-exclusion chromatography combined with solution X-ray scattering measurement of the heat-induced aggregates of water-soluble proteins at low ionic strength in a neutral solution. J Chromatogr A 2019; 1603:190-198. [PMID: 31277950 DOI: 10.1016/j.chroma.2019.06.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 11/15/2022]
Abstract
The heat-induced (80 ± 1 ℃, 1 h) aggregates of bovine serum albumin and ovalbumin at neutral pH and low ionic strength (10 mM sodium phosphate buffer, pH 6.9) were characterized using size-exclusion chromatography combined with small-angle X-ray scattering measurement. The values calculated for the radius of gyration and molecular weight of the eluted aggregates of the bovine serum albumin were 9-11 nm and 540,000-820,000, respectively. Those of ovalbumin were 11-16 nm and 500,000-1,820,000, respectively. The overall linear conformation of the bovine serum albumin aggregates slightly differed from that of the ovalbumin aggregates since the mass fractal dimensions were found from calculation to be 1.63-1.7 for the bovine serum albumin and 1.36-1.51 for the ovalbumin. The surface property of the aggregates of both proteins was suggested to be similar to that of their native monomer since all the surface fractal dimensions were almost equivalent. The dimensionless Kratky plots of the eluted aggregates indicated that the non-globular conformation of the bovine serum albumin aggregates differs from that of the ovalbumin aggregates. These analyses using size-exclusion chromatography combined with the solution X-ray scattering measurement will be helpful for characterization of the components of the denatured protein aggregation in solution.
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Affiliation(s)
- Yasushi Watanabe
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
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20
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Bucciarelli S, Midtgaard SR, Nors Pedersen M, Skou S, Arleth L, Vestergaard B. Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument. J Appl Crystallogr 2018; 51:1623-1632. [PMID: 30546289 PMCID: PMC6276278 DOI: 10.1107/s1600576718014462] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/13/2018] [Indexed: 11/16/2022] Open
Abstract
Coupling of size-exclusion chromatography with biological solution small-angle X-ray scattering (SEC-SAXS) on dedicated synchrotron beamlines enables structural analysis of challenging samples such as labile proteins and low-affinity complexes. For this reason, the approach has gained increased popularity during the past decade. Transportation of perishable samples to synchrotrons might, however, compromise the experiments, and the limited availability of synchrotron beamtime renders iterative sample optimization tedious and lengthy. Here, the successful setup of laboratory-based SEC-SAXS is described in a proof-of-concept study. It is demonstrated that sufficient quality data can be obtained on a laboratory instrument with small sample consumption, comparable to typical synchrotron SEC-SAXS demands. UV/vis measurements directly on the SAXS exposure cell ensure accurate concentration determination, crucial for direct molecular weight determination from the scattering data. The absence of radiation damage implies that the sample can be fractionated and subjected to complementary analysis available at the home institution after SEC-SAXS. Laboratory-based SEC-SAXS opens the field for analysis of biological samples at the home institution, thus increasing productivity of biostructural research. It may further ensure that synchrotron beamtime is used primarily for the most suitable and optimized samples.
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Affiliation(s)
- Saskia Bucciarelli
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Søren Roi Midtgaard
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Martin Nors Pedersen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | | | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
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21
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Chen YL, Sutton JL, Pollack L. How the Conformations of an Internal Junction Contribute to Fold an RNA Domain. J Phys Chem B 2018; 122:11363-11372. [PMID: 30285445 DOI: 10.1021/acs.jpcb.8b07262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like proteins, some RNAs fold to compact structures. We can model functional RNAs as a series of short, rigid, base-paired elements, connected by non-base-paired nucleotides that serve as junctions. These connecting regions bend and twist, facilitating the formation of tertiary contacts that stabilize compact states. Here, we explore the roles of salt and junction sequence in determining the structures of a ubiquitous connector: an asymmetric internal loop. We focus on the J5/5a junction from the widely studied P4-P6 domain of the Tetrahymena ribozyme. Following the addition of magnesium ions to fold P4-P6, this junction bends dramatically, bringing the two halves of the RNA domain together for tertiary contact engagement. Using single-molecule fluorescence resonance energy transfer (smFRET), we examine the role of sequence and salt on model RNA constructs that contain these junction regions. We explore the wild-type J5/5a junction as well as two sequence variants. These junctions display distinct, salt-dependent conformations. Small-angle X-ray scattering (SAXS) measurements verify that these effects persist in the full-length P4-P6 domain. These measurements underscore the importance of junction sequence and interactions with ions in facilitating RNA folding.
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Affiliation(s)
- Yen-Lin Chen
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
| | - Julie L Sutton
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
| | - Lois Pollack
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
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22
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Oide M, Sekiguchi Y, Fukuda A, Okajima K, Oroguchi T, Nakasako M. Classification of ab initio models of proteins restored from small-angle X-ray scattering. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1379-1388. [PMID: 30179176 DOI: 10.1107/s1600577518010342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
In structure analyses of proteins in solution by using small-angle X-ray scattering (SAXS), the molecular models are restored by using ab initio molecular modeling algorithms. There can be variation among restored models owing to the loss of phase information in the scattering profiles, averaging with regard to the orientation of proteins against the direction of the incident X-ray beam, and also conformational fluctuations. In many cases, a representative molecular model is obtained by averaging models restored in a number of ab initio calculations, which possibly provide nonrealistic models inconsistent with the biological and structural information about the target protein. Here, a protocol for classifying predicted models by multivariate analysis to select probable and realistic models is proposed. In the protocol, each structure model is represented as a point in a hyper-dimensional space describing the shape of the model. Principal component analysis followed by the clustering method is applied to visualize the distribution of the points in the hyper-dimensional space. Then, the classification provides an opportunity to exclude nonrealistic models. The feasibility of the protocol was examined through the application to the SAXS profiles of four proteins.
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Affiliation(s)
- Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yuki Sekiguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Asahi Fukuda
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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23
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Mahieu E, Gabel F. Biological small-angle neutron scattering: recent results and development. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:715-726. [DOI: 10.1107/s2059798318005016] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/27/2018] [Indexed: 02/06/2023]
Abstract
Small-angle neutron scattering (SANS) has increasingly been used by the structural biology community in recent years to obtain low-resolution information on solubilized biomacromolecular complexes in solution. In combination with deuterium labelling and solvent-contrast variation (H2O/D2O exchange), SANS provides unique information on individual components in large heterogeneous complexes that is perfectly complementary to the structural restraints provided by crystallography, nuclear magnetic resonance and electron microscopy. Typical systems studied include multi-protein or protein–DNA/RNA complexes and solubilized membrane proteins. The internal features of these systems are less accessible to the more broadly used small-angle X-ray scattering (SAXS) technique owing to a limited range of intra-complex and solvent electron-density variation. Here, the progress and developments of biological applications of SANS in the past decade are reviewed. The review covers scientific results from selected biological systems, including protein–protein complexes, protein–RNA/DNA complexes and membrane proteins. Moreover, an overview of recent developments in instruments, sample environment, deuterium labelling and software is presented. Finally, the perspectives for biological SANS in the context of integrated structural biology approaches are discussed.
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24
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Znamenskaya Falk Y, Engblom J, Pedersen JS, Arnebrant T, Kocherbitov V. Effects of Hydration on Structure and Phase Behavior of Pig Gastric Mucin Elucidated by SAXS. J Phys Chem B 2018; 122:7539-7546. [DOI: 10.1021/acs.jpcb.8b05496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yana Znamenskaya Falk
- Biomedical Science, Faculty of Health and Society, Malmö University, SE-205 06 Malmö, Sweden
- Biofilms—Research Center for Biointerfaces, Malmö University, SE-205 06 Malmö, Sweden
| | - Johan Engblom
- Biomedical Science, Faculty of Health and Society, Malmö University, SE-205 06 Malmö, Sweden
- Biofilms—Research Center for Biointerfaces, Malmö University, SE-205 06 Malmö, Sweden
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanosciene Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Thomas Arnebrant
- Biomedical Science, Faculty of Health and Society, Malmö University, SE-205 06 Malmö, Sweden
- Biofilms—Research Center for Biointerfaces, Malmö University, SE-205 06 Malmö, Sweden
| | - Vitaly Kocherbitov
- Biomedical Science, Faculty of Health and Society, Malmö University, SE-205 06 Malmö, Sweden
- Biofilms—Research Center for Biointerfaces, Malmö University, SE-205 06 Malmö, Sweden
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25
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Zabelskii DV, Vlasov AV, Ryzhykau YL, Murugova TN, Brennich M, Soloviov DV, Ivankov OI, Borshchevskiy VI, Mishin AV, Rogachev AV, Round A, Dencher NA, Büldt G, Gordeliy VI, Kuklin AI. Ambiguities and completeness of SAS data analysis: investigations of apoferritin by SAXS/SANS EID and SEC-SAXS methods. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1742-6596/994/1/012017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Watanabe Y. Assessment study of ion-exchange chromatography combined with solution X-ray scattering measurement for protein characterization. J Chromatogr A 2018; 1539:103-107. [PMID: 29395159 DOI: 10.1016/j.chroma.2018.01.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 11/29/2022]
Abstract
The performance of ion-exchange chromatography combined with small-angle X-ray scattering measurement was evaluated by characterization of the hen egg white lysozyme as a model protein. The X-ray transmittance was estimated using a micro-ionization chamber equipped with a sample cell holder for the real-time monitoring of the X-ray beam strength through the salt gradient elution. The radius of gyration of the eluted protein was estimated to be 1.50 ± 0.06 (n = 3) nm and 1.4 ± 0.1 nm as the value at the zero protein concentration. By using the X-ray transmittance values for the scattering intensity correction, the molecular weight of the eluted protein was estimated to be 15,200 ± 500 (n = 3) and 14,400 ± 200 as the value at the zero protein concentration. These values are close to those of the monomer of this protein. The ion-exchange chromatography combined with the small-angle X-ray scattering measurement system equipped with the X-ray transmittance monitor is a reliable method for protein characterization in solution.
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Affiliation(s)
- Yasushi Watanabe
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
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27
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Bernadó P, Shimizu N, Zaccai G, Kamikubo H, Sugiyama M. Solution scattering approaches to dynamical ordering in biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:253-274. [PMID: 29107147 DOI: 10.1016/j.bbagen.2017.10.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 01/09/2023]
Abstract
Clarification of solution structure and its modulation in proteins and protein complexes is crucially important to understand dynamical ordering in macromolecular systems. Small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are among the most powerful techniques to derive structural information. Recent progress in sample preparation, instruments and software analysis is opening up a new era for small-angle scattering. In this review, recent progress and trends of SAXS and SANS are introduced from the point of view of instrumentation and analysis, touching on general features and standard methods of small-angle scattering. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Giuseppe Zaccai
- Institut Laue Langevin, Institut de Biologie Structurale, CNRS, CNRS, UGA, Grenoble, France
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan..
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28
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Brennich ME, Round AR, Hutin S. Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline. J Vis Exp 2017. [PMID: 28117806 PMCID: PMC5409194 DOI: 10.3791/54861] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biological small angle X-ray scattering (BioSAXS) is a powerful technique in molecular and structural biology used to determine solution structure, particle size and shape, and surface-to-volume ratio of macromolecules. The technique is applicable to a very wide variety of solution conditions spanning a broad range of concentrations, pH values, ionic strengths, temperatures, additives, etc., but the sample is required to be monodisperse. This caveat led to the implementation of liquid chromatography systems on SAXS beamlines. Here, we describe the upstream integration of size-exclusion (SEC) and ion-exchange chromatography (IEC) on a beamline, different methods for optimal background subtraction, and data reduction. As an example, we describe how we use SEC- and IEC-SAXS on a fragment of the essential vaccinia virus protein D5, consisting of a D5N helicase domain. We determine its overall shape and molecular weight, showing the hexameric structure of the protein.
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Affiliation(s)
| | - Adam R Round
- European Molecular Biology Laboratory; School of Chemical and Physical Sciences, Keele University
| | - Stephanie Hutin
- Groupe de Microscopie Electronique et Méthodes, Institut de Biologie Structurale;
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29
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How to Analyze and Present SAS Data for Publication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:47-64. [PMID: 29218553 DOI: 10.1007/978-981-10-6038-0_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SAS is a powerful technique to investigate oligomeric state and domain organization of macromolecules, e.g. proteins and nucleic acids, under physiological, functional and even time resolved conditions. However, reconstructing three dimensional structures from SAS data is inherently ambiguous, as no information about orientation and phase is available. In addition experimental artifacts such as radiation damage, concentration effects and incorrect background subtraction can hinder the interpretation of even lead to wrong results. In this chapter, explanations on how to analyze data and how to assess and minimize the influence of experimental artifacts on the data. Furthermore, guidelines on how to present the resulting data and models to demonstrate the data supports the conclusion being made and that it is not biased by artifacts, will be given.
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30
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Small Angle Scattering: Historical Perspective and Future Outlook. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:1-10. [DOI: 10.1007/978-981-10-6038-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Pérez J, Vachette P. A Successful Combination: Coupling SE-HPLC with SAXS. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:183-199. [PMID: 29218560 DOI: 10.1007/978-981-10-6038-0_11] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A monodispersed and ideal solution is a central (unique?) requirement of SAXS to allow one to extract structural information from the recorded pattern. On-line Size Exclusion Chromatography (SEC) marked a major breakthrough, separating particles present in solution according to their size. Identical frames under an elution peak can be averaged and further processed free from contamination. However, this is not always straightforward, separation is often incomplete and software have been developed to deconvolve the contributions from the different species (molecules or oligomeric forms) within the sample. In this chapter, we present the general workflow of a SEC-SAXS experiment. We present recent instrumental and data analysis improvements that have improved the quality of recorded data, extended its potential and turn it into a mainstream approach. We describe into some details two specific applications of SEC-SAXS that provide more than just separating associated forms from the particle of interest.
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Affiliation(s)
- Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin BP48, 91192, Gif-sur-Yvette Cedex, France.
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Université Paris-Sud, 91405, Orsay Cedex, France
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32
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Kirby N, Cowieson N, Hawley AM, Mudie ST, McGillivray DJ, Kusel M, Samardzic-Boban V, Ryan TM. Improved radiation dose efficiency in solution SAXS using a sheath flow sample environment. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1254-1266. [PMID: 27917826 PMCID: PMC5137223 DOI: 10.1107/s2059798316017174] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 12/24/2022]
Abstract
Coflow is a new method for delivering radiation-sensitive biological and other solution-based samples to high-brightness X-ray beamlines that exploits laminar flow to ameliorate radiation-damage limitations and provides a host of practical improvements associated with these types of experiments. Radiation damage is a major limitation to synchrotron small-angle X-ray scattering analysis of biomacromolecules. Flowing the sample during exposure helps to reduce the problem, but its effectiveness in the laminar-flow regime is limited by slow flow velocity at the walls of sample cells. To overcome this limitation, the coflow method was developed, where the sample flows through the centre of its cell surrounded by a flow of matched buffer. The method permits an order-of-magnitude increase of X-ray incident flux before sample damage, improves measurement statistics and maintains low sample concentration limits. The method also efficiently handles sample volumes of a few microlitres, can increase sample throughput, is intrinsically resistant to capillary fouling by sample and is suited to static samples and size-exclusion chromatography applications. The method unlocks further potential of third-generation synchrotron beamlines to facilitate new and challenging applications in solution scattering.
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Affiliation(s)
- Nigel Kirby
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Nathan Cowieson
- B21 SAXS, Diamond Light Source Ltd, Hartwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Adrian M Hawley
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Stephen T Mudie
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Duncan J McGillivray
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Michael Kusel
- Kusel Design, 6 Hambleton Street, Albert Park, Victoria 3206, Australia
| | - Vesna Samardzic-Boban
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Timothy M Ryan
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
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33
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Hutin S, Brennich M, Maillot B, Round A. Online ion-exchange chromatography for small-angle X-ray scattering. Acta Crystallogr D Struct Biol 2016; 72:1090-1099. [PMID: 27710930 PMCID: PMC5053136 DOI: 10.1107/s2059798316012833] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 08/09/2016] [Indexed: 11/22/2022] Open
Abstract
Biological small-angle X-ray scattering (BioSAXS) is a powerful technique to determine the solution structure, particle size, shape and surface-to-volume ratio of macromolecules. However, a drawback is that the sample needs to be monodisperse. To ensure this, size-exclusion chromatography (SEC) has been implemented on many BioSAXS beamlines. Here, the integration of ion-exchange chromatography (IEC) using both continuous linear and step gradients on a beamline is described. Background subtraction for continuous gradients by shifting a reference measurement and two different approaches for step gradients, which are based on interpolating between two background measurements, are discussed. The results presented here serve as a proof of principle for online IEC and subsequent data treatment.
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Affiliation(s)
- Stephanie Hutin
- Institut de Biologie Structurale, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Martha Brennich
- European Synchrotron Radiation Facilty, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Benoit Maillot
- European Synchrotron Radiation Facilty, 71 Avenue des Martyrs, 38042 Grenoble, France
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, BP 10142, 67404 Illkirch, France
| | - Adam Round
- EMBL Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
- EPSAM, Keele University, Keele, England
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34
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Malaby AW, Chakravarthy S, Irving TC, Kathuria SV, Bilsel O, Lambright DG. Methods for analysis of size-exclusion chromatography-small-angle X-ray scattering and reconstruction of protein scattering. J Appl Crystallogr 2015; 48:1102-1113. [PMID: 26306089 DOI: 10.1107/s1600576715010420] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 05/31/2015] [Indexed: 11/10/2022] Open
Abstract
Size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) has emerged as an important method for investigation of heterogeneous and self-associating systems, but presents specific challenges for data processing including buffer subtraction and analysis of overlapping peaks. This paper presents novel methods based on singular value decomposition (SVD) and Guinier-optimized linear combination (LC) to facilitate analysis of SEC-SAXS data sets and high-quality reconstruction of protein scattering directly from peak regions. It is shown that Guinier-optimized buffer subtraction can reduce common subtraction artifacts and that Guinier-optimized linear combination of significant SVD basis components improves signal-to-noise and allows reconstruction of protein scattering, even in the absence of matching buffer regions. In test cases with conventional SAXS data sets for cytochrome c and SEC-SAXS data sets for the small GTPase Arf6 and the Arf GTPase exchange factors Grp1 and cytohesin-1, SVD-LC consistently provided higher quality reconstruction of protein scattering than either direct or Guinier-optimized buffer subtraction. These methods have been implemented in the context of a Python-extensible Mac OS X application known as Data Evaluation and Likelihood Analysis (DELA), which provides convenient tools for data-set selection, beam intensity normalization, SVD, and other relevant processing and analytical procedures, as well as automated Python scripts for common SAXS analyses and Guinier-optimized reconstruction of protein scattering.
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Affiliation(s)
- Andrew W Malaby
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Thomas C Irving
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Sagar V Kathuria
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - David G Lambright
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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Chaudhuri BN. Emerging applications of small angle solution scattering in structural biology. Protein Sci 2015; 24:267-76. [PMID: 25516491 PMCID: PMC4353354 DOI: 10.1002/pro.2624] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/05/2014] [Indexed: 12/12/2022]
Abstract
Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu.
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Affiliation(s)
- Barnali N Chaudhuri
- Faculty of Life Sciences and Biotechnology, South Asian UniversityAkbar Bhawan, Chanakyapuri, New Delhi, India
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Bras W, Koizumi S, Terrill NJ. Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments. IUCRJ 2014; 1:478-91. [PMID: 25485128 PMCID: PMC4224466 DOI: 10.1107/s2052252514019198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 08/25/2014] [Indexed: 05/20/2023]
Abstract
Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments.
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Affiliation(s)
- Wim Bras
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP 220, 6 Rue Jules Horowitz, Grenoble 38043, France
| | - Satoshi Koizumi
- College of Engineering, Ibaraki University, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Nicholas J Terrill
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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Zhu J, Li L, Chen L, Li X. Nano-structure of octenyl succinic anhydride modified starch micelle. Food Hydrocoll 2013. [DOI: 10.1016/j.foodhyd.2012.11.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Watanabe Y, Inoko Y. Characterization of a large glycoprotein proteoglycan by size-exclusion chromatography combined with light and X-ray scattering methods. J Chromatogr A 2013; 1303:100-4. [PMID: 23859798 DOI: 10.1016/j.chroma.2013.06.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/17/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
Abstract
The molecular weight and chain conformation of a proteoglycan derived from shark cartilage in solution were characterized by size-exclusion chromatography combined with low-angle laser light scattering and small-angle X-ray scattering methods. The total molecular weight of the proteoglycan was 3.9±0.2 million and the molecular weight of the main component was about 2.0±0.2 million. The X-ray scattering data revealed that the main components of the proteoglycan are nearly equal to a chain with excluded volume and their persistence lengths range from 13.5 to 16.4nm. These results show that size-exclusion chromatography combined with low-angle laser light scattering and small-angle X-ray scattering measurements are complementarily useful for characterization of large biopolymers in solution.
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Affiliation(s)
- Yasushi Watanabe
- National Food Research Institute, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
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Pérez J, Nishino Y. Advances in X-ray scattering: from solution SAXS to achievements with coherent beams. Curr Opin Struct Biol 2012; 22:670-8. [DOI: 10.1016/j.sbi.2012.07.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/15/2022]
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Receveur-Brechot V, Durand D. How random are intrinsically disordered proteins? A small angle scattering perspective. Curr Protein Pept Sci 2012; 13:55-75. [PMID: 22044150 PMCID: PMC3394175 DOI: 10.2174/138920312799277901] [Citation(s) in RCA: 267] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 01/08/2023]
Abstract
While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex, are then reviewed. Indeed, recent computational advances have made it possible to readily extract maximum information from the scattering curve with a special emphasis on highly flexible systems, such as multidomain proteins and IDPs. Furthermore, integrated computational approaches now enable the generation of ensembles of conformers to translate the unique flexible characteristics of IDPs by taking into consideration the constraints of more and more various complementary experiment. In particular, a combination of SAXS with high-resolution techniques, such as x-ray crystallography and NMR, allows us to provide reliable models and to gain unique structural insights about the protein over multiple structural scales. The latest neutron scattering experiments also promise new advances in the study of the conformational changes of macromolecules involving more complex systems.
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Effect of frozen storage on molecular weight, size distribution and conformation of gluten by SAXS and SEC-MALLS. Molecules 2012; 17:7169-82. [PMID: 22692241 PMCID: PMC6268907 DOI: 10.3390/molecules17067169] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/31/2012] [Accepted: 05/31/2012] [Indexed: 11/21/2022] Open
Abstract
In this study, the effects of frozen (−18 °C) storage time on molecular weight, size distribution, conformation, free amino groups and free sulfhydryl groups of gluten were studied by small-angle X-ray scattering (SAXS), multi-angle laser light scattering (MALLS) in conjunction with a size exclusion chromatography (SEC) and spectrophotometrically. The results showed that the gluten dissolved in 50 mM acetic acid appeared to be similar to quasi-spherical of the chain conformation and the slope of theconformation plot decreased during the storage. Both the molecular weight and radius of gyration of the frozen gluten decreased with the storage time showing a depolymerization in the high molecular weight fraction of gluten (105 Da ~ 109 Da). Therefore, at constant molecular weight the change of the chain conformation did not show a clear correlation with the storage time. The free amino groups content changed little and the free sulfhydryl groups content of the gluten increased from 9.8 μmol/g for the control to 12.87 μmol/g for 120-day-stored gluten, indicating that the water redistribution and ice recrystallization lead to the breakage of the disulphide bonds and may be one of the reasons for the depolymerization of gluten polymer.
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Watanabe Y, Inoko Y. Further application of size-exclusion chromatography combined with small-angle X-ray scattering optics for characterization of biological macromolecules. Anal Bioanal Chem 2010; 399:1449-53. [PMID: 20811739 DOI: 10.1007/s00216-010-4140-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/16/2010] [Accepted: 08/17/2010] [Indexed: 11/26/2022]
Abstract
Size-exclusion chromatography (gel filtration chromatography or gel permeation chromatography) in conjunction with online synchrotron radiation solution small-angle X-ray scattering optics, absorbance, and/or refractive index detectors was further assessed by application of biological macromolecules, such as the hollow sphere protein complex, apoferritin, and a linear polysaccharide, pullulan. The net X-ray scattering patterns of the eluted 24-mer molecule of apoferritin showed the specific character for the hollow spherical shape. The chromatographic (time-resolved) X-ray scattering data of the linear polysaccharide pullulan revealed the flexible chain structure during the chromatographic separation in an aqueous solution. These further applications demonstrated that the present measurement technique will be useful for not only the determination of the radius of gyration value of less than about 10 nm and molecular weight below several hundred thousand but also for the structural characterization of the various macromolecules during the chromatography.
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Affiliation(s)
- Yasushi Watanabe
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
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