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Solomon TL, Chao K, Gingras G, Aubin Y, O'Dell WB, Marino JP, Brinson RG. Backbone NMR assignment of the yeast expressed Fab fragment of the NISTmAb reference antibody. Biomol NMR Assign 2023; 17:75-81. [PMID: 36856943 DOI: 10.1007/s12104-023-10123-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/08/2023] [Indexed: 06/02/2023]
Abstract
The monoclonal antibody (mAb) protein class has become a primary therapeutic platform for the production of new life saving drug products. MAbs are comprised of two domains: the antigen-binding fragment (Fab) and crystallizable fragment (Fc). Despite the success in the clinic, NMR assignments of the complete Fab domain have been elusive, in part due to problems in production of properly folded, triply-labeled 2H,13C,15N Fab domain. Here, we report the successful recombinant expression of a triply-labeled Fab domain, derived from the standard IgG1κ known as NISTmAb, in yeast. Using the 2H,13C,15N Fab domain, we assigned 94% of the 1H, 13C, and 15N backbone atoms.
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Affiliation(s)
- Tsega L Solomon
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Kinlin Chao
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Genevieve Gingras
- Centre for Oncology, Radiopharmaceuticals and Research, Biologics and Radiotherapeutic Drugs Directorate, Health Canada, 251 Sir Frederick Banting Driveway, K1A 0K9, Ottawa, ON, Canada
| | - Yves Aubin
- Centre for Oncology, Radiopharmaceuticals and Research, Biologics and Radiotherapeutic Drugs Directorate, Health Canada, 251 Sir Frederick Banting Driveway, K1A 0K9, Ottawa, ON, Canada
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA.
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2
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Schröder GC, O'Dell WB, Webb SP, Agarwal PK, Meilleur F. Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Chem Sci 2022; 13:13303-13320. [PMID: 36507176 PMCID: PMC9683017 DOI: 10.1039/d2sc05031e] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022] Open
Abstract
Metalloproteins perform a diverse array of redox-related reactions facilitated by the increased chemical functionality afforded by their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that are responsible for the breakdown of recalcitrant polysaccharides via oxidative cleavage at the glycosidic bond. The activated copper-oxygen intermediates and their mechanism of formation remains to be established. Neutron protein crystallography which permits direct visualization of protonation states was used to investigate the initial steps of oxygen activation directly following active site copper reduction in Neurospora crassa LPMO9D. Herein, we cryo-trap an activated dioxygen intermediate in a mixture of superoxo and hydroperoxo states, and we identify the conserved second coordination shell residue His157 as the proton donor. Density functional theory calculations indicate that both superoxo and hydroperoxo active site states are stable. The hydroperoxo formed is potentially an early LPMO catalytic reaction intermediate or the first step in the mechanism of hydrogen peroxide formation in the absence of substrate. We observe that the N-terminal amino group of the copper coordinating His1 remains doubly protonated directly following molecular oxygen reduction by copper. Aided by molecular dynamics and mining minima free energy calculations we establish that the conserved second-shell His161 in MtPMO3* displays conformational flexibility in solution and that this flexibility is also observed, though to a lesser extent, in His157 of NcLPMO9D. The imidazolate form of His157 observed in our structure following oxygen intermediate protonation can be attributed to abolished His157 flexibility due steric hindrance in the crystal as well as the solvent-occluded active site environment due to crystal packing. A neutron crystal structure of NcLPMO9D at low pH further supports occlusion of the active site since His157 remains singly protonated even at acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Simon P. Webb
- VeraChem LLC12850 Middlebrook Rd. Ste 205GermantownMD 20874-5244USA
| | - Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterOK 74078USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
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3
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Borgstahl GEO, O'Dell WB, Egli M, Kern JF, Kovalevsky A, Lin JYY, Myles D, Wilson MA, Zhang W, Zwart P, Coates L. EWALD: A macromolecular diffractometer for the second target station. Rev Sci Instrum 2022; 93:064103. [PMID: 35778015 DOI: 10.1063/5.0090810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Revealing the positions of all the atoms in large macromolecules is powerful but only possible with neutron macromolecular crystallography (NMC). Neutrons provide a sensitive and gentle probe for the direct detection of protonation states at near-physiological temperatures and clean of artifacts caused by x rays or electrons. Currently, NMC use is restricted by the requirement for large crystal volumes even at state-of-the-art instruments such as the macromolecular neutron diffractometer at the Spallation Neutron Source. EWALD's design will break the crystal volume barrier and, thus, open the door for new types of experiments, the study of grand challenge systems, and the more routine use of NMC in biology. EWALD is a single crystal diffractometer capable of collecting data from macromolecular crystals on orders of magnitude smaller than what is currently feasible. The construction of EWALD at the Second Target Station will cause a revolution in NMC by enabling key discoveries in the biological, biomedical, and bioenergy sciences.
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Affiliation(s)
- Gloria E O Borgstahl
- Eppley Institute for Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA
| | - William B O'Dell
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA and Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Jiao Y Y Lin
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Dean Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Petrus Zwart
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
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4
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Reddy PT, O'Dell WB. Fusing an insoluble protein to GroEL apical domain enhances soluble expression in Escherichia coli. Methods Enzymol 2021; 659:171-188. [PMID: 34752284 DOI: 10.1016/bs.mie.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A protocol for increasing soluble protein expression by fusing the chaperone GroEL apical domain with a gene of interest is described herein. GroEL apical domain, the minichaperone that functions independently of GroES and ATP in protein folding, is cloned downstream of the lambda CII ribosome binding site in the parent pRE vector. The pRE vector has tightly controlled transcription suitable for expressing toxic proteins. The GroEL minichaperone is fused to a glycine-serine rich linker followed by the enterokinase protease recognition sequence. A number of genes that are recalcitrant to protein production in the parent pRE vector 5were cloned into the pRE:GroEL fusion vector and successfully expressed as fusion proteins in Escherichia coli.
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Affiliation(s)
- Prasad T Reddy
- Biomolecular Measurement Division, National institute of Standards and Technology, Gaithersburg, MD, United States; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, United States.
| | - William B O'Dell
- Biomolecular Measurement Division, National institute of Standards and Technology, Gaithersburg, MD, United States; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
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5
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Leith EM, O'Dell WB, Ke N, McClung C, Berkmen M, Bergonzo C, Brinson RG, Kelman Z. Characterization of the internal translation initiation region in monoclonal antibodies expressed in Escherichia coli. J Biol Chem 2019; 294:18046-18056. [PMID: 31604819 DOI: 10.1074/jbc.ra119.011008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 09/09/2019] [Revised: 10/07/2019] [Indexed: 01/16/2023] Open
Abstract
Monoclonal antibodies (mAbs) represent an important platform for the development of biotherapeutic products. Most mAbs are produced in mammalian cells, but several mAbs are made in Escherichia coli, including therapeutic fragments. The NISTmAb is a well-characterized reference material made widely available to facilitate the development of both originator biologics and biosimilars. Here, when expressing NISTmAb from codon-optimized constructs in E. coli (eNISTmAb), a truncated variant of its heavy chain was observed. N-terminal protein sequencing and mutagenesis analyses indicated that the truncation resulted from an internal translation initiation from a GTG codon (encoding Val) within eNISTmAb. Using computational and biochemical approaches, we demonstrate that this translation initiates from a weak Shine-Dalgarno sequence and is facilitated by a putative ribosomal protein S1-binding site. We also observed similar internal initiation in the mAb adalimumab (the amino acid sequence of the drug Humira) when expressed in E. coli Of note, these internal initiation regions were likely an unintended result of the codon optimization for E. coli expression, and the amino acid pattern from which it is derived was identified as a Pro-Ser-X-X-X-Val motif. We discuss the implications of our findings for E. coli protein expression and codon optimization and outline possible strategies for reducing the likelihood of internal translation initiation and truncated product formation.
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Affiliation(s)
- Erik M Leith
- Biomolecular Labeling Laboratory, National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - William B O'Dell
- Biomolecular Labeling Laboratory, National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850; National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - Na Ke
- New England Biolabs, Ipswich, Massachusetts 01938
| | | | | | - Christina Bergonzo
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - Robert G Brinson
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - Zvi Kelman
- Biomolecular Labeling Laboratory, National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850; National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850.
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6
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. Acta Crystallogr D Struct Biol 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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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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Bodenheimer AM, O'Dell WB, Oliver RC, Qian S, Stanley CB, Meilleur F. Structural investigation of cellobiose dehydrogenase IIA: Insights from small angle scattering into intra- and intermolecular electron transfer mechanisms. Biochim Biophys Acta Gen Subj 2018; 1862:1031-1039. [DOI: 10.1016/j.bbagen.2018.01.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/18/2017] [Accepted: 01/23/2018] [Indexed: 01/08/2023]
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Bodenheimer AM, O'Dell WB, Stanley CB, Meilleur F. Structural studies of Neurospora crassa LPMO9D and redox partner CDHIIA using neutron crystallography and small-angle scattering. Carbohydr Res 2017; 448:200-204. [PMID: 28291519 DOI: 10.1016/j.carres.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 01/12/2023]
Abstract
Sensitivity to hydrogen/deuterium and lack of observable radiation damage makes cold neutrons an ideal probe the structural studies of proteins with highly photosensitive groups such as the copper center of lytic polysaccharide monooxygenases (LPMOs) and flavin adenine dinucleotide (FAD) and heme redox cofactors of cellobiose dehydrogenases (CDHs). Here, neutron crystallography and small-angle neutron scattering are used to investigate Neurospora crassa LPMO9D (NcLPMO9D) and CDHIIA (NcCDHIIA), respectively. The presence of LPMO greatly enhances the efficiency of commercial glycoside hydrolase cocktails in the depolymerization of cellulose. LPMOs can receive electrons from CDHs to activate molecular dioxygen for the oxidation of cellulose resulting in chain cleavage and disruption of local crystallinity. Using neutron protein crystallography, the hydrogen/deuterium atoms of NcLPMO9D could be located throughout the structure. At the copper active site, the protonation states of the side chains of His1, His84, His157 and Tyr168, and the orientation of water molecules could be determined. Small-angle neutron scattering measurements provided low resolution models of NcCDHIIA with both the dehydrogenase and cytochrome domains in oxidized states that exhibited elongated conformations. This work demonstrates the suitability of neutron diffraction and scattering for characterizing enzymes critical to oxidative cellulose deconstruction.
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Affiliation(s)
- Annette M Bodenheimer
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - William B O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Christopher B Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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10
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O'Dell WB, Agarwal PK, Meilleur F. Inside Cover: Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase (Angew. Chem. Int. Ed. 3/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201611987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
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11
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O'Dell WB, Agarwal PK, Meilleur F. Innentitelbild: Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase (Angew. Chem. 3/2017). Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201611987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
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12
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Affiliation(s)
- William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
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O'Dell WB, Agarwal PK, Meilleur F. Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angew Chem Int Ed Engl 2016; 56:767-770. [PMID: 28004877 DOI: 10.1002/anie.201610502] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 10/26/2016] [Indexed: 01/26/2023]
Abstract
Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. We have determined high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed "pre-bound" molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygen activation. These results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme-substrate complex.
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Affiliation(s)
- William B O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
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O'Dell WB, Bodenheimer AM, Meilleur F. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. Arch Biochem Biophys 2016; 602:48-60. [DOI: 10.1016/j.abb.2015.11.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
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Liberton M, Collins AM, Page LE, O'Dell WB, O'Neill H, Urban VS, Timlin JA, Pakrasi HB. Probing the consequences of antenna modification in cyanobacteria. Photosynth Res 2013; 118:17-24. [PMID: 24132812 DOI: 10.1007/s11120-013-9940-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
Photosynthetic organisms rely on antenna systems to harvest and deliver energy from light to reaction centers. In fluctuating photic environments, regulation of light harvesting is critical for a photosynthetic organism's survival. Here, we describe the use of a suite of phycobilisome mutants to probe the consequences of antenna truncation in the cyanobacterium Synechocystis sp. PCC 6803. Studies using transmission electron microscopy (TEM), hyperspectral confocal fluorescence microscopy (HCFM), small-angle neutron scattering (SANS), and an optimized photobioreactor system have unraveled the adaptive strategies that cells employ to compensate for antenna reduction. As the phycobilisome antenna size decreased, changes in thylakoid morphology were more severe and physical segregation of the two photosystems increased. Repeating distances between thylakoid membranes measured by SANS were correlated with TEM data, and corresponded to the degree of phycobilisome truncation. Thylakoid membranes were found to have a high degree of structural flexibility, and changes in the membrane system upon illumination were rapid and reversible. Phycobilisome truncation in Synechocystis 6803 reduced the growth rate and lowered biomass accumulation. Together, these results lend a dynamic perspective to the intracellular membrane organization in cyanobacteria cells and suggest an adaptive mechanism that allows cells to adjust to altered light absorption capabilities, while highlighting the cell-wide implications of antenna truncation.
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Affiliation(s)
- Michelle Liberton
- Department of Biology, Washington University, One Brookings Drive, St. Louis, MO, 63130, USA
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Busch S, Pardo LC, O'Dell WB, Bruce CD, Lorenz CD, McLain SE. On the structure of water and chloride ion interactions with a peptide backbone in solution. Phys Chem Chem Phys 2013; 15:21023-33. [DOI: 10.1039/c3cp53831a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liberton M, Page LE, O'Dell WB, O'Neill H, Mamontov E, Urban VS, Pakrasi HB. Organization and flexibility of cyanobacterial thylakoid membranes examined by neutron scattering. J Biol Chem 2012; 288:3632-40. [PMID: 23255600 DOI: 10.1074/jbc.m112.416933] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteria are prokaryotes that can use photosynthesis to convert sunlight into cellular fuel. Knowledge of the organization of the membrane systems in cyanobacteria is critical to understanding the metabolic processes in these organisms. We examined the wild-type strain of Synechocystis sp. PCC 6803 and a series of mutants with altered light-harvesting phycobilisome antenna systems for changes in thylakoid membrane architecture under different conditions. Using small-angle neutron scattering, it was possible to resolve correlation distances of subcellular structures in live cells on the nanometer scale and capture dynamic light-induced changes to these distances. Measurements made from samples with varied scattering contrasts confirmed that these distances could be attributed to the thylakoid lamellar system. We found that the changes to the thylakoid system were reversible between light- and dark-adapted states, demonstrating a robust structural flexibility in the architecture of cyanobacterial cells. Chemical disruption of photosynthetic electron transfer diminished these changes, confirming the involvement of the photosynthetic apparatus. We have correlated these findings with electron microscopy data to understand the origin of the changes in the membranes and found that light induces an expansion in the center-to-center distances between the thylakoid membrane layers. These combined data lend a dynamic dimension to the intracellular organization in cyanobacterial cells.
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Affiliation(s)
- Michelle Liberton
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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O'Dell WB, Baker DC, McLain SE. Structural evidence for inter-residue hydrogen bonding observed for cellobiose in aqueous solution. PLoS One 2012; 7:e45311. [PMID: 23056199 PMCID: PMC3462749 DOI: 10.1371/journal.pone.0045311] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [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: 04/29/2012] [Accepted: 08/21/2012] [Indexed: 11/19/2022] Open
Abstract
The structure of the disaccharide cellulose subunit cellobiose (4-O-β-D-glucopyranosyl-D-glucose) in solution has been determined via neutron diffraction with isotopic substitution (NDIS), computer modeling and nuclear magnetic resonance (NMR) spectroscopic studies. This study shows direct evidence for an intramolecular hydrogen bond between the reducing ring HO3 hydroxyl group and the non-reducing ring oxygen (O5') that has been previously predicted by computation and NMR analysis. Moreover, this work shows that hydrogen bonding to the non-reducing ring O5' oxygen is shared between water and the HO3 hydroxyl group with an average of 50% occupancy by each hydrogen-bond donor. The glycosidic torsion angles φ(H) and ψ(H) from the neutron diffraction-based model show a fairly tight distribution of angles around approximately 22(°) and -40(°), respectively, in solution, consistent with the NMR measurements. Similarly, the hydroxymethyl torsional angles for both reducing and non-reducing rings are broadly consistent with the NMR measurements in this study, as well as with those from previous measurements for cellobiose in solution.
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Affiliation(s)
- William B. O'Dell
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, United States of America
| | - David C. Baker
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sylvia E. McLain
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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O'Dell WB, Beatty KJ, Kuo-Hsiang Tang J, Blankenship RE, Urban VS, O'Neill H. Sol–gel entrapped light harvesting antennas: immobilization and stabilization of chlorosomes for energy harvesting. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm34357f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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