Publications from Research Conducted at MANDI

Macromolecular Neutron Diffractometer

MANDI | BL-11B | SNS

Publications from Research Conducted at MANDI

The following 76 publications were retrieved from PuSH (Publications of SNS and HFIR)

2024 2 Publications

Borgstahl G.E., Azadmanesh J., Slobodnik K., Struble L., Lutz W.E., Coates L., Weiss K., Myles D.A., Kroll T., "Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition", Nature Portfolio, (2024).

Drago V., Devos J.M., Blakeley M.P., Forsyth V.T., Parks J.M., Kovalevsky A., Mueser T.C., "Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase", Cell Reports Physical Science, 5, 2, 101827 (2024).

2023 4 Publications

Drago V., Campos C., Hooper M., Collins A., Gerlits O., Weiss K., Blakeley M.P., Phillips R.S., Kovalevsky A., "Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography", Communications Chemistry, 6, 162 (2023).

Loyd M., Shikhaliev P., "Scintillator-Based Detectors", 171-214 Neutron Detectors for Scattering Applications Springer Nature (2023).

Lutz W.E., Azadmanesh J., Lovelace J., Kolar C., Coates L., Weiss K., Borgstahl G.E., "Perfect Crystals: microgravity capillary counterdiffusion crystallization of human manganese superoxide dismutase for neutron crystallography", npj Microgravity, 9, 39 (2023).

Tandrup T., Lo Leggio L., Meilleur F., "Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature", Acta Crystallographica Section F, F79, 1-7 (2023).

2022 7 Publications

Azadmanesh J., Lutz W.E., Coates L., Weiss K., Borgstahl G.E., "Cryotrapping peroxide in the active site of human mitochondrial manganese superoxide dismutase crystals for neutron diffraction", Acta Crystallographica Section F, 78, 8-16 (2022).

Correy G.J., Kneller D.W., Phillips G., Pant S., Russi S., Cohen A.E., Meigs G., Holton J.M., Gahbauer S., Thompson M.C., Ashworth A., Coates L., Kovalevsky A., Meilleur F., Fraser J.S., "The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature", Science Advances, 8, 21, eabo5083 (2022).

David F., Setzler C., Sorescu A., Lieberman R.L., Meilleur F., Petty J.T., "Mapping H+ in the Nanoscale (A2C4)2-Ag8 Fluorophore", Journal of Physical Chemistry Letters, 13, 11317-11322 (2022).

Harp J., Lybrand T.P., Pallan P.S., Coates L., Sullivan B., Egli M., "Cryo neutron crystallography demonstrates influence of RNA 2′-OH orientation on conformation, sugar pucker and water structure", Nucleic Acids Research, 50, 7721-7738 (2022).

Hussein Ali R.E., "Investigations of the structural dynamics of the water and proton channels in Photosystem II", Ph.D. Dissertation, Humboldt University Berlin (2022).

Kneller D.W., Li H., Phillips G., Weiss K., Zhang Q., Arnould M.A., Jonsson C.B., Surendranathan S., Parvathareddy J., Blakeley M.P., Coates L., Louis J.M., Bonnesen P.V., Kovalevsky A., "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease", Nature Communications, 13, 2268 (2022).

Schroder G.C., O'Dell W.B., Webb S., Agarwal P.K., Meilleur F., "Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase", Chemical Science, 13, 13303-13320 (2022).

2021 8 Publications

Azadmanesh J., Lutz W.E., Coates L., Weiss K., Borgstahl G.E., "Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase", Nature Communications, 12, 2079 (2021).

Harp J., Coates L., Sullivan B., Egli M., "Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography", Nucleic Acids Research, 49, 4782-4792 (2021).

Hiromoto T., Nishikawa K., Tamada T., Higuchi Y., "The Challenge of Visualizing the Bridging Hydride at the Active Site and Proton Network of [NiFe]-Hydrogenase by Neutron Crystallography", Topics in Catalysis, 64, 622-630 (2021).

Kneller D.W., Li H., Galanie S., Phillips G., Labbe A., Weiss K., Zhang Q., Arnould M.A., Clyde A., Ma H., Ramanathan A., Jonsson C.B., Head M.S., Coates L., Louis J.M., Bonnesen P.V., Kovalevsky A., "Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease", Journal of Medicinal Chemistry, 64, 17366-17383 (2021).

Kneller D.W., Phillips G., Weiss K., Zhang Q., Coates L., Kovalevsky A., "Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography", Journal of Medicinal Chemistry, 64, 8, 4991–5000 (2021).

Kono F., Tamada T., "Neutron crystallography for the elucidation of enzyme catalysis", Current Opinion in Structural Biology, 71, 36-42 (2021).

Schroder G.C., "Dissecting Metalloprotein Chemistry: Characterization of a Copper Containing Lytic Polysaccharide Monooxygenase and a Heme Cytochrome P450 using X-ray and Neutron Scattering.", Ph.D. Dissertation, North Carolina State University (2021).

Schroder G.C., O'Dell W.B., Swartz P.D., Meilleur F., "Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions", Acta Crystallographica Section F, F77, 128-133 (2021).

2020 9 Publications

Coates L., "Ion Permeation in Potassium Ion Channels", Acta Crystallographica Section D, D76, 326-331 (2020).

Coates L., Sullivan B., "The macromolecular neutron diffractometer at the spallation neutron source", Methods in Enzymology, 634, 87-99 (2020).

Doucet M., Samarakoon A.M., Do C., Heller W.T., Archibald R., Tennant D.A., Proffen T., Granroth G.E., "Machine learning for neutron scattering at ORNL", Machine Learning: Science and Technology, 2, 023001 (2020).

Hiromoto T., Nishikawa K., Inoue S., Matsuura H., Hirano Y., Kurihara K., Kusaka K., Cuneo M.J., Coates L., Tamada T., Higuchi Y., "Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase", Acta Crystallographica Section D, 76, 10, (2020).

Kneller D.W., Phillips G., Kovalevsky A., Coates L., "Room-temperature neutron and X-ray data collection of 3CL Mpro from SARS-CoV-2", Acta Crystallographica Section F, 76, Part 10, 483-487 (2020).

Kneller D.W., Phillips G., Weiss K., Pant S., Zhang Q., O'Neill H.M., Coates L., Kovalevsky A., "Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography", Journal of Biological Chemistry, 295, 50, 17365-17373 (2020).

Langan P.S., Sullivan B., Weiss K., Coates L., "Probing the role of the conserved residue Glu166 in a class A b-lactamase using neutron and X-ray protein crystallography", Acta Crystallographica Section D, D76, 2, 118-123 (2020).

Schroder G.C., Meilleur F., "Neutron crystallography data collection and processing for modelling hydrogen atoms in protein structures", JoVE, 166, e61903 (2020).

Shukla S., "Probing structure, function and dynamics in bacterial primary and secondary transporter-associated binding proteins", Ph.D. Dissertation, University of Tennessee (2020).

2019 11 Publications

Caldararu O., Manzoni F., Oksanen E., Logan D.T., Ryde U., "Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data", Acta Crystallographica Section D, 75, 368-380 (2019).

Caldararu O., Oksanen E., Ryde U., Hedegard E.D., "Correction: Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase", Chemical Science, 10, 8262-8263 (2019).

Caldararu O., Oksanen E., Ryde U., Hedegard E.D., "Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase", Chemical Science, 10, 2, 576-586 (2019).

Coates L., "Protein Crystallography at the Spallation Neutron Source", 3rd International Symposium of Quantum Beam Science at Ibaraki University "Quantum Beam Science in Biology and Soft Materials (ISQBSS2018), JPS Conf. Proc. 25, 011002, (2019).

Kumar P., Agarwal P.K., Waddell M.B., Mittag T., Serpersu E.H., Cuneo M.J., "Low-barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad", Angewandte Chemie International Edition, 131, 16406-16412 (2019).

Langan P.S., Vandavasi V., Sullivan B., Harp J., Weiss K., Coates L., "Crystallization of a potassium ion channel and X-ray and neutron data collection", Acta Crystallographica Section F, 75, 6, (2019).

Lu X.Y., Selvaraj B., Ghimire-Rijal S., Orf G.S., Meilleur F., Blankenship R.E., Cuneo M.J., Myles D.A., "Neutron and X-ray analysis of the Fenna–Matthews–Olson photosynthetic antenna complex from Prosthecochloris aestuarii", Acta Crystallographica Section F, 75, 3, 1-5 (2019).

Ogutu I., "Investigation of the Active Site Maturation and Catalytic Mechanism of Nitrile Hydratases (NHase, E.C.4.2.1.84)", Ph.D. Dissertation, Marquette University (2019).

Sullivan B., Archibald R., Vadavasi V., Langan P.S., Coates L., Lynch V.E., "Volumetric Segmentation via Neural Networks Improves Neutron Crystallography Data Analysis", 2019 19th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing (CCGRID), (2019).

Sullivan B., Archibald R., Vandavasi V., Langan P., Langan P.S., Coates L., Azadmanesh J., Lynch V.E., "BraggNet: integrating Bragg peaks using neural networks", Journal of Applied Crystallography, 52, 854-863 (2019).

Yamada T., Yano N., Hosoya T., Kusaka K., "Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27", Journal of Applied Crystallography, 52, (2019).

2018 14 Publications

Azadmanesh J., Borgstahl G.E., "A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase", Antioxidants, 7, 2, 25 (2018).

Azadmanesh J., Lutz W.E., Weiss K., Coates L., Borgstahl G.E., "Redox manipulation of the manganese metal in human manganese superoxide dismutase for neutron diffraction", Acta Crystallographica Section F, 74, 10, 677-687 (2018).

Coates L., Cao H.B., Chakoumakos B.C., Frontzek M., Hoffmann C., Kovalevsky A., Liu Y., Meilleur F., Dos Santos A.M., Myles D.A., Wang X.P., Ye F., "A suite-level review of the neutron single-crystal diffraction instruments at Oak Ridge National Laboratory", Review of Scientific Instruments, 89, 9, 092802 (2018).

Harp J., Coates L., Sullivan B., Egli M., "Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG)", Acta Crystallographica Section F, 74, 9, 603-609 (2018).

Hussein R., Ibrahim M., Chatterjee R., Coates L., Muh F., Yachandra V.K., Yano J., Kern J., Dobbek H., Zouni A., "Optimizing Crystal Size of Photosystem II by Macroseeding: Towards Neutron Protein Crystallography", Crystal Growth and Design, 18, 1, 85–94 (2018).

Kovalevsky A., Aggarwal M., Velazquez H., Cuneo M.J., Blakeley M.P., Weiss K., Smith J.C., Fisher S.Z., McKenna R., ""To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation", Structure, 26, 3, 383–390 (2018).

Kumar P., Serpersu E.H., Cuneo M.J., "A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad", Science Advances, 4, 4, eaas8667 (2018).

Kwon H., Langan P.S., Coates L., Raven E.L., Moody P.C., "The rise of neutron cryo-crystallography", Acta Crystallographica Section D, 74, 8, 792-799 (2018).

Langan P.S., Vandavasi V., Cooper S.J., Weiss K., Ginell S.L., Parks J.M., Coates L., "Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis", ACS Catalysis, 8, 2428–2437 (2018).

Manzoni F., Wallerstein J., Schrader T.E., Ostermann A., Coates L., Akke M., Blakeley M.P., Oksanen E., Logan D.T., "Elucidation of hydrogen bonding patterns in ligand-free, lactose- and glycerol-bound galectin-3C by neutron crystallography to guide drug design", Journal of Medicinal Chemistry, 61, 10, 4412-4420 (2018).

Meilleur F., Coates L., Cuneo M.J., Kovalevsky A., Myles D.A., "The Neutron Macromolecular Crystallography Instruments at Oak Ridge National Laboratory: Advances, Challenges, and Opportunities", Crystals, 8, 10, 388 (2018).

Prashasti F.N., "Molecular determinants of ligand specificity of aminoglycoside acetyltransferases", Ph.D. Dissertation, University of Tennessee (2018).

Sullivan B., Archibald R., Dobbek H., Bommer M., McFeeters R.L., Coates L., Wang X.P., Gallmeier F.X., Carpenter J.M., Lynch V.E., Langan P., Langan P.S., "Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space", Acta Crystallographica Section D, D74, 10, 946-1038 (2018).

Wang C.L., Paranthaman M.P., Riedel R.A., Hodges J.P., Karlic J.J., Veatch R.A., Li L., Bridges C.A., "Bright Eu2+-activated polycrystalline ceramic neutron scintillators", Nuclear Instruments and Methods in Physics Research Section A, 883, 1-8 (2018).

2017 8 Publications

Azadmanesh J., Trickel S.R., Weiss K., Coates L., Borgstahl G.E., "Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals", Acta Crystallographica Section F, 73, 4, 235-240 (2017).

Bacik J.P., Mekasha S., Forsberg Z., Kovalevsky A., Vaaje-Kolstad G., Eijsink V.G., Nix J.C., Coates L., Cuneo M.J., Unkefer C.J., Chen J.C., "Neutron and atomic resolution X-ray structures of a lytic polysac-charide monooxygenase reveal copper-mediated dioxygen binding and evidence for N-terminal deprotonation", Biochemistry, 56, 20, 2529–2532 (2017).

Bommer M., Coates L., Dau H., Zouni A., Dobbek H., "Protein crystallization and initial neutron diffraction studies of the photosystem II subunit PsbO", Acta Crystallographica Section F, 73, 9, 525-531 (2017).

Coates L., Robertson L., "Ewald: an extended wide-angle Laue diffractometer for the second target station of the Spallation Neutron Source", Journal of Applied Crystallography, 50, 4, 1174-1178 (2017).

Fisher S.Z., Jackson A.J., Kovalevsky A., Oksanen E., Wacklin H., "Chapter 1 - Biological Structures", Vol 49, 1-75 Experimental Methods in the Physical Sciences Elsevier (2017).

Li L., Shukla S., Meilleur F., Standaert R.F., Pierce J., Myles D.A., Cuneo M.J., "Neutron crystallographic studies of T4 lysozyme at cryogenic temperature", Protein Science, 26, 10, 2098–2104 (2017).

Schaffner I., Mlynek G., Flego N., Puehringer D., Libiseller-Egger J., Coates L., Hofbauer S., Bellei M., Furtmuller P.G., Battistuzzi G., Smulevich G., Djinovic-Carugo K., Obinger C., "Molecular mechanism of enzymatic chlorite detoxification: insights from structural and kinetic studies", ACS Catalysis, 7, 11, 7962-7976 (2017).

Vandavasi V., Langan P.S., Weiss K., Parks J.M., Cooper J.B., Ginell S.L., Coates L., "Active Site Protonation States in an Acyl-enzyme Intermediate of a Class A β-lactamase with a Monobactam Substrate", Antimicrobial Agents and Chemotherapy (AAC), 21, 1, e01636-16 (2017).

2016 6 Publications

Langan P.S., Close D.W., Coates L., Rocha R.C., Ghosh K., Kiss C., Waldo G., Freyer J., Kovalevsky A., Bradbury A.R., "Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail", Journal of Molecular Biology, 428, 9, 1776-1789 (2016).

Manzoni F., Saraboji K., Sprenger J., Kumar R., Noresson A.L., Nilsson U.J., Leffler H., Fisher S.Z., Schrader T.E., Ostermann A., Coates L., Blakeley M.P., Oksanen E., Logan D.T., "Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C", Acta Crystallographica Section D, D72, 1194-1202 (2016).

McFeeters H., Vandavasi V., Weiss K., Coates L., McFeeters R.L., "Neutron diffraction analysis of Pseudomonas aeruginosa peptidyl-tRNA hydrolase 1", Acta Crystallographica Section F, 72, Part 3, 220-223 (2016).

O'Dell W.B., Bodenheimer A.M., Meilleur F., "Neutron Protein Crystallography: A Complementary Tool for Locating Hydrogens in Proteins", Archives of Biochemistry and Biophysics, 602, 48-60 (2016).

Vandavasi V., Weiss K., Cooper J.B., Erskine P., Tomanicek S.J., Ostermann A., Schrader T.E., Ginell S.L., Coates L., "Exploring the Mechanism of beta-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography", Journal of Medicinal Chemistry, 59, 1, 474–479 (2016).

Wang C.L., Riedel R.A., "Improved neutron-gamma discrimination for a 6Li-glass neutron detector using digital signal analysis methods", Review of Scientific Instruments, 87, 01, 013301 (2016).

2015 4 Publications

Bacik J.P., Mekasha S., Forsberg Z., Kovalevsky A., Nix J.C., Cuneo M.J., Coates L., Vaaje-Kolstad G., Chen J.C., Eijsink V.G., Unkefer C.J., "Neutron and high-resolution room temperature X-ray diffraction studies of a lytic polysaccharide monooxygenase", Acta Crystallographica Section F, 71, 1448-1452 (2015).

Coates L., "Recent improvements to the macromolecular neutron diffractometer MaNDi at the Spallation Neutron Source", Neutron News, 26, 4, 17-18 (2015).

Coates L., Cuneo M.J., Frost M., He J., Weiss K., Tomanicek S.J., McFeeters H., Vandavasi V., Langan P., Iverson E.B., "The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source", Journal of Applied Crystallography, 48, 4, 1302-1306 (2015).

Wan Q., Parks J.M., Hanson B.L., Fisher S.Z., Ostermann A., Schrader T.E., Graham D.E., Coates L., Langan P., Kovalevsky A., "Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography", Proceedings of the National Academy of Sciences of the United States of America, 112, 40, 12384–12389 (2015).

2014 2 Publications

Coates L., Tomanicek S.J., Schrader T.E., Weiss K., Ng J.D., Juttner P., Ostermann A., "Cryogenic neutron protein crystallography: routine methods and potential benefits", Journal of Applied Crystallography, 47, 4, 1431-1434 (2014).

Golden E.A., Vrielink A., "Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function", Australian Journal of Chemistry, 67, 12, 1751-1762 (2014).