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Mohammed ASA, Soloviov D, Jeffries CM. Perspectives on solution-based small angle X-ray scattering for protein and biological macromolecule structural biology. Phys Chem Chem Phys 2024; 26:25268-25286. [PMID: 39323216 DOI: 10.1039/d4cp02001d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Small-angle X-ray scattering (SAXS) is used to extract structural information from a wide variety of non-crystalline samples in different fields (e.g., materials science, physics, chemistry, and biology). This review provides an overview of SAXS as applied to structural biology, specifically for proteins and other biomacromolecules in solution with an emphasis on extracting key structural parameters and the interpretation of SAXS data using a diverse array of techniques. These techniques cover aspects of building and assessing models to describe data measured from monodispersed and ideal dilute samples through to more complicated structurally polydisperse systems. Ab initio modelling, rigid body modelling as well as normal-mode analysis, molecular dynamics, mixed component and structural ensemble modelling are discussed. Dealing with polydispersity both physically in terms of component separation as well as approaching the analysis and modelling of data of mixtures and evolving systems are described, including methods for data decomposition such as single value decomposition/principle component analysis and evolving factor analysis. This review aims to highlight that solution SAXS, with the cohort of developments in data analysis and modelling, is well positioned to build upon the traditional 'single particle view' foundation of structural biology to take the field into new areas for interpreting the structures of proteins and biomacromolecules as population-states and dynamic structural systems.
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Affiliation(s)
- Ahmed S A Mohammed
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, co/DESY, Notkestrasse 85, D-22607 Hamburg, Germany.
- Physics Department, Faculty of Science, Fayoum University, 63514 Fayoum, Egypt
- Department of Biomedical Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Dmytro Soloviov
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, co/DESY, Notkestrasse 85, D-22607 Hamburg, Germany.
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, co/DESY, Notkestrasse 85, D-22607 Hamburg, Germany.
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2
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Zuo X, Tiede DM. Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications. J Appl Crystallogr 2024; 57:1446-1455. [PMID: 39387080 PMCID: PMC11460383 DOI: 10.1107/s1600576724007222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 07/21/2024] [Indexed: 10/12/2024] Open
Abstract
X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclo-dextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0, which is available to download from https://12idb.xray.aps.anl.gov/solx.html.
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Affiliation(s)
- Xiaobing Zuo
- X-ray Science DivisionArgonne National LaboratoryLemontIllinoisUSA
| | - David M. Tiede
- Chemical Sciences and Engineering DivisionArgonne National LaboratoryLemontIllinoisUSA
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3
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Lee S, Ki H, Lee SJ, Ihee H. Single-Molecule X-ray Scattering Used to Visualize the Conformation Distribution of Biological Molecules via Single-Object Scattering Sampling. Int J Mol Sci 2023; 24:17135. [PMID: 38138965 PMCID: PMC10743147 DOI: 10.3390/ijms242417135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Biological macromolecules, the fundamental building blocks of life, exhibit dynamic structures in their natural environment. Traditional structure determination techniques often oversimplify these multifarious conformational spectra by capturing only ensemble- and time-averaged molecular structures. Addressing this gap, in this work, we extend the application of the single-object scattering sampling (SOSS) method to diverse biological molecules, including RNAs and proteins. Our approach, referred to as "Bio-SOSS", leverages ultrashort X-ray pulses to capture instantaneous structures. In Bio-SOSS, we employ two gold nanoparticles (AuNPs) as labels, which provide strong contrast in the X-ray scattering signal, to ensure precise distance determinations between labeled sites. We generated hypothetical Bio-SOSS images for RNAs, proteins, and an RNA-protein complex, each labeled with two AuNPs at specified positions. Subsequently, to validate the accuracy of Bio-SOSS, we extracted distances between these nanoparticle labels from the images and compared them with the actual values used to generate the Bio-SOSS images. Specifically, for a representative RNA (1KXK), the standard deviation in distance discrepancies between molecular dynamics snapshots and Bio-SOSS retrievals was found to be optimally around 0.2 Å, typically within 1 Å under practical experimental conditions at state-of-the-art X-ray free-electron laser facilities. Furthermore, we conducted an in-depth analysis of how various experimental factors, such as AuNP size, X-ray properties, and detector geometry, influence the accuracy of Bio-SOSS. This comprehensive investigation highlights the practicality and potential of Bio-SOSS in accurately capturing the diverse conformation spectrum of biological macromolecules, paving the way for deeper insights into their dynamic natures.
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Affiliation(s)
- Seonggon Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; (S.L.); (H.K.); (S.J.L.)
- Center for Advanced Reaction Dynamics (CARD), Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; (S.L.); (H.K.); (S.J.L.)
- Center for Advanced Reaction Dynamics (CARD), Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; (S.L.); (H.K.); (S.J.L.)
- Center for Advanced Reaction Dynamics (CARD), Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; (S.L.); (H.K.); (S.J.L.)
- Center for Advanced Reaction Dynamics (CARD), Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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4
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Delhommel F, Martínez-Lumbreras S, Sattler M. Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes. Methods Enzymol 2022; 678:263-297. [PMID: 36641211 DOI: 10.1016/bs.mie.2022.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Understanding the structure and dynamics of biological macromolecules is essential to decipher the molecular mechanisms that underlie cellular functions. The description of structure and conformational dynamics often requires the integration of complementary techniques. In this review, we highlight the utility of combining nuclear magnetic resonance (NMR) spectroscopy with small angle scattering (SAS) to characterize these challenging biomolecular systems. NMR can assess the structure and conformational dynamics of multidomain proteins, RNAs and biomolecular complexes. It can efficiently provide information on interaction surfaces, long-distance restraints and relative domain orientations at residue-level resolution. Such information can be readily combined with high-resolution structural data available on subcomponents of biomolecular assemblies. Moreover, NMR is a powerful tool to characterize the dynamics of biomolecules on a wide range of timescales, from nanoseconds to seconds. On the other hand, SAS approaches provide global information on the size and shape of biomolecules and on the ensemble of all conformations present in solution. Therefore, NMR and SAS provide complementary data that are uniquely suited to investigate dynamic biomolecular assemblies. Here, we briefly review the type of data that can be obtained by both techniques and describe different approaches that can be used to combine them to characterize biomolecular assemblies. We then provide guidelines on which experiments are best suited depending on the type of system studied, ranging from fully rigid complexes, dynamic structures that interconvert between defined conformations and systems with very high structural heterogeneity.
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Affiliation(s)
- Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany.
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5
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Smith KP, Lee W, Tonelli M, Lee Y, Light SH, Cornilescu G, Chakravarthy S. Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach. Protein Sci 2022; 31:e4282. [PMID: 35137487 PMCID: PMC9047041 DOI: 10.1002/pro.4282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/11/2022]
Abstract
The bacterial pathogen Vibrio cholerae use a type III secretion system to inject effector proteins into a host cell. Recently, a putative Toxic GTPase Activating Protein (ToxGAP) called Vibrio outer protein E (VopE) was identified as a T3SS substrate and virulence factor that affected host mitochondrial dynamics and immune response. However, biophysical and structural characterization has been absent. Here, we describe solution NMR structure of the putative GTPase-activating protein (GAP) domain (73-204) of VopE. Using size exclusion chromatography coupled with small-angle x-ray scattering and residual dipolar coupling data, we restrained the MD process to efficiently determine the overall fold and improve the quality of the output calculated structures. Comparing the structure of VopE with other ToxGAP's revealed a similar overall fold with several features unique to VopE. Specifically, the "Bulge 1," α1 helix, and noteworthy "backside linker" elements on the N-terminus are dissimilar to the other ToxGAP's. By using NMR relaxation dispersion experiments, we demonstrate that these regions undergo motions on a > 6 s-1 timescale. Based on the disposition of these mobile regions relative to the putative catalytic arginine residue, we hypothesize that the protein may undergo structural changes to bind cognate GTPases.
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Affiliation(s)
- Kyle P. Smith
- Department of Cell & Developmental BiologyNorthwestern University ChicagoIllinoisUSA
- Xilio TherapeuticsWalthamMassachusettsUSA
| | - Woonghee Lee
- Department of ChemistryUniversity of Colorado‐DenverDenverColoradoUSA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Yeongjoon Lee
- Department of ChemistryUniversity of Colorado‐DenverDenverColoradoUSA
| | - Samuel H. Light
- Department of MicrobiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Gabriel Cornilescu
- Advanced Technology Research Facility, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research, Inc., National Cancer Institute, National Institutes of HealthFrederickMarylandUSA
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6
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Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS. Biophys J 2021; 120:3664-3675. [PMID: 34310942 DOI: 10.1016/j.bpj.2021.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/25/2021] [Accepted: 07/20/2021] [Indexed: 11/23/2022] Open
Abstract
Na+/Ca2+ exchangers (NCXs) are secondary active transporters that couple the translocation of Na+ with the transport of Ca2+ in the opposite direction. The exchanger is an essential Ca2+ extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+ sensor called CBD12. Binding of intracellular Ca2+ to CBD12 activates the NCX but inhibits the NCX of Drosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant interdomain flexibility in the apo state but assume rigid interdomain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N residual dipolar couplings), and small-angle x-ray scattering (SAXS) data in a combined strategy to select an ensemble of conformations in agreement with the experimental data. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, whereas the wide-open interdomain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+ binding shifts the CBD12 conformational ensemble toward extended conformers, which could be a key step in the NCXs' allosteric regulation mechanism. This strategy, combining MD with NMR and SAXS, provides a powerful approach to select ensembles of conformations that could be applied to other flexible multidomain systems.
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7
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Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
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Roskamp KW, Paulson CN, Brubaker WD, Martin RW. Function and Aggregation in Structural Eye Lens Crystallins. Acc Chem Res 2020; 53:863-874. [PMID: 32271004 DOI: 10.1021/acs.accounts.0c00014] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Crystallins are transparent, refractive proteins that contribute to the focusing power of the vertebrate eye lens. These proteins are extremely soluble and resist aggregation for decades, even under crowded conditions. Crystallins have evolved to avoid strong interprotein interactions and have unusual hydration properties. Crystallin aggregation resulting from mutation, damage, or aging can lead to cataract, a disease state characterized by opacity of the lens.Different aggregation mechanisms can occur, following multiple pathways and leading to aggregates with varied morphologies. Studies of variant proteins found in individuals with childhood-onset cataract have provided insight into the molecular factors underlying crystallin stability and solubility. Modulation of exposed hydrophobic surface is critical, as is preventing specific intermolecular interactions that could provide nucleation sites for aggregation. Biophysical measurements and structural biology techniques are beginning to provide a detailed picture of how crystallins crowd into the lens, providing high refractivity while avoiding excessively tight binding that would lead to aggregation.Despite the central biological importance of refractivity, relatively few experimental measurements have been made for lens crystallins. Our work and that of others have shown that hydration is important to the high refractive index of crystallin proteins, as are interactions between pairs of aromatic residues and potentially other specific structural features.This Account describes our efforts to understand both the functional and disease states of vertebrate eye lens crystallins, particularly the γ-crystallins. We use a variety of biophysical techniques, notably NMR spectroscopy, to investigate crystallin stability and solubility. In the first section, we describe efforts to understand the relative stability and aggregation propensity of different γS-crystallin variants. The second section focuses on interactions of these proteins with the holdase chaperone αB-crystallin. The third, fourth, and fifth sections explore different modes of aggregation available to crystallin proteins, and the final section highlights the importance of refractive index and the sometimes conflicting demands of selection for refractivity and solubility.
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Affiliation(s)
- Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Carolyn N. Paulson
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - William D. Brubaker
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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9
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Integrating Non-NMR Distance Restraints to Augment NMR Depiction of Protein Structure and Dynamics. J Mol Biol 2020; 432:2913-2929. [DOI: 10.1016/j.jmb.2020.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 11/24/2022]
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10
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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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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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12
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Sunday DF, Martin TB, Chang AB, Burns AB, Grubbs RH. Addressing the challenges of modeling the scattering from bottlebrush polymers in solution. JOURNAL OF POLYMER SCIENCE 2020; 58:10.1002/pol.20190289. [PMID: 33305292 PMCID: PMC7724922 DOI: 10.1002/pol.20190289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/02/2020] [Indexed: 12/17/2022]
Abstract
Small-angle scattering measurements of complex macromolecules in solution are used to establish relationships between chemical structure and conformational properties. Interpretation of the scattering data requires an inverse approach where a model is chosen and the simulated scattering intensity from that model is iterated to match the experimental scattering intensity. This raises challenges in the case where the model is an imperfect approximation of the underlying structure, or where there are significant correlations between model parameters. We examine three bottlebrush polymers (consisting of polynorbornene backbone and polystyrene side chains) in a good solvent using a model commonly applied to this class of polymers: the flexible cylinder model. Applying a series of constrained Monte-Carlo Markov Chain analyses demonstrates the severity of the correlations between key parameters and the presence of multiple close minima in the goodness of fit space. We demonstrate that a shape-agnostic model can fit the scattering with significantly reduced parameter correlations and less potential for complex, multimodal parameter spaces. We provide recommendations to improve the analysis of complex macromolecules in solution, highlighting the value of Bayesian methods. This approach provides richer information for understanding parameter sensitivity compared to methods which produce a single, best fit.
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Affiliation(s)
- Daniel F. Sunday
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Tyler B. Martin
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Alice B. Chang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Adam B. Burns
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Robert H. Grubbs
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
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NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes. Biophys Rev 2019; 12:155-174. [PMID: 31838649 DOI: 10.1007/s12551-019-00609-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022] Open
Abstract
Allostery is a ubiquitous biological mechanism in which a distant binding site is coupled to and drastically alters the function of a catalytic site in a protein. Allostery provides a high level of spatial and temporal control of the integrity and activity of biomolecular assembles composed of proteins, nucleic acids, or small molecules. Understanding the physical forces that drive allosteric coupling is critical to harnessing this process for use in bioengineering, de novo protein design, and drug discovery. Current microscopic models of allostery highlight the importance of energetics, structural rearrangements, and conformational fluctuations, and in this review, we discuss the synergistic use of solution NMR spectroscopy and computational methods to probe these phenomena in allosteric systems, particularly protein-nucleic acid complexes. This combination of experimental and theoretical techniques facilitates an unparalleled detection of subtle changes to structural and dynamic equilibria in biomolecules with atomic resolution, and we provide a detailed discussion of specialized NMR experiments as well as the complementary methods that provide valuable insight into allosteric pathways in silico. Lastly, we highlight two case studies to demonstrate the adaptability of this approach to enzymes of varying size and mechanistic complexity.
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Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol 2019; 58:197-213. [PMID: 31204190 PMCID: PMC6778498 DOI: 10.1016/j.sbi.2019.04.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 11/27/2022]
Abstract
Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Chris A Brosey
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - John A Tainer
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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15
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Takeuchi K, Baskaran K, Arthanari H. Structure determination using solution NMR: Is it worth the effort? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:195-201. [PMID: 31345771 DOI: 10.1016/j.jmr.2019.07.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
It has been almost 40 years since solution NMR joined X-ray crystallography as a technique for determining high-resolution structures of proteins. Since then NMR derived structure has contributed in fundamental ways to our understanding of the function of biomolecules. With the already existing mature field of X-ray crystallography and the emergence of cryo-EM as techniques to tackle high-resolution structures of large protein complexes, the role of NMR in structure determination has been questioned. However, NMR has the unique ability to recapitulate the dynamic motion of proteins in their structures, while size limitations of the biomolecular systems that can be routinely studied still present challenges. The field has continually developed methodology and instrumentation since its introduction, pushing its frontiers and redefining its limits. Here we present a brief overview of NMR-based structure determination over the past 40 years. We outline the current state of the field and look ahead to the challenges that still need to be addressed to realize the future potential of NMR as a structural technique.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Kumaran Baskaran
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr, Madison, WI 53706, United States
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
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16
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Gronenborn AM. Integrated BioNMR - "getting by with a little help from my friends". JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:192-194. [PMID: 31320228 PMCID: PMC6703907 DOI: 10.1016/j.jmr.2019.07.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 03/20/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Single types of methodologies are insufficient to adequately describe complex biological structures. As a result, integrated approaches that combine complementary data are being developed. Here, I describe the benefits of integrating solution and magic angle spinning BioNMR approaches to characterize structure and dynamics of protein assemblies.
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Affiliation(s)
- A M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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17
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Rodríguez-Zamora P. Conjugation of NMR and SAXS for flexible and multidomain protein structure determination: From sample preparation to model refinement. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:140-144. [PMID: 31445067 DOI: 10.1016/j.pbiomolbio.2019.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 10/26/2022]
Abstract
Experimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magnetic resonance (NMR) spectroscopy data for the improvement of protein structure determination, particularly for flexible, multidomain or intrinsically disordered proteins. Individually, each of these techniques presents capabilities and limitations: NMR excels in local information, providing atomic resolution, but is limited by protein size, whereas SAXS yields a global envelope of the protein with lower resolution, but revealing domain positions. Different conjugation methodologies use the complementarity of both techniques' independent constraints to achieve comprehensive protein structure determination and resolve dynamics at a moderate computational expense.
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Affiliation(s)
- P Rodríguez-Zamora
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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18
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Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Front Mol Biosci 2019; 6:64. [PMID: 31475155 PMCID: PMC6705226 DOI: 10.3389/fmolb.2019.00064] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) play important roles in many aspects of normal cell physiology, such as signal transduction and transcription, as well as pathological states, including Alzheimer's, Parkinson's, and Huntington's disease. Unlike their globular counterparts that are defined by a few structures and free energy minima, IDP/IDR comprise a large ensemble of rapidly interconverting structures and a corresponding free energy landscape characterized by multiple minima. This aspect has precluded the use of structural biological techniques, such as X-ray crystallography and nuclear magnetic resonance (NMR) for resolving their structures. Instead, low-resolution techniques, such as small-angle X-ray or neutron scattering (SAXS/SANS), have become a mainstay in characterizing coarse features of the ensemble of structures. These are typically complemented with NMR data if possible or computational techniques, such as atomistic molecular dynamics, to further resolve the underlying ensemble of structures. However, over the past 10–15 years, it has become evident that the classical, pairwise-additive force fields that have enjoyed a high degree of success for globular proteins have been somewhat limited in modeling IDP/IDR structures that agree with experiment. There has thus been a significant effort to rehabilitate these models to obtain better agreement with experiment, typically done by optimizing parameters in a piecewise fashion. In this work, we take a different approach by optimizing a set of force field parameters simultaneously, using machine learning to adapt force field parameters to experimental SAXS scattering profiles. We demonstrate our approach in modeling three biologically IDP ensembles based on experimental SAXS profiles and show that our optimization approach significantly improve force field parameters that generate ensembles in better agreement with experiment.
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Affiliation(s)
- Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Utsab R Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Loukas Petridis
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Arvind Ramanathan
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States
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19
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Urzhumtsev AG, Lunin VY. Introduction to crystallographic refinement of macromolecular atomic models. CRYSTALLOGR REV 2019. [DOI: 10.1080/0889311x.2019.1631817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexandre G. Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
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20
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Kaptein R, Wagner G. Integrative methods in structural biology. JOURNAL OF BIOMOLECULAR NMR 2019; 73:261-263. [PMID: 31313058 DOI: 10.1007/s10858-019-00267-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Rob Kaptein
- Bijvoet Centre, Utrecht University, 3584 CH, Utrecht, The Netherlands.
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
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21
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Russell RW, Fritz MP, Kraus J, Quinn CM, Polenova T, Gronenborn AM. Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'. JOURNAL OF BIOMOLECULAR NMR 2019; 73:333-346. [PMID: 30847635 PMCID: PMC6693955 DOI: 10.1007/s10858-019-00233-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
We present a systematic investigation into the attainable accuracy and precision of protein structures determined by heteronuclear magic angle spinning solid-state NMR for a set of four proteins of varied size and secondary structure content. Structures were calculated using synthetically generated random sets of C-C distances up to 7 Å at different degrees of completeness. For single-domain proteins, 9-15 restraints per residue are sufficient to derive an accurate model structure, while maximum accuracy and precision are reached with over 15 restraints per residue. For multi-domain proteins and protein assemblies, additional information on domain orientations, quaternary structure and/or protein shape is needed. As demonstrated for the HIV-1 capsid protein assembly, this can be accomplished by integrating MAS NMR with cryoEM data. In all cases, inclusion of TALOS-derived backbone torsion angles improves the accuracy for small number of restraints, while no further increases are noted for restraint completeness above 40%. In contrast, inclusion of TALOS-derived torsion angle restraints consistently increases the precision of the structural ensemble at all degrees of distance restraint completeness.
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Affiliation(s)
- Ryan W Russell
- Department of Chemistry and Biochemistry, University of Delaware, 19716, Newark, DE, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA
| | - Matthew P Fritz
- Department of Chemistry and Biochemistry, University of Delaware, 19716, Newark, DE, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA
| | - Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, 19716, Newark, DE, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, 19716, Newark, DE, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 19716, Newark, DE, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA.
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA.
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA.
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22
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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23
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Interpreting solution X-ray scattering data using molecular simulations. Curr Opin Struct Biol 2018; 49:18-26. [DOI: 10.1016/j.sbi.2017.11.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/20/2017] [Accepted: 11/04/2017] [Indexed: 01/23/2023]
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24
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Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:237-258. [PMID: 30617833 DOI: 10.1007/978-981-13-2200-6_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Small-angle X-ray scattering (SAXS) is an efficient experimental tool to measure the overall shape of macromolecular structures in solution. However, due to the low resolution of SAXS data, high-resolution data obtained from X-ray crystallography or NMR and computational methods such as molecular dynamics (MD) simulations are complementary to SAXS data for understanding protein functions based on their structures at atomic resolution. Because MD simulations provide a physicochemically proper structural ensemble for flexible proteins in solution and a precise description of solvent effects, the hybrid analysis of SAXS and MD simulations is a promising method to estimate reasonable solution structures and structural ensembles in solution. Here, we review typical and useful in silico methods for modeling three dimensional protein structures, calculating theoretical SAXS profiles, and analyzing ensemble structures consistent with experimental SAXS profiles. We also review two examples of the hybrid analysis, termed MD-SAXS method in which MD simulations are carried out without any knowledge of experimental SAXS data, and the experimental SAXS data are used only to assess the consistency of the solution model from MD simulations with those observed in experiments. One example is an investigation of the intrinsic dynamics of EcoO109I using the computational method to obtain a theoretical profile from the trajectory of an MD simulation. The other example is a structural investigation of the vitamin D receptor ligand-binding domain using snapshots generated by MD simulations and assessment of the snapshots by experimental SAXS data.
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25
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Harnessing the Combined Power of SAXS and NMR. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:171-180. [DOI: 10.1007/978-981-13-2200-6_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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26
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Trewhella J. Small Angle Scattering and Structural Biology: Data Quality and Model Validation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:77-100. [PMID: 30617825 DOI: 10.1007/978-981-13-2200-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This chapter provides a brief review of the current state-of-the-art in small-angle scattering (SAS) from biomolecules in solution in regard to: (1) sample preparation and instrumentation, (2) data reduction and analysis, and (3) three-dimensional structural modelling and validation. In this context, areas of ongoing research in regard to the interpretation of SAS data will be discussed with a particular focus on structural modelling using computational methods and data from different experimental techniques, including SAS (hybrid methods). Finally, progress made in establishing community accepted publication guidelines and a standard reporting framework that includes SAS data deposition in a public data bank will be described. Importantly, SAS data with associated meta-data can now be held in a format that supports exchange between data archives and seamless interoperability with the world-wide Protein Data Bank (wwPDB). Biomolecular SAS is thus well positioned to contribute to an envisioned federation of data archives in support of hybrid structural biology.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia. .,Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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27
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Sønderby P, Rinnan Å, Madsen JJ, Harris P, Bukrinski JT, Peters GHJ. Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape. J Chem Inf Model 2017; 57:2463-2475. [DOI: 10.1021/acs.jcim.6b00789] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Pernille Sønderby
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Åsmund Rinnan
- Department
of Food Science, Faculty of Science, University of Copenhagen, DK-1958 Frederiksberg C, Denmark
| | - Jesper J. Madsen
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | | | - Günther H. J. Peters
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
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28
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Bhandari YR, Fan L, Fang X, Zaki GF, Stahlberg EA, Jiang W, Schwieters CD, Stagno JR, Wang YX. Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering. J Mol Biol 2017; 429:3635-3649. [PMID: 28918093 DOI: 10.1016/j.jmb.2017.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
Knowledge of RNA three-dimensional topological structures provides important insight into the relationship between RNA structural components and function. It is often likely that near-complete sets of biochemical and biophysical data containing structural restraints are not available, but one still wants to obtain knowledge about approximate topological folding of RNA. In this regard, general methods for determining such topological structures with minimum readily available restraints are lacking. Naked RNAs are difficult to crystallize and NMR spectroscopy is generally limited to small RNA fragments. By nature, sequence determines structure and all interactions that drive folding are self-contained within sequence. Nevertheless, there is little apparent correlation between primary sequences and three-dimensional folding unless supplemented with experimental or phylogenetic data. Thus, there is an acute need for a robust high-throughput method that can rapidly determine topological structures of RNAs guided by some experimental data. We present here a novel method (RS3D) that can assimilate the RNA secondary structure information, small-angle X-ray scattering data, and any readily available tertiary contact information to determine the topological fold of RNA. Conformations are firstly sampled at glob level where each glob represents a nucleotide. Best-ranked glob models can be further refined against solvent accessibility data, if available, and then converted to explicit all-atom coordinates for refinement against SAXS data using the Xplor-NIH program. RS3D is widely applicable to a variety of RNA folding architectures currently present in the structure database. Furthermore, we demonstrate applicability and feasibility of the program to derive low-resolution topological structures of relatively large multi-domain RNAs.
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Affiliation(s)
- Yuba R Bhandari
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States.
| | - Lixin Fan
- Leidos Biomedical Research Inc., Frederick, MD 21702, United States
| | - Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - George F Zaki
- Data Science and Information Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
| | - Eric A Stahlberg
- Data Science and Information Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
| | - Wei Jiang
- Argonne National Laboratory, Argonne, IL 60439, United States
| | - Charles D Schwieters
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States; NCI Small Angle X-ray Scattering Core Facility, Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States.
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29
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. 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)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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30
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Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics. Arch Biochem Biophys 2017; 628:33-41. [PMID: 28501583 PMCID: PMC5553349 DOI: 10.1016/j.abb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/25/2023]
Abstract
Small-angle X-ray scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules. NMR is arguably the most powerful technique for the experimental analysis of dynamics. The joint application of these two highly complementary techniques provides an extremely useful approach that facilitates comprehensive characterization of biomacromolecular solutions. SAXS and NMR are effective and highly complementary techniques in structural biology. Constraints from SAXS can be readily incorporated in NMR structure calculations. High resolution NMR models of domains can serve as building blocks for SAXS-based rigid body modeling. Flexible systems can be well described using ensemble approaches combining SAXS and NMR. Dynamics studies can be enhanced by combining SAXS and NMR.
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31
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Thompson MK, Ehlinger AC, Chazin WJ. Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR. Methods Enzymol 2017; 592:49-76. [PMID: 28668130 DOI: 10.1016/bs.mie.2017.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples.
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Affiliation(s)
- Matthew K Thompson
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Aaron C Ehlinger
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.
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32
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Sedlak SM, Bruetzel LK, Lipfert J. Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements. J Appl Crystallogr 2017; 50:621-630. [PMID: 28381982 PMCID: PMC5377352 DOI: 10.1107/s1600576717003077] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
A model is presented for the errors in small-angle X-ray scattering profiles that takes into account the physics of the measurement process. The model agrees quantitatively with the variations observed in experimental measurements and provides a straightforward prescription to add realistic errors to simulated scattering profiles. A new model is proposed for the measurement errors incurred in typical small-angle X-ray scattering (SAXS) experiments, which takes into account the setup geometry and physics of the measurement process. The model accurately captures the experimentally determined errors from a large range of synchrotron and in-house anode-based measurements. Its most general formulation gives for the variance of the buffer-subtracted SAXS intensity σ2(q) = [I(q) + const.]/(kq), where I(q) is the scattering intensity as a function of the momentum transfer q; k and const. are fitting parameters that are characteristic of the experimental setup. The model gives a concrete procedure for calculating realistic measurement errors for simulated SAXS profiles. In addition, the results provide guidelines for optimizing SAXS measurements, which are in line with established procedures for SAXS experiments, and enable a quantitative evaluation of measurement errors.
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Affiliation(s)
- Steffen M Sedlak
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich , Amalienstrasse 54, Munich, 80799, Germany
| | - Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich , Amalienstrasse 54, Munich, 80799, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich , Amalienstrasse 54, Munich, 80799, Germany
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33
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Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition. Methods 2017; 118-119:119-136. [PMID: 28315749 DOI: 10.1016/j.ymeth.2017.03.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/19/2017] [Accepted: 03/13/2017] [Indexed: 12/20/2022] Open
Abstract
Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain arrangements and dynamics. Principles of protein-RNA recognition and current approaches are reviewed and illustrated with recent studies.
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34
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Prischi F, Pastore A. Hybrid Methods in Iron-Sulfur Cluster Biogenesis. Front Mol Biosci 2017; 4:12. [PMID: 28349052 PMCID: PMC5346568 DOI: 10.3389/fmolb.2017.00012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
Hybrid methods, which combine and integrate several biochemical and biophysical techniques, have rapidly caught up in the last twenty years to provide a way to obtain a fuller description of proteins and molecular complexes with sizes and complexity otherwise not easily affordable. Here, we review the use of a robust hybrid methodology based on a mixture of NMR, SAXS, site directed mutagenesis and molecular docking which we have developed to determine the structure of weakly interacting molecular complexes. We applied this technique to gain insights into the structure of complexes formed amongst proteins involved in the molecular machine, which produces the essential iron-sulfur cluster prosthetic groups. Our results were validated both by X-ray structures and by other groups who adopted the same approach. We discuss the advantages and the limitations of our methodology and propose new avenues, which could improve it.
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Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex Colchester, UK
| | - Annalisa Pastore
- Maurice Wohl Institute, King's College LondonLondon, UK; Molecular Medicine Department, University of PaviaPavia, Italy
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35
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Hybrid Applications of Solution Scattering to Aid Structural Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:215-227. [PMID: 29218562 DOI: 10.1007/978-981-10-6038-0_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biomolecular applications of solution X-ray and neutron scattering (SAXS and SANS, respectively) started in late 1960s - early 1970s but were relatively limited in their ability to provide a detailed structural picture and lagged behind what became the two primary methods of experimental structural biology - X-ray crystallography and NMR. However, improvements in both data analysis and instrumentation led to an explosive growth in the number of studies that used small-angle scattering (SAS) for investigation of macromolecular structure, often in combination with other biophysical techniques. Such hybrid applications are nowadays quickly becoming a norm whenever scattering data are used for two reasons. First, it is generally accepted that SAS data on their own cannot lead to a uniquely defined high-resolution structural model, creating a need for supplementing them with information from complementary techniques. Second, solution scattering data are frequently applied in situations when a method such NMR or X-ray crystallography cannot provide a satisfactory structural picture, which makes these additional restraints highly desirable. Maturation of the hybrid bio-SAS approaches brings to light new questions including completeness of the conformational space sampling, model validation, and data compatibility.
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36
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Yadav DK, Lukavsky PJ. NMR solution structure determination of large RNA-protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:57-81. [PMID: 27888840 DOI: 10.1016/j.pnmrs.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.
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Affiliation(s)
- Deepak Kumar Yadav
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Peter J Lukavsky
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic.
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37
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Small-angle scattering and 3D structure interpretation. Curr Opin Struct Biol 2016; 40:1-7. [DOI: 10.1016/j.sbi.2016.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022]
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38
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Vestergaard B. Analysis of biostructural changes, dynamics, and interactions – Small-angle X-ray scattering to the rescue. Arch Biochem Biophys 2016; 602:69-79. [DOI: 10.1016/j.abb.2016.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/17/2016] [Accepted: 02/26/2016] [Indexed: 12/27/2022]
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39
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Björling A, Niebling S, Marcellini M, van der Spoel D, Westenhoff S. Deciphering solution scattering data with experimentally guided molecular dynamics simulations. J Chem Theory Comput 2016; 11:780-7. [PMID: 25688181 PMCID: PMC4325560 DOI: 10.1021/ct5009735] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Indexed: 01/26/2023]
Abstract
![]()
Time-resolved
X-ray solution scattering is an increasingly popular
method to measure conformational changes in proteins. Extracting structural
information from the resulting difference X-ray scattering data is
a daunting task. We present a method in which the limited but precious
information encoded in such scattering curves is combined with the
chemical knowledge of molecular force fields. The molecule of interest
is then refined toward experimental data using molecular dynamics
simulation. Therefore, the energy landscape is biased toward conformations
that agree with experimental data. We describe and verify the method,
and we provide an implementation in GROMACS.
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Affiliation(s)
- Alexander Björling
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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40
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Abstract
Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus, elucidating the forces that drive allostery is critical to understanding the complex transformations of biomolecules. Currently, a number of models exist to describe allosteric behavior, taking into account energetics as well as conformational rearrangements and fluctuations. In the following Review, we discuss the use of solution NMR techniques designed to probe allosteric mechanisms in enzymes. NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method. We also provide a detailed technical discussion of several specialized NMR experiments that are ideally suited for the study of enzymatic allostery.
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Affiliation(s)
- George P. Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - J. Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
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41
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Yabukarski F, Leyrat C, Martinez N, Communie G, Ivanov I, Ribeiro EA, Buisson M, Gerard FC, Bourhis JM, Jensen MR, Bernadó P, Blackledge M, Jamin M. Ensemble Structure of the Highly Flexible Complex Formed between Vesicular Stomatitis Virus Unassembled Nucleoprotein and its Phosphoprotein Chaperone. J Mol Biol 2016; 428:2671-94. [PMID: 27107640 DOI: 10.1016/j.jmb.2016.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/08/2023]
Abstract
Nucleocapsid assembly is an essential process in the replication of the non-segmented, negative-sense RNA viruses (NNVs). Unassembled nucleoprotein (N(0)) is maintained in an RNA-free and monomeric form by its viral chaperone, the phosphoprotein (P), forming the N(0)-P complex. Our earlier work solved the structure of vesicular stomatitis virus complex formed between an N-terminally truncated N (NΔ21) and a peptide of P (P60) encompassing the N(0)-binding site, but how the full-length P interacts with N(0) remained unknown. Here, we combine several experimental biophysical methods including size exclusion chromatography with detection by light scattering and refractometry, small-angle X-ray and neutron scattering and nuclear magnetic resonance spectroscopy with molecular dynamics simulation and computational modeling to characterize the NΔ21(0)-PFL complex formed with dimeric full-length P. We show that for multi-molecular complexes, simultaneous multiple-curve fitting using small-angle neutron scattering data collected at varying contrast levels provides additional information and can help refine structural ensembles. We demonstrate that (a) vesicular stomatitis virus PFL conserves its high flexibility within the NΔ21(0)-PFL complex and interacts with NΔ21(0) only through its N-terminal extremity; (b) each protomer of P can chaperone one N(0) client protein, leading to the formation of complexes with stoichiometries 1N:P2 and 2N:P2; and (c) phosphorylation of residues Ser60, Thr62 and Ser64 provides no additional interactions with N(0) but creates a metal binding site in PNTR. A comparison with the structures of Nipah virus and Ebola virus N(0)-P core complex suggests a mechanism for the control of nucleocapsid assembly that is common to all NNVs.
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Affiliation(s)
- Filip Yabukarski
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Cedric Leyrat
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Nicolas Martinez
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France; Institut Laue Langevin, Grenoble, France
| | - Guillaume Communie
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Ivan Ivanov
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France; Institut Laue Langevin, Grenoble, France
| | - Euripedes A Ribeiro
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Marlyse Buisson
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France; Laboratoire de Virologie, Centre Hospitalo-Universitaire de Grenoble, Grenoble, France
| | - Francine C Gerard
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Jean-Marie Bourhis
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, Montpellier, France
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France
| | - Marc Jamin
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble 38044, France.
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42
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Zhang Y, Wen B, Peng J, Zuo X, Gong Q, Zhang Z. Determining structural ensembles of flexible multi-domain proteins using small-angle X-ray scattering and molecular dynamics simulations. Protein Cell 2016; 6:619-23. [PMID: 25944044 PMCID: PMC4506289 DOI: 10.1007/s13238-015-0162-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Yonghui Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
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43
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Rambo RP, Tainer JA. Modeling macromolecular motions by x-ray-scattering-constrained molecular dynamics. Biophys J 2016; 108:2421-2423. [PMID: 25992719 DOI: 10.1016/j.bpj.2015.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/20/2015] [Accepted: 04/20/2015] [Indexed: 12/19/2022] Open
Affiliation(s)
- Robert P Rambo
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom.
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California; Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.
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44
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Lisi GP, Loria JP. Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:1-17. [PMID: 26952190 PMCID: PMC4785347 DOI: 10.1016/j.pnmrs.2015.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 05/04/2023]
Abstract
Conformational motions play an essential role in enzyme function, often facilitating the formation of enzyme-substrate complexes and/or product release. Although considerable debate remains regarding the role of molecular motions in the conversion of enzymatic substrates to products, numerous examples have found motions to be crucial for optimization of enzyme scaffolds, effective substrate binding, and product dissociation. Conformational fluctuations are often rate-limiting to enzyme catalysis, primarily through product release, with the chemical reaction occurring much more quickly. As a result, the direct involvement of motions at various stages along the enzyme reaction coordinate remains largely unknown and untested. In the following review, we describe the use of solution NMR techniques designed to probe various timescales of molecular motions and detail examples in which motions play a role in propagating catalytic effects from the active site and directly participate in essential aspects of enzyme function.
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Affiliation(s)
- George P Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520, United States; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States.
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45
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Bruetzel LK, Fischer S, Salditt A, Sedlak SM, Nickel B, Lipfert J. A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:025103. [PMID: 26931887 DOI: 10.1063/1.4940936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We demonstrate the use of a molybdenum-anode-based in-house small-angle X-ray scattering (SAXS) setup to study biological macromolecules in solution. Our system consists of a microfocus X-ray tube delivering a highly collimated flux of 2.5 × 10(6) photons/s at a beam size of 1.2 × 1.2 mm(2) at the collimation path exit and a maximum beam divergence of 0.16 mrad. The resulting observable scattering vectors q are in the range of 0.38 Å(-1) down to 0.009 Å(-1) in SAXS configuration and of 0.26 Å(-1) up to 5.7 Å(-1) in wide-angle X-ray scattering (WAXS) mode. To determine the capabilities of the instrument, we collected SAXS data on weakly scattering biological macromolecules including proteins and a nucleic acid sample with molecular weights varying from ∼12 to 69 kDa and concentrations of 1.5-24 mg/ml. The measured scattering data display a high signal-to-noise ratio up to q-values of ∼0.2 Å(-1) allowing for an accurate structural characterization of the samples. Moreover, the in-house source data are of sufficient quality to perform ab initio 3D structure reconstructions that are in excellent agreement with the available crystallographic structures. In addition, measurements for the detergent decyl-maltoside show that the setup can be used to determine the size, shape, and interactions (as characterized by the second virial coefficient) of detergent micelles. This demonstrates that the use of a Mo-anode based in-house source is sufficient to determine basic geometric parameters and 3D shapes of biomolecules and presents a viable alternative to valuable beam time at third generation synchrotron sources.
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Affiliation(s)
- Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Stefan Fischer
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Annalena Salditt
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Steffen M Sedlak
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Bert Nickel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
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46
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Tomlinson JH, Thompson GS, Kalverda AP, Zhuravleva A, O'Neill AJ. A target-protection mechanism of antibiotic resistance at atomic resolution: insights into FusB-type fusidic acid resistance. Sci Rep 2016; 6:19524. [PMID: 26781961 PMCID: PMC4725979 DOI: 10.1038/srep19524] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/09/2015] [Indexed: 11/09/2022] Open
Abstract
Antibiotic resistance in clinically important bacteria can be mediated by proteins that physically associate with the drug target and act to protect it from the inhibitory effects of an antibiotic. We present here the first detailed structural characterization of such a target protection mechanism mediated through a protein-protein interaction, revealing the architecture of the complex formed between the FusB fusidic acid resistance protein and the drug target (EF-G) it acts to protect. Binding of FusB to EF-G induces conformational and dynamic changes in the latter, shedding light on the molecular mechanism of fusidic acid resistance.
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Affiliation(s)
- Jennifer H Tomlinson
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Gary S Thompson
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Arnout P Kalverda
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Anastasia Zhuravleva
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Alex J O'Neill
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
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47
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Prischi F, Pastore A. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:351-68. [PMID: 27165336 DOI: 10.1007/978-3-319-27216-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.
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Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King's College London, Denmark Hill Campus, London, UK.
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48
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Vammi V, Song G. Ensembles of a small number of conformations with relative populations. JOURNAL OF BIOMOLECULAR NMR 2015; 63:341-351. [PMID: 26474790 DOI: 10.1007/s10858-015-9993-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 10/14/2015] [Indexed: 06/05/2023]
Abstract
In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assigning relative populations to protein ensembles could significantly improve their quality. To demonstrate that ESP indeed is an excellent alternative to represent protein native states, in this work we compare the quality of two ESP ensembles of Ubiquitin with several well-known regular ensembles or average structure representations. Extensive amount of significant experimental data are employed to achieve a thorough assessment. Our results demonstrate that ESP ensembles, though much smaller in size comparing to regular ensembles, perform equally or even better sometimes in all four different types of experimental data used in the assessment, namely, the residual dipolar couplings, residual chemical shift anisotropy, hydrogen exchange rates, and solution scattering profiles. This work further underlines the significance of having relative populations in describing the native states.
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Affiliation(s)
- Vijay Vammi
- Bioinformatics and Computational Biology Program, Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA, 50011, USA.
| | - Guang Song
- Bioinformatics and Computational Biology Program, Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA, 50011, USA
- Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA, USA
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49
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Kikhney AG, Svergun DI. A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 2015; 589:2570-7. [PMID: 26320411 DOI: 10.1016/j.febslet.2015.08.027] [Citation(s) in RCA: 392] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/17/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a biophysical method to study the overall shape and structural transitions of biological macromolecules in solution. SAXS provides low resolution information on the shape, conformation and assembly state of proteins, nucleic acids and various macromolecular complexes. The technique also offers powerful means for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs). Here, the basic principles of SAXS are presented, and profits and pitfalls of the characterization of multidomain flexible proteins and IDPs using SAXS are discussed from the practical point of view. Examples of the synergistic use of SAXS with high resolution methods like X-ray crystallography and nuclear magnetic resonance (NMR), as well as other experimental and in silico techniques to characterize completely, or partially unstructured proteins, are presented.
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Affiliation(s)
- Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany.
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50
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Putnam DK, Weiner BE, Woetzel N, Lowe EW, Meiler J. BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles. Proteins 2015; 83:1500-12. [PMID: 26018949 PMCID: PMC4797635 DOI: 10.1002/prot.24838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/08/2015] [Accepted: 05/19/2015] [Indexed: 12/25/2022]
Abstract
Small angle X-ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. Here, we introduce BCL::SAXS--an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of hen egg white lysozyme. Using this protein we show how to generate SAXS profiles representing: (1) complete models, (2) models with approximated side chain coordinates, and (3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non-redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC) > 99%. We show how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAχS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native.
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Affiliation(s)
- Daniel K. Putnam
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA
| | - Brian E. Weiner
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Nils Woetzel
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Edward W. Lowe
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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