1
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Azadmanesh J, Slobodnik K, Struble LR, Lutz WE, Coates L, Weiss KL, Myles DAA, Kroll T, Borgstahl GEO. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. bioRxiv 2024:2024.01.26.577433. [PMID: 38328249 PMCID: PMC10849630 DOI: 10.1101/2024.01.26.577433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ●- to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.
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2
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Bras W, Myles DAA, Felici R. When x-rays alter the course of your experiments. J Phys Condens Matter 2021; 33:423002. [PMID: 34298526 DOI: 10.1088/1361-648x/ac1767] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
The continuing increase in the brilliance of synchrotron radiation beamlines allows for many new and exciting experiments that were impossible before the present generation of synchrotron radiation sources came on line. However, the exposure to such intense beams also tests the limits of what samples can endure. Whilst the effects of radiation induced damage in a static experiment often can easily be recognized by changes in the diffraction or spectroscopy curves, the influence of radiation on chemical or physical processes, where one expects curves to change, is less often recognized and can be misinterpreted as a 'real' result instead of as a 'radiation influenced result'. This is especially a concern in time-resolved materials science experiments using techniques as powder diffraction, small angle scattering and x-ray absorption spectroscopy. Here, the effects of radiation (5-50 keV) on some time-resolved processes in different types of materials and in different physical states are discussed. We show that such effects are not limited to soft matter and biology but rather can be found across the whole spectrum of materials research, over a large range of radiation doses and is not limited to very high brilliance beamlines.
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Affiliation(s)
- Wim Bras
- Chemical Sciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge TN 37831, United States of America
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge TN 37831, United States of America
| | - Roberto Felici
- CNR-SPIN, Area della ricerca di Tor Vergata, via del Fosso del Cavaliere 100, 00133 Roma, Italy
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3
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Nickels JD, Poudel S, Chatterjee S, Farmer A, Cordner D, Campagna SR, Giannone RJ, Hettich RL, Myles DAA, Standaert RF, Katsaras J, Elkins JG. Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome. Front Microbiol 2020; 11:914. [PMID: 32499768 PMCID: PMC7243436 DOI: 10.3389/fmicb.2020.00914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/17/2020] [Indexed: 12/22/2022] Open
Abstract
Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells – as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins.
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Affiliation(s)
- Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, United States
| | - Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sneha Chatterjee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Abigail Farmer
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Destini Cordner
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, United States
| | - Shawn R Campagna
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert F Standaert
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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4
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Abstract
IMAGINE is a high intensity, quasi-Laue neutron crystallography beamline developed at the 85MW High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). This state-of-the-art facility for neutron-diffraction enables neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of <1mm3 and unit cell edges of <150Å. The beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0×3.2mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. The beamline is equipped with a single-axis goniometer, neutron-sensitive cylindrical image plate detector and room temperature and cryogenic sample environments. This article describes the beamline components, the diffractometer and the data collection and data analysis protocols that are used, and outlines the protein deuteration, crystallization and conventional crystallography capabilities that are available to users at ORNL's neutron facilities. We also present examples of the scientific questions being addressed at this beamline and highlight important findings in enzyme chemistry that have been made possible by IMAGINE.
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Affiliation(s)
- Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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5
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Lu X, Selvaraj B, Ghimire-Rijal S, Orf GS, Meilleur F, Blankenship RE, Cuneo MJ, Myles DAA. Neutron and X-ray analysis of the Fenna-Matthews-Olson photosynthetic antenna complex from Prosthecochloris aestuarii. Acta Crystallogr F Struct Biol Commun 2019; 75:171-175. [PMID: 30839291 DOI: 10.1107/s2053230x19000724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/16/2019] [Indexed: 11/10/2022]
Abstract
The Fenna-Matthews-Olson protein from Prosthecochloris aestuarii (PaFMO) has been crystallized in a new form that is amenable to high-resolution X-ray and neutron analysis. The crystals belonged to space group H3, with unit-cell parameters a = b = 83.64, c = 294.78 Å, and diffracted X-rays to ∼1.7 Å resolution at room temperature. Large PaFMO crystals grown to volumes of 0.3-0.5 mm3 diffracted neutrons to 2.2 Å resolution on the MaNDi neutron diffractometer at the Spallation Neutron Source. The resolution of the neutron data will allow direct determination of the positions of H atoms in the structure, which are believed to be fundamentally important in tuning the individual excitation energies of bacteriochlorophylls in this archetypal photosynthetic antenna complex. This is one of the largest unit-cell systems yet studied using neutron diffraction, and will allow the first high-resolution neutron analysis of a photosynthetic antenna complex.
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Affiliation(s)
- Xun Lu
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Brinda Selvaraj
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sudipa Ghimire-Rijal
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gregory S Orf
- Departments of Biology and Chemistry, Washington University in St Louis, St Louis, MO 63130, USA
| | - Flora Meilleur
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St Louis, St Louis, MO 63130, USA
| | - Matthew J Cuneo
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dean A A Myles
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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6
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Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry 2018; 57:5864-5876. [PMID: 30204415 PMCID: PMC6189639 DOI: 10.1021/acs.biochem.8b00783] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genome of the hyperthermophile Thermotoga maritima contains three isoforms of maltose binding protein (MBP) that are high-affinity receptors for di-, tri-, and tetrasaccharides. Two of these proteins (tmMBP1 and tmMBP2) share significant sequence identity, approximately 90%, while the third (tmMBP3) shares less than 40% identity. MBP from Escherichia coli (ecMBP) shares 35% sequence identity with the tmMBPs. This subset of MBP isoforms offers an interesting opportunity to investigate the mechanisms underlying the evolution of substrate specificity and affinity profiles in a genome where redundant MBP genes are present. In this study, the X-ray crystal structures of tmMBP1, tmMBP2, and tmMBP3 are reported in the absence and presence of oligosaccharides. tmMBP1 and tmMBP2 have binding pockets that are larger than that of tmMBP3, enabling them to bind to larger substrates, while tmMBP1 and tmMBP2 also undergo substrate-induced hinge bending motions (∼52°) that are larger than that of tmMBP3 (∼35°). Small-angle X-ray scattering was used to compare protein behavior in solution, and computer simulations provided insights into dynamics of these proteins. Comparing quantitative protein-substrate interactions and dynamical properties of tmMBPs with those of the promiscuous ecMBP and disaccharide selective Thermococcus litoralis MBP provides insights into the features that enable selective binding. Collectively, the results provide insights into how the structure and dynamics of tmMBP homologues enable them to differentiate between a myriad of chemical entities while maintaining their common fold.
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Affiliation(s)
- Shantanu Shukla
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
| | - Caeley Gullett
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dean A. A. Myles
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee
| | - Matthew J. Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Deparment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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7
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Coates L, Cao HB, Chakoumakos BC, Frontzek MD, Hoffmann C, Kovalevsky AY, Liu Y, Meilleur F, Dos Santos AM, Myles DAA, Wang XP, Ye F. A suite-level review of the neutron single-crystal diffraction instruments at Oak Ridge National Laboratory. Rev Sci Instrum 2018; 89:092802. [PMID: 30278686 DOI: 10.1063/1.5030896] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
The nascent suite of single-crystal neutron diffractometers at the Oak Ridge National Laboratory has no equal at any other neutron scattering facility worldwide and offers the potential to re-assert single-crystal diffraction using neutrons as a significant tool to study nuclear and magnetic structures of small unit cell crystals, nuclear structures of macromolecules, and diffuse scattering. Signature applications and features of single-crystal neutron diffraction are high resolution nuclear structure analysis, magnetic structure and spin density determinations, contrast variation (particularly D2O/H2O) for nuclear structural studies, lack of radiation damage when using crystals of biological molecules such as proteins, and the fidelity to measure nuclear and magnetic diffuse scattering with elastic discrimination.
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Affiliation(s)
- L Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - H B Cao
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - B C Chakoumakos
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - M D Frontzek
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - C Hoffmann
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - A Y Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Y Liu
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - F Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - A M Dos Santos
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - D A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - X P Wang
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - F Ye
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
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8
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Haberl B, Dissanayake S, Wu Y, Myles DAA, Dos Santos AM, Loguillo M, Rucker GM, Armitage DP, Cochran M, Andrews KM, Hoffmann C, Cao H, Matsuda M, Meilleur F, Ye F, Molaison JJ, Boehler R. Next-generation diamond cell and applications to single-crystal neutron diffraction. Rev Sci Instrum 2018; 89:092902. [PMID: 30278728 DOI: 10.1063/1.5031454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
A diamond cell optimized for single-crystal neutron diffraction is described. It is adapted for work at several of the single-crystal diffractometers of the Spallation Neutron Source and the High Flux Isotope Reactor at the Oak Ridge National Laboratory (ORNL). A simple spring design improves portability across the facilities and affords load maintenance from offline pressurization and during temperature cycling. Compared to earlier prototypes, pressure stability of polycrystalline diamond (Versimax®) has been increased through double-conical designs and ease of use has been improved through changes to seat and piston setups. These anvils allow ∼30%-40% taller samples than possible with comparable single-crystal anvils. Hydrostaticity and the important absence of shear pressure gradients have been established with the use of glycerin as a pressure medium. Large single-crystal synthetic diamonds have also been used for the first time with such a clamp-diamond anvil cell for pressures close to 20 GPa. The cell is made from a copper beryllium alloy and sized to fit into ORNL's magnets for future ultra-low temperature and high-field studies. We show examples from the Spallation Neutron Source's SNAP and CORELLI beamlines and the High Flux Isotope Reactor's HB-3A and IMAGINE beamlines.
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Affiliation(s)
- Bianca Haberl
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Sachith Dissanayake
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yan Wu
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Dean A A Myles
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Antonio M Dos Santos
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mark Loguillo
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald M Rucker
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Douglas P Armitage
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Malcolm Cochran
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Katie M Andrews
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Christina Hoffmann
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Huibo Cao
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Masaaki Matsuda
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Flora Meilleur
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Feng Ye
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jamie J Molaison
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Reinhard Boehler
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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9
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Schröder GC, O'Dell WB, Myles DAA, Kovalevsky A, Meilleur F. IMAGINE: neutrons reveal enzyme chemistry. Acta Crystallogr D Struct Biol 2018; 74:778-786. [DOI: 10.1107/s2059798318001626] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 11/10/2022]
Abstract
Neutron diffraction is exquisitely sensitive to the positions of H atoms in protein crystal structures. IMAGINE is a high-intensity, quasi-Laue neutron crystallography beamline developed at the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. This state-of-the-art facility for neutron diffraction has enabled detailed structural analysis of macromolecules. IMAGINE is especially suited to resolve individual H atoms in protein structures, enabling neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of less than 1 mm3 and unit-cell edges of less than 150 Å. Beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0 × 3.2 mm focal spot at the sample position, and variable short- and long-wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. This review gives an overview of the IMAGINE beamline at the HFIR, presents examples of the scientific questions being addressed at this beamline, and highlights important findings in enzyme chemistry that have been made using the neutron diffraction capabilities offered by IMAGINE.
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10
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Duff MR, Borreguero JM, Cuneo MJ, Ramanathan A, He J, Kamath G, Chennubhotla SC, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK. Modulating Enzyme Activity by Altering Protein Dynamics with Solvent. Biochemistry 2018; 57:4263-4275. [PMID: 29901984 DOI: 10.1021/acs.biochem.8b00424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ∼3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent khydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzyme's ability to access its functionally relevant conformational substates, explaining the decreased khydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering.
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Affiliation(s)
- Michael R Duff
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States
| | - Jose M Borreguero
- Neutron Data Analysis and Visualization Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Matthew J Cuneo
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Arvind Ramanathan
- Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Junhong He
- Neutron Technologies Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Ganesh Kamath
- Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology , University of Pittsburgh , Pittsburgh , Pennsylvania , United States
| | - Flora Meilleur
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States.,Molecular and Structural Biochemistry Department , North Carolina State University , Raleigh , North Carolina , United States
| | - Elizabeth E Howell
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States
| | - Kenneth W Herwig
- Neutron Technologies Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Dean A A Myles
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Pratul K Agarwal
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States.,Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
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11
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Nickels JD, Chatterjee S, Mostofian B, Stanley CB, Ohl M, Zolnierczuk P, Schulz R, Myles DAA, Standaert RF, Elkins JG, Cheng X, Katsaras J. Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane. J Phys Chem Lett 2017; 8:4214-4217. [PMID: 28825491 DOI: 10.1021/acs.jpclett.7b01877] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. We advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at ( http://cmb.ornl.gov/members/cheng ). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.
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Affiliation(s)
| | | | | | | | - Michael Ohl
- Jülich Center for Neutron Science, Forschungszentrum Juelich GmbH , Outstation at SNS, Oak Ridge, Tennessee 37831, United States
| | - Piotr Zolnierczuk
- Jülich Center for Neutron Science, Forschungszentrum Juelich GmbH , Outstation at SNS, Oak Ridge, Tennessee 37831, United States
| | - Roland Schulz
- Intel Corporation , Hillsboro, Oregon 97124, United States of America
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12
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Li L, Shukla S, Meilleur F, Standaert RF, Pierce J, Myles DAA, Cuneo MJ. Neutron crystallographic studies of T4 lysozyme at cryogenic temperature. Protein Sci 2017; 26:2098-2104. [PMID: 28707382 DOI: 10.1002/pro.3231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022]
Abstract
Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics, and stability. Approximately 700 mutants of this protein and their respective complexes have been characterized by X-ray crystallography; however, despite the high resolution diffraction limits attained in several studies, no hydrogen atoms were reported being visualized in the electron density maps. To address this, a 2.2 Å-resolution neutron data set was collected at 80 K from a crystal of perdeuterated T4L pseudo-wild type. We describe a near complete atomic structure of T4L, which includes the positions of 1737 hydrogen atoms determined by neutron crystallography. The cryogenic neutron model reveals explicit detail of the hydrogen bonding interactions in the protein, in addition to the protonation states of several important residues.
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Affiliation(s)
- Le Li
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
| | - Shantanu Shukla
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Flora Meilleur
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Robert F Standaert
- Energy and Environmental Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Josh Pierce
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
| | - Dean A A Myles
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Matthew J Cuneo
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
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13
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Selvaraj B, Lu X, Cuneo MJ, Myles DAA. Investigation of the bacteriochlorin rings and its environment in Fenna–Matthews–Olsen antenna complex revealed by neutron and ultra-high resolution X-ray crystallography. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317096520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Nickels JD, Chatterjee S, Stanley CB, Qian S, Cheng X, Myles DAA, Standaert RF, Elkins JG, Katsaras J. The in vivo structure of biological membranes and evidence for lipid domains. PLoS Biol 2017; 15:e2002214. [PMID: 28542493 PMCID: PMC5441578 DOI: 10.1371/journal.pbio.2002214] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/11/2017] [Indexed: 12/19/2022] Open
Abstract
Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge, as cells are dynamic, chemically diverse, and fragile. A case in point is the cell membrane, which is too small to be seen directly with optical microscopy and provides little observational contrast for other methods. As a consequence, nanoscale characterization of the membrane has been performed ex vivo or in the presence of exogenous labels used to enhance contrast and impart specificity. Here, we introduce an isotopic labeling strategy in the gram-positive bacterium Bacillus subtilis to investigate the nanoscale structure and organization of its plasma membrane in vivo. Through genetic and chemical manipulation of the organism, we labeled the cell and its membrane independently with specific amounts of hydrogen (H) and deuterium (D). These isotopes have different neutron scattering properties without altering the chemical composition of the cells. From neutron scattering spectra, we confirmed that the B. subtilis cell membrane is lamellar and determined that its average hydrophobic thickness is 24.3 ± 0.9 Ångstroms (Å). Furthermore, by creating neutron contrast within the plane of the membrane using a mixture of H- and D-fatty acids, we detected lateral features smaller than 40 nm that are consistent with the notion of lipid rafts. These experiments-performed under biologically relevant conditions-answer long-standing questions in membrane biology and illustrate a fundamentally new approach for systematic in vivo investigations of cell membrane structure.
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Affiliation(s)
- Jonathan D. Nickels
- Shull Wollan Center—A Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sneha Chatterjee
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Christopher B. Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Shuo Qian
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Xiaolin Cheng
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Dean A. A. Myles
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert F. Standaert
- Shull Wollan Center—A Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RFS); (JGE); (JK)
| | - James G. Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RFS); (JGE); (JK)
| | - John Katsaras
- Shull Wollan Center—A Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RFS); (JGE); (JK)
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15
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Perticaroli S, Ehlers G, Stanley CB, Mamontov E, O'Neill H, Zhang Q, Cheng X, Myles DAA, Katsaras J, Nickels JD. Description of Hydration Water in Protein (Green Fluorescent Protein) Solution. J Am Chem Soc 2016; 139:1098-1105. [PMID: 27783480 DOI: 10.1021/jacs.6b08845] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological study and industrial formulation. We present an experimental description of the dynamical perturbation of hydration water around green fluorescent protein in solution. Less than two shells (∼5.5 Å) were perturbed, with dynamics a factor of 2-10 times slower than bulk water, depending on their distance from the protein surface and the probe length of the measurement. This dependence on probe length demonstrates that hydration water undergoes subdiffusive motions (τ ∝ q-2.5 for the first hydration shell, τ ∝ q-2.3 for perturbed water in the second shell), an important difference with neat water, which demonstrates diffusive behavior (τ ∝ q-2). These results help clarify the seemingly conflicting range of values reported for hydration water retardation as a logical consequence of the different length scales probed by the analytical techniques used.
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Affiliation(s)
- Stefania Perticaroli
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Georg Ehlers
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Christopher B Stanley
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Eugene Mamontov
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Hugh O'Neill
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Qiu Zhang
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Xiaolin Cheng
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Dean A A Myles
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - John Katsaras
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jonathan D Nickels
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
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16
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Nickels JD, Cheng X, Mostofian B, Stanley C, Lindner B, Heberle FA, Perticaroli S, Feygenson M, Egami T, Standaert RF, Smith JC, Myles DAA, Ohl M, Katsaras J. Mechanical Properties of Nanoscopic Lipid Domains. J Am Chem Soc 2015; 137:15772-80. [DOI: 10.1021/jacs.5b08894] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan D. Nickels
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Department
of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Xiaolin Cheng
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Barmak Mostofian
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | | | - Benjamin Lindner
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frederick A. Heberle
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Stefania Perticaroli
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Mikhail Feygenson
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Takeshi Egami
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Robert F. Standaert
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dean A. A. Myles
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Michael Ohl
- Jülich Center for Neutron Science, Oak
Ridge, Tennessee 37831, United States
| | - John Katsaras
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Department
of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
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17
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Heberle FA, Myles DAA, Katsaras J. Biomembranes research using thermal and cold neutrons. Chem Phys Lipids 2015; 192:41-50. [PMID: 26241882 DOI: 10.1016/j.chemphyslip.2015.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/25/2015] [Accepted: 07/27/2015] [Indexed: 01/26/2023]
Abstract
In 1932 James Chadwick discovered the neutron using a polonium source and a beryllium target (Chadwick, 1932). In a letter to Niels Bohr dated February 24, 1932, Chadwick wrote: "whatever the radiation from Be may be, it has most remarkable properties." Where it concerns hydrogen-rich biological materials, the "most remarkable" property is the neutron's differential sensitivity for hydrogen and its isotope deuterium. Such differential sensitivity is unique to neutron scattering, which unlike X-ray scattering, arises from nuclear forces. Consequently, the coherent neutron scattering length can experience a dramatic change in magnitude and phase as a result of resonance scattering, imparting sensitivity to both light and heavy atoms, and in favorable cases to their isotopic variants. This article describes recent biomembranes research using a variety of neutron scattering techniques.
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Affiliation(s)
- F A Heberle
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge, TN, 37831, United States; Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States
| | - D A A Myles
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge, TN, 37831, United States
| | - J Katsaras
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge, TN, 37831, United States; Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, 37996, United States.
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18
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Bodenheimer AM, Cuneo MJ, Swartz PD, He J, O'Neill HM, Myles DAA, Evans BR, Meilleur F. Crystallization and preliminary X-ray diffraction analysis of Hypocrea jecorina Cel7A in two new crystal forms. Acta Crystallogr F Struct Biol Commun 2014; 70:773-6. [PMID: 24915091 DOI: 10.1107/s2053230x14008851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022]
Abstract
Cel7A (previously known as cellobiohydrolase I) from Hypocrea jecorina was crystallized in two crystalline forms, neither of which have been previously reported. Both forms co-crystallize under the same crystallization conditions. The first crystal form belonged to space group C2, with unit-cell parameters a=152.5, b=44.9, c=57.6 Å, β=101.2°, and diffracted X-rays to 1.5 Å resolution. The second crystal form belonged to space group P6₃22, with unit-cell parameters a=b≃155, c≃138 Å, and diffracted X-rays to 2.5 Å resolution. The crystals were obtained using full-length Cel7A, which consists of a large 434-residue N-terminal catalytic domain capable of cleaving cellulose, a 27-residue flexible linker and a small 36-residue C-terminal carbohydrate-binding module (CBM). However, a preliminary analysis of the electron-density maps suggests that the linker and CBM are disordered in both crystal forms. Complete refinement and structure analysis are currently in progress.
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Affiliation(s)
- Annette M Bodenheimer
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Matthew J Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul D Swartz
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Junhong He
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Hugh M O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dean A A Myles
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Barbara R Evans
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Flora Meilleur
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
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19
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Munshi P, Snell EH, van der Woerd MJ, Judge RA, Myles DAA, Ren Z, Meilleur F. Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant. ACTA ACUST UNITED AC 2014; 70:414-20. [DOI: 10.1107/s1399004713029684] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/28/2013] [Indexed: 11/10/2022]
Abstract
Ketol-isomerases catalyze the reversible isomerization between aldoses and ketoses. D-Xylose isomerase carries out the first reaction in the catabolism of D-xylose, but is also able to convert D-glucose to D-fructose. The first step of the reaction is an enzyme-catalyzed ring opening of the cyclic substrate. The active-site amino-acid acid/base pair involved in ring opening has long been investigated and several models have been proposed. Here, the structure of the xylose isomerase E186Q mutant with cyclic glucose bound at the active site, refined against joint X-ray and neutron diffraction data, is reported. Detailed analysis of the hydrogen-bond networks at the active site of the enzyme suggests that His54, which is doubly protonated, is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl groupviaan activated water molecule. The structure also reveals an extended hydrogen-bonding network that connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186, which is a glutamic acid to glutamine mutation.
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20
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Meilleur F, Munshi P, Robertson L, Stoica AD, Crow L, Kovalevsky A, Koritsanszky T, Chakoumakos BC, Blessing R, Myles DAA. The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 2013; 69:2157-60. [DOI: 10.1107/s0907444913019604] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/15/2013] [Indexed: 11/11/2022]
Abstract
The first high-resolution neutron protein structure of perdeuterated rubredoxin fromPyrococcus furiosus(PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory is reported. Neutron diffraction data extending to 1.65 Å resolution were collected from a relatively small 0.7 mm3PfRd crystal using 2.5 d (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the D atoms of the protein and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolution (1.5 Å) from crystals with volume <1.0 mm3and with unit-cell edges <100 Å. Beamline features include novel elliptical focusing mirrors that deliver neutrons into a 2.0 × 3.2 mm focal spot at the sample position with full-width vertical and horizontal divergences of 0.5 and 0.6°, respectively. Variable short- and long-wavelength cutoff optics provide automated exchange between multiple-wavelength configurations (λmin= 2.0, 2.8, 3.3 Å to λmax= 3.0, 4.0, 4.5, ∼20 Å). These optics produce a more than 20-fold increase in the flux density at the sample and should help to enable more routine collection of high-resolution data from submillimetre-cubed crystals. Notably, the crystal used to collect thesePfRd data was 5–10 times smaller than those previously reported.
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21
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Ankner JF, Heller WT, Herwig KW, Meilleur F, Myles DAA. Neutron scattering techniques and applications in structural biology. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.16. [PMID: 23546619 DOI: 10.1002/0471140864.ps1716s72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.
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Affiliation(s)
- John F Ankner
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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22
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Abstract
Techniques and equipment have been developed that enable large protein crystals (1–6 mm3) flash-cooled in liquid nitrogen at 77 K to be transferred and mounted on a liquid helium Displex cryorefrigerator and cooled to temperatures down to 15 K for accurate neutron diffraction analysis. In preliminary experiments, it was possible to collect high-quality high-resolution neutron diffraction data to 1.55 Å resolution from several large crystals of triclinic hen egg white lysozyme cooled to 15 K. This enabled the subsequent cryogenic analysis of two further proteins, rubredoxin and concanavalin A, at 1.7 and 2.5 Å, respectively, demonstrating the generality of the approach. The ability to flash-cool such large crystals for cryogenic neutron analysis should significantly broaden the range of scientific questions examined by neutron protein crystallography, allowing the analysis of structures and transitions as a function of temperature and enabling freeze-trapped capture of kinetic intermediates in protein systems.
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23
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Munshi P, Chung SL, Blakeley MP, Weiss KL, Myles DAA, Meilleur F. Rapid visualization of hydrogen positions in protein neutron crystallographic structures. Acta Crystallogr D Biol Crystallogr 2011; 68:35-41. [PMID: 22194331 DOI: 10.1107/s0907444911048402] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/15/2011] [Indexed: 11/10/2022]
Abstract
Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.
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Affiliation(s)
- Parthapratim Munshi
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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24
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Li X, Shew CY, He L, Meilleur F, Myles DAA, Liu E, Zhang Y, Smith GS, Herwig KW, Pynn R, Chen WR. Scattering functions of Platonic solids. J Appl Crystallogr 2011. [DOI: 10.1107/s0021889811011691] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The single-particle small-angle scattering properties of five Platonic solids, including the tetrahedron, hexahedron, octahedron, dodecahedron and icosahedron, are systematically investigated. For each given geometry, the Debye spatial autocorrelation function, pair distance distribution function and intraparticle structure factor (form factor) are calculated and compared with the corresponding scattering function of a spherical reference system. From the theoretical models, the empirical relationship between the dodecahedral and icosahedral structural characteristics and those of the equivalent spheres is found. Moreover, the single-particle scattering properties of icosahedral and spherical shells with identical volume are investigated, and the prospect of using different data analysis approaches to explore their structural differences is presented and discussed.
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25
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He L, Piper A, Meilleur F, Myles DAA, Hernandez R, Brown DT, Heller WT. The structure of Sindbis virus produced from vertebrate and invertebrate hosts as determined by small-angle neutron scattering. J Virol 2010; 84:5270-6. [PMID: 20219936 PMCID: PMC2863847 DOI: 10.1128/jvi.00044-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 02/25/2010] [Indexed: 01/14/2023] Open
Abstract
The complex natural cycle of vectored viruses that transition between host species, such as between insects and mammals, makes understanding the full life cycle of the virus an incredibly complex problem. Sindbis virus, an arbovirus and prototypic alphavirus having an inner protein shell and an outer glycoprotein coat separated by a lipid membrane, is one example of a vectored virus that transitions between vertebrate and insect hosts. While evidence of host-specific differences in Sindbis virus has been observed, no work has been performed to characterize the impact of the host species on the structure of the virus. Here, we report the first study of the structural differences between Sindbis viruses grown in mammalian and insect cells, which were determined by small-angle neutron scattering (SANS), a nondestructive technique that did not decrease the infectivity of the Sindbis virus particles studied. The scattering data and modeling showed that, while the radial position of the lipid bilayer did not change significantly, it was possible to conclude that it did have significantly more cholesterol when the virus was grown in mammalian cells. Additionally, the outer protein coat was found to be more extended in the mammalian Sindbis virus. The SANS data also demonstrated that the RNA and nucleocapsid protein share a closer interaction in the mammalian-cell-grown virus than in the virus from insect cells.
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Affiliation(s)
- Lilin He
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Amanda Piper
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Flora Meilleur
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dean A. A. Myles
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Raquel Hernandez
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dennis T. Brown
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - William T. Heller
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
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Gardberg AS, Del Castillo AR, Weiss KL, Meilleur F, Blakeley MP, Myles DAA. Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography. Acta Crystallogr D Biol Crystallogr 2010; 66:558-67. [PMID: 20445231 DOI: 10.1107/s0907444910005494] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 02/09/2010] [Indexed: 11/10/2022]
Abstract
The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.
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Wilkinson C, Lehmann MS, Meilleur F, Blakeley MP, Myles DAA, Vogelmeier S, Thoms M, Walsh M, McIntyre GJ. Characterization of image plates for neutron diffraction. J Appl Crystallogr 2009. [DOI: 10.1107/s0021889809024856] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A method to measure the overall gain and point-spread function of an image-plate detector system (converter, phosphor, readout electronics) online from single-crystal diffraction patterns is derived. Only with a knowledge of these quantities can one estimate without bias the true standard deviations of the observed integrated intensities of Bragg reflections measured with such a detector. The gain corrected for the point-spread function should ideally be approximately 1.0 to avoid loss of data or precision due to the upper and lower limits of digitization of the diffraction patterns. The gain and the point-spread function are derived for several configurations of the three neutron Laue image-plate diffractometers, LADI, VIVALDI and LADI-III, at the Institut Laue–Langevin. The detective quantum efficiencies (DQE) of these instruments have been measured to be 0.16 (1), 0.57 (2) and 0.46 (3), respectively. It has also been found that the DQE is effectively constant for different times of exposure, despite the fading of the photostimulated luminescent signal during that time. While the results described in this paper concern neutron detection by image plates, the method is equally valid for other integrating detectors and radiations,e.g.CCD detectors and X-rays.
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Gardberg AS, Blakeley MP, Myles DAA. A preliminary neutron crystallographic study of proteinase K at pD 6.5. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:184-187. [PMID: 19194016 PMCID: PMC2635872 DOI: 10.1107/s1744309109000566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 01/07/2009] [Indexed: 05/27/2023]
Abstract
A preliminary neutron crystallographic study of the proteolytic enzyme proteinase K is presented. Large hydrogenated crystals were prepared in deuterated crystallization buffer using the vapor-diffusion method. Data were collected to a resolution of 2.3 A on the LADI-III diffractometer at the Institut Laue-Langevin (ILL) in 2.5 d. The results demonstrate the feasibility of a full neutron crystallographic analysis of this structure with the aim of providing relevant information on the location of H atoms, particularly at the active site. This information will contribute to further understanding of the molecular mechanisms underlying the catalytic activity of proteinase K and to an enriched understanding of the subtilisin clan of serine proteases.
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Teixeira SCM, Ankner J, Bellissent-Funel MC, Bewley R, Blakeley MP, Coates L, Dahint R, Dalgliesh R, Dencher N, Dhont J, Fischer P, Forsyth VT, Fragneto G, Frick B, Geue T, Gilles R, Gutberlet T, Haertlein M, Hauß T, Häußler W, Heller WT, Herwig K, Holderer O, Juranyi F, Kampmann R, Knott R, Kohlbrecher J, Kreuger S, Langan P, Lechner R, Lynn G, Majkrzak C, May R, Meilleur F, Mo Y, Mortensen K, Myles DAA, Natali F, Neylon C, Niimura N, Ollivier J, Ostermann A, Peters J, Pieper J, Rühm A, Schwahn D, Shibata K, Soper AK, Straessle T, Suzuki UI, Tanaka I, Tehei M, Timmins P, Torikai N, Unruh T, Urban V, Vavrin R, Weiss K, Zaccai G. New sources and instrumentation for neutrons in biology. Chem Phys 2009; 345:133-151. [PMID: 19132140 PMCID: PMC2614686 DOI: 10.1016/j.chemphys.2008.02.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.
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Affiliation(s)
- S C M Teixeira
- Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble cedex 9, France
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Abstract
Neutron scattering and diffraction provide detailed information on the structure and dynamics of biological materials across time and length scales that range from picoseconds to nanoseconds and from 1 to 10,000 A, respectively. The particular sensitivity of neutrons to the isotopes of hydrogen makes selective deuterium labeling of biological systems an essential tool for maximizing the return from neutron scattering experiments. In neutron protein crystallography, the use of fully deuterated protein crystals improves the signal-to-noise ratio of the data by an order of magnitude and enhances the visibi-lity of the molecular structure (Proc Natl Acad Sci U S A 97:3872-3877, 2000; Acta Crystallogr D Biol Crystallogr 61:1413-1417, 2005; Acta Crystallogr D Biol Crystallogr 61:539-544, 2005). In solution and surface scattering experiments, the incorporation of deuterium-labeled subunits or components into complex assemblies or structures makes it possible to deconvolute the scattering of the labeled and unlabeled subunits and to determine their relative dispositions within the complex (J Mol Biol 93:255-265, 1975). With multiple labeling patterns, it is also possible to reconstruct the locations of multiple subunits in ternary and higher-order complexes (Science 238:1403-1406, 1987; J Mol Biol 271:588-601, 1997; J Biol Chem 275:14432-14439, 2000; Biochemistry 42:7790-7800, 2003). In inelastic neutron scattering experiments, which probe hydrogen dynamics in biological materials, the application of site, residue, or region-specific hydrogen-deuterium-labeling patterns can be used to distinguish and highlight the specific dynamics within a system (Proc Natl Acad Sci U S A 95:4970-4975, 1998).Partial, selective, or fully deuterated proteins can be readily produced by endogenous expression of recombinant proteins in bacterial systems that are adapted to growth in D(2)O solution and using selectively deuterated carbon sources. Adaptation can be achieved either by gradual step-wise increase in D(2)O concentration or, more directly, by plating cells on media of choice and selecting colonies that perform best for subsequent culture and inoculation. Scale-up growth and expression is typically performed in standard shaker flasks using either commercial or "home-grown" rich media (derived, for example, from cell lysates produced from algae grown in D(2)O) or under more controlled conditions in defined minimal media. Cell growth is typically slower in deuterated media (>5 times slower) and yields are correspondingly lower. Once the target protein has been expressed, purification proceeds by the protocols developed for the hydrogenated protein. The deuteration levels of the final product are determined by mass spectrometry.
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Affiliation(s)
- Flora Meilleur
- Department of Molecular & Structural Biochemistry, North Carolina State University, Oak Ridge National Laboratory, Raleigh, Oak Ridge, NC, TN, USA
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Meilleur F, Myles DAA, Blakeley MP. Neutron Laue macromolecular crystallography. Eur Biophys J 2006; 35:611-20. [PMID: 16897039 DOI: 10.1007/s00249-006-0074-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 04/27/2006] [Accepted: 05/04/2006] [Indexed: 11/26/2022]
Abstract
Recent progress in neutron protein crystallography such as the use of the Laue technique and improved neutron optics and detector technologies have dramatically improved the speed and precision with which neutron protein structures can now be determined. These studies are providing unique and complementary insights on hydrogen and hydration in protein crystal structures that are not available from X-ray structures alone. Parallel improvements in modern molecular biology now allow fully (per)deuterated protein samples to be produced for neutron scattering that essentially eradicate the large-and ultimately limiting-hydrogen incoherent scattering background that has hampered such studies in the past. High quality neutron data can now be collected to near atomic resolution (approximately 2.0 A) for proteins of up to approximately 50 kDa molecular weight using crystals of volume approximately 0.1 mm3 on the Laue diffractometer at ILL. The ability to flash-cool and collect high resolution neutron data from protein crystals at cryogenic temperature (15 K) has opened the way for kinetic crystallography on freeze trapped systems. Current instrument developments now promise to reduce crystal volume requirements by a further order of magnitude, making neutron protein crystallography a more accessible and routine technique.
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Affiliation(s)
- Flora Meilleur
- Institut Laue Langevin, BP 156, 38042, Grenoble Cedex 9, France.
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Snell EH, van der Woerd MJ, Damon M, Judge RA, Myles DAA, Meilleur F. Optimizing crystal volume for neutron diffraction: D-xylose isomerase. Eur Biophys J 2006; 35:621-32. [PMID: 16724195 DOI: 10.1007/s00249-006-0068-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 03/27/2006] [Accepted: 04/04/2006] [Indexed: 10/24/2022]
Abstract
Neutron diffraction is uniquely sensitive to hydrogen positions and protonation state. In that context structural information from neutron data is complementary to that provided through X-ray diffraction. However, there are practical obstacles to overcome in fully exploiting the potential of neutron diffraction, i.e. low flux and weak scattering. Several approaches are available to overcome these obstacles and we have investigated the simplest: increasing the diffracting volume of the crystals. Volume is a quantifiable metric that is well suited for experimental design and optimization techniques. By using response surface methods we have optimized the xylose isomerase crystal volume, enabling neutron diffraction while we determined the crystallization parameters with a minimum of experiments. Our results suggest a systematic means of enabling neutron diffraction studies for a larger number of samples that require information on hydrogen position and/or protonation state.
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Affiliation(s)
- Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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Coates L, Erskine PT, Mall S, Gill R, Wood SP, Myles DAA, Cooper JB. X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases. Eur Biophys J 2006; 35:559-66. [PMID: 16673078 DOI: 10.1007/s00249-006-0065-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2006] [Revised: 03/24/2006] [Accepted: 04/04/2006] [Indexed: 11/24/2022]
Abstract
Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing non-hydrolysable analogues of the scissile peptide bond. Until recent years, the positions of protons on the catalytic aspartates and the ligand in these complexes had not been determined with certainty due to the inadequate resolution of these analyses. There has been much interest in locating the catalytic protons at the active site of aspartic proteinases since this has major implications for detailed understanding of the mechanism of action and the design of improved transition state mimics for therapeutic applications. In this review we discuss the results of studies which have shed light on the locations of protons at the catalytic centre. The first direct determination of the proton positions stemmed from neutron diffraction data collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex at a resolution of 2.1 A provided evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. Atomic resolution X-ray studies of inhibitor complexes have corroborated this finding. A similar study of the native enzyme established that it, unexpectedly, has a dipeptide bound at the catalytic site which is consistent with classical reports of inhibition by short peptides and the ability of pepsins to catalyse transpeptidation reactions. Studies by NMR have confirmed the findings of low-barrier and single-well hydrogen bonds in the complexes with transition state analogues.
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Affiliation(s)
- Leighton Coates
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, SO16 7PX, England
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Meilleur F, Snell EH, van der Woerd MJ, Judge RA, Myles DAA. A quasi-Laue neutron crystallographic study of d-xylose isomerase. Eur Biophys J 2006; 35:601-9. [PMID: 16673077 DOI: 10.1007/s00249-006-0066-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 03/29/2006] [Accepted: 04/04/2006] [Indexed: 10/24/2022]
Abstract
The location of hydrogen atoms in enzyme structures can bring critical understanding of catalytic mechanism. However, whilst it is often difficult to determine the position of hydrogen atoms using X-ray crystallography even with subatomic (<1.0 A) resolution data available, neutron crystallography provides an experimental tool to directly localize hydrogen/deuterium atoms in biological macromolecules at resolution of 1.5-2.0 A. D-Xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) is a 43 kDa enzyme that catalyses the first reaction in the catabolism of D-xylose. Linearization and isomerization of D-xylose at the active site of D-xylose isomerase rely upon a complex hydrogen transfer. Neutron quasi-Laue data at 2.2 A resolution were collected at room temperature on a partially deuterated Streptomyces rubiginosus D-xylose isomerase crystal using the LADI instrument at ILL with the objective to provide insight into the enzymatic mechanism. The neutron structure shows unambiguously that residue His 53 is doubly protonated at the active site of the enzyme. This suggests that the reaction proceeds through an acid catalyzed opening of the sugar ring, which is in accord with the mechanism suggested by Fenn et al. (Biochemistry 43(21): 6464-6474, 2004). This is the first report of direct observation of double protonation of His 53 and the first validation of the ring opening mechanism at the active site of D-xylose isomerase.
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Affiliation(s)
- Flora Meilleur
- Institut Laue Langevin, BP 156, 38042, Grenoble, France.
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35
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Blakeley MP, Mitschler A, Hazemann I, Meilleur F, Myles DAA, Podjarny A. Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase-inhibitor complex. Eur Biophys J 2006; 35:577-83. [PMID: 16622654 DOI: 10.1007/s00249-006-0064-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 03/22/2006] [Indexed: 10/24/2022]
Abstract
Protonation states determination by neutron (2.2 A at room temperature) and X-ray (0.66 A at 100 K) crystallographic studies were compared for a medium size enzyme, human aldose reductase (MW=36 kDa), complexed with its NADP+ coenzyme and a selected inhibitor of therapeutic interest. The neutron resolution could be achieved only with the ab initio fully deuterated protein and the subsequent crystallization in D2O of the complex. We used the largest good-quality crystal (1.00x0.67x0.23 mm, i.e. volume of 0.15 mm3) that we were able to grow so far. Both studies enable the determination of protonation states, with a clear advantage for neutrons in the case of less-ordered atoms (B>5 A2). Hydrogen atoms are best determined by a complementary analysis of the Fourier maps obtained from both methods.
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Affiliation(s)
- M P Blakeley
- EMBL, 6 Rue Jules Horowitz, BP 181 Cedex 9, 38042, Grenoble, France
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36
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Budayova-Spano M, Fisher SZ, Dauvergne MT, Agbandje-McKenna M, Silverman DN, Myles DAA, McKenna R. Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 62:6-9. [PMID: 16511248 PMCID: PMC2150928 DOI: 10.1107/s1744309105038248] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 11/18/2005] [Indexed: 11/11/2022]
Abstract
Human carbonic anhydrase II (HCA II) is a zinc metalloenzyme that catalyzes the reversible hydration and dehydration of carbon dioxide and bicarbonate, respectively. The rate-limiting step in catalysis is the intramolecular transfer of a proton between the zinc-bound solvent (H2O/OH-) and the proton-shuttling residue His64. This distance (approximately 7.5 A) is spanned by a well defined active-site solvent network stabilized by amino-acid side chains (Tyr7, Asn62, Asn67, Thr199 and Thr200). Despite the availability of high-resolution (approximately 1.0 A) X-ray crystal structures of HCA II, there is currently no definitive information available on the positions and orientations of the H atoms of the solvent network or active-site amino acids and their ionization states. In preparation for neutron diffraction studies to elucidate this hydrogen-bonding network, perdeuterated HCA II has been expressed, purified, crystallized and its X-ray structure determined to 1.5 A resolution. The refined structure is highly isomorphous with hydrogenated HCA II, especially with regard to the active-site architecture and solvent network. This work demonstrates the suitability of these crystals for neutron macromolecular crystallography.
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Affiliation(s)
- Monika Budayova-Spano
- European Molecular Biology Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Institut Laue–Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble, France
| | - S. Zoë Fisher
- Department of Biochemistry and Molecular Biology, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
| | - Marie-Thérèse Dauvergne
- European Molecular Biology Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
| | - David N. Silverman
- Department of Pharmacology and Therapeutics, PO Box 100267, University of Florida, Gainesville, FL 32610, USA
| | - Dean A. A. Myles
- European Molecular Biology Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
- Correspondence e-mail:
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Schultz AJ, Thiyagarajan P, Hodges JP, Rehm C, Myles DAA, Langan P, Mesecar AD. Conceptual design of a macromolecular neutron diffractometer (MaNDi) for the SNS. J Appl Crystallogr 2005. [DOI: 10.1107/s0021889805030256] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This paper describes the design criteria, calculations and simulations for a high-resolution macromolecular neutron diffractometer (MaNDi) for the Spallation Neutron Source (SNS). MaNDi is optimized to achieve 1.5 Å resolution from crystals of 0.1–1 mm3with lattice repeats in the range of 150 Å. It was determined that locating MaNDi on a decoupled hydrogen moderator beamline with a curved guide will provide data of higher resolution and higher signal-to-noise than a coupled hydrogen moderator at the SNS. In addition, for an instrument with an initial flight path of 24 m at the 60 Hz source and a wavelength bandwidth of Δλ≃ 2.7 Å, bandwidth selection disk choppers can shift the wavelength range higher or lower for different experiments. With a wavelength range of 1.5–4.2 Å anddmin= 2.0 Å, simulations predict experiment duration times of 1–7 d, which is expected to revolutionize neutron macromolecular crystallography (NMC) for applications in the fields of structural biology, enzymology and computational chemistry.
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Hazemann I, Dauvergne MT, Blakeley MP, Meilleur F, Haertlein M, Van Dorsselaer A, Mitschler A, Myles DAA, Podjarny A. High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductase. Acta Crystallogr D Biol Crystallogr 2005; 61:1413-7. [PMID: 16204895 DOI: 10.1107/s0907444905024285] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Accepted: 07/28/2005] [Indexed: 11/10/2022]
Abstract
Neutron diffraction data have been collected to 2.2 Angstrom resolution from a small (0.15 mm(3)) crystal of perdeuterated human aldose reductase (h-AR; MW = 36 kDa) in order to help to determine the protonation state of the enzyme. h-AR belongs to the aldo-keto reductase family and is implicated in diabetic complications. Its ternary complexes (h-AR-coenzyme NADPH-selected inhibitor) provide a good model to study both the enzymatic mechanism and inhibition. Here, the successful production of fully deuterated human aldose reductase [h-AR(D)], subsequent crystallization of the ternary complex h-AR(D)-NADPH-IDD594 and neutron Laue data collection at the LADI instrument at ILL using a crystal volume of just 0.15 mm(3) are reported. Neutron data were recorded to 2 Angstrom resolution, with subsequent data analysis using data to 2.2 Angstrom. This is the first fully deuterated enzyme of this size (36 kDa) to be solved by neutron diffraction and represents a milestone in the field, as the crystal volume is at least one order of magnitude smaller than those usually required for other high-resolution neutron structures determined to date. This illustrates the significant increase in the signal-to-noise ratio of data collected from perdeuterated crystals and demonstrates that good-quality neutron data can now be collected from more typical protein crystal volumes. Indeed, the signal-to-noise ratio is then dominated by other sources of instrument background, the nature of which is under investigation. This is important for the design of future instruments, which should take maximum advantage of the reduction in the intrinsic diffraction pattern background from fully deuterated samples.
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Affiliation(s)
- I Hazemann
- IGBMC, 1 Rue Laurent Fries, 67404 Strasbourg-Illkirch, France
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Meilleur F, Dauvergne MT, Schlichting I, Myles DAA. Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam. Acta Crystallogr D Biol Crystallogr 2005; 61:539-44. [PMID: 15858263 DOI: 10.1107/s0907444905003872] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2004] [Accepted: 02/03/2005] [Indexed: 11/10/2022]
Abstract
Neutron protein crystallography allows H-atom positions to be located in biological structures at the relatively modest resolution of 1.5-2.0 A. A difficulty of this technique arises from the incoherent scattering from hydrogen, which considerably reduces the signal-to-noise ratio of the data. This can be overcome by preparing fully deuterated samples. Efficient protocols for routine and low-cost production of in vivo deuterium-enriched proteins have been developed. Here, the overexpression and crystallization of highly (>99%) deuterium-enriched cytochrome P450cam for neutron analysis is reported. Cytochrome P450cam from Pseudomonas putida catalyses the hydroxylation of camphor from haem-bound molecular O(2) via a mechanism that is thought to involve a proton-shuttle pathway to the active site. Since H atoms cannot be visualized in available X-ray structures, neutron diffraction is being used to determine the protonation states and water structure at the active site of the enzyme. Analysis of both hydrogenated and perdeuterated P450cam showed no significant changes between the X-ray structures determined at 1.4 and 1.7 A, respectively. This work demonstrates that the fully deuterated protein is highly isomorphous with the native (hydrogenated) protein and is appropriate for neutron protein crystallographic analysis.
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Affiliation(s)
- Flora Meilleur
- European Molecular Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France.
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Bennett BC, Meilleur F, Myles DAA, Howell EE, Dealwis CG. Preliminary neutron diffraction studies of Escherichia coli dihydrofolate reductase bound to the anticancer drug methotrexate. Acta Crystallogr D Biol Crystallogr 2005; 61:574-9. [PMID: 15858267 DOI: 10.1107/s0907444905004804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Accepted: 02/10/2005] [Indexed: 11/10/2022]
Abstract
The contribution of H atoms in noncovalent interactions and enzymatic reactions underlies virtually all aspects of biology at the molecular level, yet their 'visualization' is quite difficult. To better understand the catalytic mechanism of Escherichia coli dihydrofolate reductase (ecDHFR), a neutron diffraction study is under way to directly determine the accurate positions of H atoms within its active site. Despite exhaustive investigation of the catalytic mechanism of DHFR, controversy persists over the exact pathway associated with proton donation in reduction of the substrate, dihydrofolate. As the initial step in a proof-of-principle experiment which will identify ligand and residue protonation states as well as precise solvent structures, a neutron diffraction data set has been collected on a 0.3 mm(3) D(2)O-soaked crystal of ecDHFR bound to the anticancer drug methotrexate (MTX) using the LADI instrument at ILL. The completeness in individual resolution shells dropped to below 50% between 3.11 and 3.48 A and the I/sigma(I) in individual shells dropped to below 2 at around 2.46 A. However, reflections with I/sigma(I) greater than 2 were observed beyond these limits (as far out as 2.2 A). To our knowledge, these crystals possess one of the largest primitive unit cells (P6(1), a = b = 92, c = 73 A) and one of the smallest crystal volumes so far tested successfully with neutrons.
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Affiliation(s)
- Brad C Bennett
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
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41
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Blakeley MP, Kalb AJ, Helliwell JR, Myles DAA. The 15-K neutron structure of saccharide-free concanavalin A. Proc Natl Acad Sci U S A 2004; 101:16405-10. [PMID: 15525703 PMCID: PMC534515 DOI: 10.1073/pnas.0405109101] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Indexed: 11/18/2022] Open
Abstract
The positions of the ordered hydrogen isotopes of a protein and its bound solvent can be determined by using neutron crystallography. Furthermore, by collecting neutron data at cryo temperatures, the dynamic disorder within a protein crystal is reduced, which may lead to improved definition of the nuclear density. It has proved possible to cryo-cool very large Con A protein crystals (>1.5 mm3) suitable for high-resolution neutron and x-ray structure analysis. We can thereby report the neutron crystal structure of the saccharide-free form of Con A and its bound water, including 167 intact D2O molecules and 60 oxygen atoms at 15 K to 2.5-A resolution, along with the 1.65-A x-ray structure of an identical crystal at 100 K. Comparison with the 293-K neutron structure shows that the bound water molecules are better ordered and have lower average B factors than those at room temperature. Overall, twice as many bound waters (as D2O) are identified at 15 K than at 293 K. We note that alteration of bound water orientations occurs between 293 and 15 K; such changes, as illustrated here with this example, could be important more generally in protein crystal structure analysis and ligand design. Methodologically, this successful neutron cryo protein structure refinement opens up categories of neutron protein crystallography, including freeze-trapped structures and cryo to room temperature comparisons.
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Affiliation(s)
- M P Blakeley
- European Molecular Biology Laboratory, 6 Rue Jules Horowitz, B.P. 181, 38042 Grenoble 9, France
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42
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Abstract
Perdeuterated and hydrogenated cytochrome P450cam (P450cam), from Pseudomonas putida, has been characterized concerning thermal stability and structural dynamics. For the first time, Fourier transform infrared (FTIR) spectroscopy was used to characterize a perdeuterated protein. The secondary structure compositions were determined from the fitted amide I' spectral region, giving band populations at 10 degrees C for the perdeuterated protein of 22% between 1605 and 1624 cm(-1) (beta-sheets), 47% between 1633 and 1650 cm(-1) (alpha-helix (29%) plus unordered/3(10)-helix (18%)), and 28% between 1657 and 1677 cm(-1) (turns) and for the hydrogenated protein of 22% between 1610 and 1635 cm(-1) (beta-sheets), 52% between 1640 and 1658 cm(-1) (alpha-helix (41%) plus unordered/3(10)-helix (11%)), and 24% between 1665 and 1680 cm(-1) (turns). Thermal unfolding experiments revealed that perdeuterated P450cam was less stable than the hydrogenated protein. The midpoint transition temperatures were 60.8 and 64.4 degrees C for the perdeuterated and hydrogenated P450cam, respectively. Step-scan time-resolved FTIR was applied to the P450cam-CO complex to study the ligand-rebinding process after flash photolysis. Rebinding of the ligand occurred with the same kinetics and rate constants k(on), 8.9 x 10(4) and 8.3 x 10(4) M(-1) s(-1) for the perdeuterated and hydrogenated P450cam, respectively.Perdeuterated P450cam was expressed for a neutron crystallographic study to determine the specific hydration states and hydrogen-bonding networks at the active site. The analyses presented here show that perdeuterated P450cam is structurally similar to its hydrogenated counterpart, despite its reduced thermal stability, suggesting that information obtained from the neutron structure will be representative of the normal hydrogenated P450cam.
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Affiliation(s)
- Flora Meilleur
- EMBL-Grenoble Outstation, BP 181, 38042 Grenoble Cedex 9, France
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43
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Abstract
The number of protein crystal structures being refined to atomic resolution is increasing each year as well as the size of proteins being studied. There are currently 346 structures in the protein data bank which have been refined to or beyond atomic resolution. The benefits of atomic resolution X-ray data are discussed along with a number of structural examples of biomedically relevant proteins. The complementary role of neutron diffraction will also be discussed.
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Affiliation(s)
- L Coates
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
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44
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Tuominen VU, Myles DAA, Dauvergne MT, Lahti R, Heikinheimo P, Goldman A. Production and preliminary analysis of perdeuterated yeast inorganic pyrophosphatase crystals suitable for neutron diffraction. Acta Crystallogr D Biol Crystallogr 2004; 60:606-9. [PMID: 14993708 DOI: 10.1107/s0907444903029585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2003] [Accepted: 12/22/2003] [Indexed: 04/29/2023]
Abstract
Yeast inorganic pyrophosphatase (Y-PPase) is a model system for studying phosphoryl-transfer reactions catalysed by multiple metal ions. To understand the process requires knowledge of the positions of the protons in the active site, which can be best achieved by neutron diffraction analysis. In order to reduce the hydrogen incoherent-scattering background and to improve the signal-to-noise ratio of the neutron reflections, deuterated protein was produced. Deuterated protein 96% enriched with deuterium was produced in high yield and crystals as large as 2 mm on one side were obtained. These crystals have unit-cell parameters a = 58.9, b = 103.9, c = 117.0 A, alpha = beta = gamma = 90 degrees at 273 K and diffract neutrons to resolutions of 2.5-3 A. The X-ray structure of the perdeuterated protein has also been refined at 273 K to 1.9 A resolution.
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Affiliation(s)
- Vesa U Tuominen
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, PO Box 123, FIN-20521 Turku, Finland
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45
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Erskine PT, Coates L, Mall S, Gill RS, Wood SP, Myles DAA, Cooper JB. Atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides. Protein Sci 2003; 12:1741-9. [PMID: 12876323 PMCID: PMC2323960 DOI: 10.1110/ps.0305203] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The X-ray structures of native endothiapepsin and a complex with a hydroxyethylene transition state analog inhibitor (H261) have been determined at atomic resolution. Unrestrained refinement of the carboxyl groups of the enzyme by using the atomic resolution data indicates that both catalytic aspartates in the native enzyme share a single negative charge equally; that is, in the crystal, one half of the active sites have Asp 32 ionized and the other half have Asp 215 ionized. The electron density map of the native enzyme refined at 0.9 A resolution demonstrates that there is a short peptide (probably Ser-Thr) bound noncovalently in the active site cleft. The N-terminal nitrogen of the dipeptide interacts with the aspartate diad of the enzyme by hydrogen bonds involving the carboxyl of Asp 215 and the catalytic water molecule. This is consistent with classical findings that the aspartic proteinases can be inhibited weakly by short peptides and that these enzymes can catalyze transpeptidation reactions. The dipeptide may originate from autolysis of the N-terminal Ser-Thr sequence of the enzyme during crystallization.
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Affiliation(s)
- Peter T Erskine
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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Prince SM, Howard TD, Myles DAA, Wilkinson C, Papiz MZ, Freer AA, Cogdell RJ, Isaacs NW. Detergent structure in crystals of the integral membrane light-harvesting complex LH2 from Rhodopseudomonas acidophila strain 10050. J Mol Biol 2003; 326:307-15. [PMID: 12547211 DOI: 10.1016/s0022-2836(02)01361-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Integral membrane proteins are solubilized by their incorporation into a detergent micelle. The detergent micelle has a critical influence on the formation of a three-dimensional crystal lattice. The bulk detergent phase is not seen in X-ray crystal structures of integral membrane proteins, due to its disordered character. Here, we describe the detergent structure present in crystals of the peripheral light-harvesting complex of the purple bacteria Rhodopseudomonas acidophila strain 10050 at a maximal resolution of 12A as determined by neutron crystallography. The LH2 molecule has a toroidal shape and spans the membrane completely in vivo. A volume of 16% of the unit cell could be ascribed to detergent tails, localized on both the inner and outer hydrophobic surfaces of the molecule. The detergent tail volumes were found to be associated with individual LH2 molecules and had no direct role in the formation of the crystalline lattice.
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Affiliation(s)
- S M Prince
- Department of Chemistry, University of Glasgow, G12 8QQ, Glasgow, UK.
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47
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Daniels BV, Myles DAA, Forsyth VT, Lawson CL. Crystals of trp repressor suitable for high-resolution neutron Laue diffraction studies. Acta Crystallogr D Biol Crystallogr 2003; 59:136-8. [PMID: 12499549 DOI: 10.1107/s0907444902018516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2002] [Accepted: 10/08/2002] [Indexed: 11/10/2022]
Abstract
Crystallization and preliminary neutron-diffraction measurements of wild-type variant Val58-->Ile of the Escherichia coli trp repressor are reported. A vapor-diffusion chamber suitable for initial protein-solution Volumes in the range 0.2-0.5 ml was used to grow cube-shaped crystals with edge dimensions in the range 0.8-1.4 mm. Neutron Laue measurements to a nominal resolution of 2.1 A were recorded from a D(2)O-exchanged crystal using the LADI instrument at ILL. These results demonstrate that it will be possible for the first time to obtain a full-atom neutron structural model of a DNA-binding protein plus its associated solvent. Direct observation of hydrogen bonding between protein and solvent should enhance understanding of the role of solvent in protein-DNA recognition.
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Affiliation(s)
- Brenda V Daniels
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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48
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Ramadan MAM, Shrive AK, Holden D, Myles DAA, Volanakis JE, DeLucas LJ, Greenhough TJ. The three-dimensional structure of calcium-depleted human C-reactive protein from perfectly twinned crystals. Acta Crystallogr D Biol Crystallogr 2002; 58:992-1001. [PMID: 12037301 DOI: 10.1107/s0907444902005693] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2001] [Accepted: 03/27/2002] [Indexed: 02/25/2023]
Abstract
C-reactive protein is a member of the pentraxin family of oligomeric serum proteins which has been conserved through evolution, homologues having been found in every species in which they have been sought. Human C-reactive protein (hCRP) is the classical acute-phase reactant produced in large amounts in response to tissue damage and inflammation and is used almost universally as a clinical indicator of infection and inflammation. The role of hCRP in host defence and the calcium-dependent ligand-binding specificity of hCRP for phosphocholine moieties have long been recognized. In order to clarify the structural rearrangements associated with calcium binding, the reported affinity of calcium-depleted hCRP for polycations and other ligands, and the role of calcium in protection against denaturation and proteolysis, the structure of calcium-depleted hCRP has been determined by X-ray crystallography. Crystals of calcium-depleted hCRP are invariably twinned and those suitable for analysis are merohedral type II twins of point group 4 single crystals. The structure has been solved by molecular replacement using the calcium-bound hCRP structure [Shrive et al. (1996), Nature Struct. Biol. 3, 346-354]. It reveals two independent pentamers which form a face-to-face decamer across a dyad near-parallel to the twinning twofold axis. Cycles of intensity deconvolution, density modification (tenfold NCS) and model building, eventually including refinement, give a final R factor of 0.19 (R(free) = 0.20). Despite poor definition in some areas arising from the limited resolution of the data and from the twinning and disorder, the structure reveals the probable mode of twinning and the conformational changes, localized in one of the calcium-binding loops, which accompany calcium binding.
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49
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Kalb (Gilboa) AJ, Myles DAA, Habash J, Raftery J, Helliwell JR. Neutron Laue diffraction experiments on a large unit cell: concanavalin A complexed with methyl-α-D-glucopyranoside. J Appl Crystallogr 2001. [DOI: 10.1107/s0021889801007245] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A neutron Laue diffraction experiment on a complex of concanavalin A with methyl-α-D-glucopyranoside extensively soaked in D2O (space groupI213,a= 167.8 Å), which resulted in 3.5 Å diffraction data, is described. In a programme of structural studies of crystalline saccharide complexes of concanavalin A, the unit cell of the cubicI213 complex of concanavalin A with methyl-α-D-glucopyranoside is one of the largest. With its cell edge of 167.8 Å and its asymmetric unit of molecular weight 50 kDa, it represents a challenge for current neutron diffraction technology. The size of the crystal used in this experiment, although large (4 × 3 × 2 mm), was not the largest ever produced for this complex. The degree of spatial overlapping observed in the Laue experiment, however, suggests that use of larger crystals would be a disadvantage. On the basis of these observations, several technical improvements for macromolecular neutron crystallography are suggested.
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Forsyth VT, Mason SA, Howard JAK, Davidson MG, Fuller W, Myles DAA. A fast new diffractometer for chemical crystallography, small proteins and fiber diffraction. ACTA ACUST UNITED AC 2001. [DOI: 10.1080/10448630108245004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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