The Thompson Lab

Publications

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity

St-Jacques AD, Rodriguez JM, Eason MG, Foster SM, Khan ST, Damry AM, Goto NK, Thompson MC, Chica RA. (2022) Nature Communications.

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Mapping Protein Dynamics at High Spatial Resolution with Temperature-Jump X-ray Crystallography

Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O’Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC. (2023) Nature Chemistry.

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Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography

Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR III, Brewster AS, Sauter NK, Young ID, Wolff AM, Tiwari VK, Kumar N, Berkowitz DB, Hadt RG, Thompson MC, Follmer AH, Wall ME, Wilson MA. (2023) bioRxiv.”

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Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods

Thompson MC (2023) Methods in Enzymology.

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Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Diaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS. (2023) bioRxiv.

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The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature

Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. (2022) Science Advances.

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Accurately positioning functional residues with robotics-inspired computational protein design

Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchuir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T. (2022) PNAS.

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Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing

Legault S, Fraser-Halberg DP, McAnelly RL, Eason MG, Thompson MC, Chica RA. (2022) Chemical Science.

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Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Diaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs M, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. (2021) Science Advances.

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An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj VV, Hoppe N, Boone M, Billesboelle C, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chi US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, Garcia-Sastre A, Ott M, Vignuzzi M, Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, Walter P, Manglik A. (2020) Science.

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Ensemble-based enzyme design can recapitulate the effects of directed evolution in silico

Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA. (2020) Nature Communications.

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Expanding the space of protein geometries by computational design of ​de novo fold families

Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. (2020) Science.

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Advances in methods for atomic resolution macromolecular structure determination

Thompson MC, Yeates TO, Rodriguez JA. (2020) F1000Res.

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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson A, Tanaka R, Tanaka T, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC. (2020) IUCrJ.

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Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

Dasgupta M, Budday D, Oliveira SHP, Madzelan P, Marchany-Rivera D, Seravalli J, Hayes B, Sierra RG, Boutet S, Hunter MS, Alonso-Mori R, Batyuk A, Wierman J, Lyubimov A, Brewster AS, Sauter NK, Applegate GA, Tiwari VK, Berkowitz DB, Thompson MC, Cohen AE, Fraser JS, Wall ME, van den Bedem H, Wilson MA. (2019) PNAS.

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Computational design of a modular protein sense/response system

Glasgow AA, Huang Y, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. (2019) Science.

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Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme

Thompson MC, Barad BA, Wolff AM, Cho HS, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. (2019) Nature Chemistry.

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Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

Thompson MC, Cascio D, Yeates TO. (2018) Acta Cryst D.

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Allosteric Inhibitors, Crystallography and Comparative Analysis Reveal Network of Coordinated Movement Across Human Herpesvirus Proteases

Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS. (2017) JACS.

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Identifying and Overcoming Crystal Pathologies: Disorder and Twinning

Thompson MC. (2017) Protein Crystallography: Methods and Protocols.

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Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin

Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS. (2017) Structure.

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Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein

Jorda J, Leibly DJ, Thompson MC, Yeates TO. (2016) Chemical Communications.

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An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein

Thompson MC, Cascio D, Leibly DJ, Yeates TO. (2015) Protein Science.

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Mapping the Conformational Landscape of a Dynamic Enzyme by Multitemperature and XFEL Crystallography

Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. (2015) eLife.

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Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor

Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO. (2014) Acta Cryst F.

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Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein

Thompson MC, Wheatley NM, Jorda J, Sawaya MR, Gidaniyan SD, Ahmed H, Yang Z, McCarty KN, Whitelegge JP, Yeates TO. (2014) J. Mol. Bio.

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A challenging interpretation of a hexagonally layered protein structure

Thompson MC, Yeates TO. (2013) Acta Cryst D.

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The protein shells of bacterial microcompartment organelles

Yeates TO, Thompson MC, Bobik TA. (2011) Curr. Opin. Struct. Bio..

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