User Ryan Knihtila at IMAGINE (CG-4D)

Publications from Research Conducted at IMAGINE

The following 69 publications were retrieved from PuSH (Publications of SNS and HFIR)

2023 1 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).

2022 9 Publications

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).
Drago V., "Microgravity Crystallization and Neutron Diffraction of PLP-Dependent Enzymes", Ph.D. Dissertation, University of Toledo (2022).
Drago V., Devos J.M., Blakeley M.P., Forsyth V.T., Kovalevsky A., Schall C.A., Mueser T.C., "Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction", npj Microgravity, 8, 13 (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).
Moreno-Chicano T., Carey L.M., Axford D., Beale J.H., Doak R.B., Duyvesteyn H.M., Ebrahim A., Henning R., Monteiro D.C., Myles D.A., et al. ., "Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature", IUCrJ, 9, 610-624 (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).
Shukla S., Myles D.A., Cuneo M.J., "Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography", Scientific Reports, 12, 17647 (2022).

2021 7 Publications

Gerlits O., Blakeley M.P., Keen D.A., Radic Z., Kovalevsky A., "Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure", Current Research in Structural Biology, 3, 206-215 (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).
Schroder G.C., O'Dell W.B., Swartza 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).
Wan Q., Bennett B.C., Wymore T., Li Z., Wilson M.A., Brooks C.L., Langan P., Kovalevsky A., Dealwis C., "Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid–Base Catalysis", ACS Catalysis, 11, 5873–5884 (2021).

2020 11 Publications

Gerlits O., Weiss K., Blakeley M.P., Veglia G., Taylor S.S., Kovalevsky A., "Protein kinase A in the neutron beam: Insights for catalysis from directly observing protons", Methods in Enzymology, 634, 311-331 (2020).
Kita A., Morimoto Y., "Hydrogen/deuterium exchange behavior in tetragonal hen egg-white lysozyme crystals affected by solution state", Journal of Applied Crystallography, 53, 837-840 (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).
Kovalevsky A., Gerlits O., Beltran K., Weiss K., Keen D.A., Blakeley M.P., Louis J.M., Weber I.T., "Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease", Methods in Enzymology, 634, 257-279 (2020).
Kumar M., Mandal K., Blakeley M.P., Wymore T., Kent S.B., Louis J.M., Das A., Kovalevsky A., "Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design", ACS Omega, 5, 11605-11617 (2020).
Meilleur F., Kovalevsky A., Myles D.A., "IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor", Methods in Enzymology, 634, 69-85 (2020).
Mueser T.C., Drago V., Kovalevsky A., Dajnowicz S., "Pyridoxal 5′-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase", Methods in Enzymology, 634, 333-359 (2020).
Pierce J., Cuneo M.J., Jennings A., Li L., Meilleur F., Zhao J.K., Myles D.A., "Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals", Methods in Enzymology, 634, 153-175 (2020).

2019 8 Publications

AlMishwat M.A., "Structural and Mechanistic Enzymology of Nucleotide Incorporation by A-Family DNA Polymerases", Ph.D. Dissertation, Pennsylvania State University (2019).
Gerlits O., Weiss K., Blakeley M.P., Veglia G., Taylor S.S., Kovalevsky A., "Zooming in on Protons: neutron structure of protein kinase A trapped in a product complex", Science Advances, 5, 3, eaav0482 (2019).
Knihtila R., Volmar A.Y., Meilleur F., Mattos C., "Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras", Acta Crystallographica Section F, 75, 2, 111-115 (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).
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).
Park J., Selvaraj B., McShan A.C., Boyken S.E., Wei K.Y., Oberdorfer G., DeGrado W., Sgourakis N.G., Cuneo M.J., Myles D.A., Baker D., "De novo design of a homo-trimeric amantadine-binding protein", eLife, 8, e47839 (2019).
Pierce J., Crow L., Cuneo M.J., Edwards M., Herwig K.W., Jennings A.R., Jones A.B., Li L., Meilleur F., Myles D.A., Robertson L., Standaert R.F., Wonder A., Zhao J.K., "A prototype system for dynamically polarized neutron protein crystallography", Nuclear Instruments and Methods in Physics Research Section A, 940, 430-434 (2019).

2018 10 Publications

Banco M.T., "The Structural, Enzymatic, and Inhibitory Studies of Three Enzymes Involved in Sulfur Metabolism", Ph.D. Dissertation, University of Toledo (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).
Dajnowicz S., "Electronic Modulation in Pyridoxal-5’-Phosphate-Dependent Enzymes", Ph.D. Dissertation, University of Toledo (2018).
Dajnowicz S., Parks J.M., Hu X., Johnston R.C., Kovalevsky A., Mueser T.C., "Hyperconjugation Promotes Catalysis in a Pyridoxal 5′-Phosphate-Dependent Enzyme", ACS Catalysis, 8, 6733–6737 (2018).
Gerlits O., Campbell J.C., Blakeley M.P., Kim C., Kovalevsky A., "Neutron Crystallography Detects Differences in Protein Dynamics: Structure of the PKG II Cyclic Nucleotide Binding Domain in Complex with an Activator", Biochemistry, 57, 12, 1833-1837 (2018).
Haberl B., Dissanayake S., Wu Y., Myles D.A., Dos Santos A.M., Loguillo M.J., Rucker G., Armitage D., Cochran M.J., Andrews K.M., Hoffmann C., Cao H.B., Matsuda M., Meilleur F., Ye F., Molaison J.J., Boehler R., "Next-generation diamond cell and applications to single-crystal neutron diffraction", Review of Scientific Instruments, 89, 9, 092902 (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).
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).
Schroder G.C., O'Dell W.B., Myles D.A., Kovalevsky A., Meilleur F., "IMAGINE: neutrons reveal enzyme chemistry", Acta Crystallographica Section D, 74, 8, 778–786 (2018).
Vandavasi V., Blakeley M.P., Keen D.A., Hu L.R., Huang Z., Kovalevsky A., "Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA", Structure, 26, 12, 1645-1650.e3 (2018).

2017 11 Publications

Bodenheimer A.M., O'Dell W.B., Stanley C.B., Meilleur F., "Structural studies of Neurospora crassa LPMO9D and redox partner CDHIIA using neutron crystallography and small-angle scattering", Carbohydrate Research, 448, 200-204 (2017).
Carey L.M., "Probing the Structure-Function Relationship of a Multifunctional Enzyme using Crystallographic Diffraction Methods", Ph.D. Dissertation, North Carolina State University (2017).
Dajnowicz S., Johnston R.C., Parks J.M., Blakeley M.P., Keen D.A., Weiss K., Gerlits O., Kovalevsky A., Mueser T.C., "Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme", Nature Communications, 8, 1, 955 (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).
Golden E.A., Yu L.J., Meilleur F., Blakeley M.P., Duff A.P., Karton A., Vrielink A., "An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase", Scientific Reports, 7, 40517 (2017).
Hiromoto T., Meilleur F., Shimizu R., Shibazaki C., Adachi M., Tamada T., Kuroki R., "Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type", Protein Science, 26, 10, 1953–1963 (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).
O'Dell W.B., Agarwal P.K., Meilleur F., "Oxygen activation at the active site of a fungal lytic polysaccharide monooxygenase", Angewandte Chemie International Edition, 56, 3, 767-770 (2017).
O'Dell W.B., Swartz P.D., Weiss K., Meilleur F., "Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction", Acta Crystallographica Section F, 73, 2, 70-78 (2017).

2016 6 Publications

Aggarwal M., Kovalevsky A., Velazquez H., Fisher S.Z., Smith J.C., McKenna R., "Neutron Structure of Human Carbonic Anhydrase II in Complex with Methazolamide: Mapping the Solvent and Hydrogen-Bonding Patterns of an Effective Clinical Drug", IUCrJ, 3, Part 5, 319-325 (2016).
Banco M.T., Mishra V., Ostermann A., Schrader T.E., Evans G.B., Kovalevsky A., Ronning D.R., "Neutron structures of the Helicobacter pylori 5′-methylthioadenosine nucleosidase highlight proton sharing and protonation states", Proceedings of the National Academy of Sciences of the United States of America, 113, 48, 13756–13761 (2016).
Bodenheimer A.M., "Structural Characterization of the Fungal Cellulose Degrading Enzymes Cel7A and Cellobiose Dehydrogenase IIA", Ph.D. Dissertation, North Carolina State University (2016).
Gerlits O., Wymore T., Das A., Shen C.H., Parks J.M., Smith J.C., Weiss K., Keen D.A., Blakeley M.P., Louis J.M., Langan P., Weber I.T., Kovalevsky A., "Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site", Angewandte Chemie International Edition, 55, 16, 4924–4927 (2016).
Knihtila R., "GTP Hydrolysis in RAS: How mutations affect hydrogen bonding and catalysis", Ph.D. Dissertation, Northeastern University (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).

2015 2 Publications

Golden E.A., "Finding hydrogens: elucidating the redox chemistry of cholesterol oxidase through neutron diffraction studies", Ph.D. Dissertation, University of Western Australia (2015).
Knihtila R., Holzapfel G., Weiss K., Meilleur F., Mattos C., "Neutron Crystal Structure of RAS GTPase puts in question the Protonation State of the GTP γ-Phosphate", Journal of Biological Chemistry, 290, 31025-31036 (2015).

2014 3 Publications

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).
Wan Q., Bennett B.C., Wilson M.A., Kovalevsky A., Langan P., Howell E.E., Dealwis C., "Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography", Proceedings of the National Academy of Sciences of the United States of America, 111, 51, 18225-18230 (2014).
Wan Q., Kovalevsky A., Wilson M.A., Bennett B.C., "Preliminary joint Xray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP", Acta Crystallographica Section F, 70, 6, 814-818 (2014).

2013 1 Publications

Meilleur F., Munshi P., Robertson L., Stoica A.D., Crow L., Kovalevsky A., Koritsanszky T., Chakoumakos B.C., Blessing R., Myles D.A., "The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography", Acta Crystallographica Section D, 69, 2157-2160 (2013).