James Holton, PhD
Professor
Biochemistry and Biophysics
School of Medicine

Websites

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• Beamline (tomalbertron.org)

Grants and Projects

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• Eliminating Critical Systematic Errors In Structural Biology With Next-Generation Simulation, NIH, 2017-2022

Publications (73)

Top publication keywords:
Photosystem II Protein ComplexX-RaysMacromolecular SubstancesConnectinPhotosynthesisCrystallizationX-Ray DiffractionProteinsSynchrotronsCrystallography, X-RayModels, MolecularLasersPhotosystem I Protein ComplexProtein ConformationMetalloproteins

• Influence of pump laser fluence on ultrafast myoglobin structural dynamics.
  Nature 2024 Barends TRM, Gorel A, Bhattacharyya S, Schirò G, Bacellar C, Cirelli C, Colletier JP, Foucar L, Grünbein ML, Hartmann E, Hilpert M, Holton JM, Johnson PJM, Kloos M, Knopp G, Marekha B, Nass K, Nass …
• Author Correction: Structural evidence for intermediates during O2 formation in photosystem II.
  Nature 2024 Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable …
• Deep residual networks for crystallography trained on synthetic data.
  Acta crystallographica. Section D, Structural biology 2024 Mendez D, Holton JM, Lyubimov AY, Hollatz S, Mathews II, Cichosz A, Martirosyan V, Zeng T, Stofer R, Liu R, Song J, McPhillips S, Soltis M, Cohen AE
• Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.
  Nature chemistry 2023 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,…
• Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.
  Journal of the American Chemical Society 2023 Doyle MD, Bhowmick A, Wych DC, Lassalle L, Simon PS, Holton J, Sauter NK, Yachandra VK, Kern JF, Yano J, Wall ME

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• Structural evidence for intermediates during O2 formation in photosystem II.
  Nature 2023 Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable …
• Large language models generate functional protein sequences across diverse families.
  Nature biotechnology 2023 Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N
• 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 2022 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
• The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature.
  bioRxiv : the preprint server for biology 2022 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
• Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition.
  Nature communications 2021 Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, …
• Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry.
  Journal of synchrotron radiation 2021 Kristensen LG, Holton JM, Rad B, Chen Y, Petzold CJ, Gupta S, Ralston CY
• Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Ibrahim M, Moriarty NW, Kern J, Holton JM, Brewster AS, Bhowmick A, Bergmann U, Zouni A, Messinger J, Yachandra VK, Yano J, Dobbek H, Sauter NK, Adams PD
• Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
  Science advances 2021 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N,…
• Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase).
  Journal of bioscience and bioengineering 2021 Gee CL, Holton JM, McPherson A
• Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking.
  bioRxiv : the preprint server for biology 2020 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz 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, …
• Beyond integration: modeling every pixel to obtain better structure factors from stills.
  IUCrJ 2020 Mendez D, Bolotovsky R, Bhowmick A, Brewster AS, Kern J, Yano J, Holton JM, Sauter NK
• Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N,…
• Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures.
  Proceedings of the National Academy of Sciences of the United States of America 2020 de la Mora E, Coquelle N, Bury CS, Rosenthal M, Holton JM, Carmichael I, Garman EF, Burghammer M, Colletier JP, Weik M
• Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction.
  Acta crystallographica. Section D, Structural biology 2020 Sauter NK, Kern J, Yano J, Holton JM
• Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.
  Cell chemical biology 2019 Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM
• Challenge data set for macromolecular multi-microcrystallography.
  Acta crystallographica. Section D, Structural biology 2019 Holton JM
• Structures of the intermediates of Kok's photosynthetic water oxidation clock.
  Nature 2018 Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, …
• Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.
  Nature structural & molecular biology 2017 Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA
• Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin.
  Scientific data 2017 Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Batyuk A, Ciftci H, Guillet S, Hayes MJ, Hayes B, Lane TJ, Liang M, Lundström U, Koglin JE, Mgbam P, Rao Y, Rendahl T, Rodriguez E,…
• Responses to `Atomic resolution': a badly abused term in structural biology.
  Acta crystallographica. Section D, Structural biology 2017 Chiu W, Holton J, Langan P, Sauter NK, Schlichting I, Terwilliger T, Martin JL, Read RJ, Wakatsuki S
• Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.
  Nature communications 2016 Hunter MS, Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Ciftci H, Guillet S, Hayes MJ, Lane TJ, Liang M, Lundström U, Koglin JE, Mgbam P, Rao Y, Zhang L, Wakatsuki S, Holton JM…
• Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.
  eLife 2016 Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT
• Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.
  eLife 2015 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, …
• Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion.
  Cell 2015 Rosenberg OS, Dovala D, Li X, Connolly L, Bendebury A, Finer-Moore J, Holton J, Cheng Y, Stroud RM, Cox JS
• Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.
  Nature methods 2014 Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC
• Goniometer-based femtosecond crystallography with X-ray free electron lasers.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman…
• The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.
  The FEBS journal 2014 Holton JM, Classen S, Frankel KA, Tainer JA
• Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Mavrici D, Marakalala MJ, Holton JM, Prigozhin DM, Gee CL, Zhang YJ, Rubin EJ, Alber T
• Protein structural ensembles are revealed by redefining X-ray electron density noise.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Lang PT, Holton JM, Fraser JS, Alber T
• Predicting the X-ray lifetime of protein crystals.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Zeldin OB, Brockhauser S, Bremridge J, Holton JM, Garman EF
• Crystallographic data processing for free-electron laser sources.
  Acta crystallographica. Section D, Biological crystallography 2013 White TA, Barty A, Stellato F, Holton JM, Kirian RA, Zatsepin NA, Chapman HN
• Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.
  Journal of applied crystallography 2013 Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer JA
• The point-spread function of fiber-coupled area detectors.
  Journal of synchrotron radiation 2012 Holton JM, Nielsen C, Frankel KA
• Time-resolved protein nanocrystallography using an X-ray free-electron laser.
  Optics express 2012 Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J, Arnlund D, Bajt S, Barends TR, Barthelmess M, Bogan MJ, Bostedt C, Bottin H, Bozek JD, Caleman C, Coppola N, Davidsson J, …
• Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser.
  Physical review. B, Condensed matter and materials physics 2011 Lomb L, Barends TR, Kassemeyer S, Aquila A, Epp SW, Erk B, Foucar L, Hartmann R, Rudek B, Rolles D, Rudenko A, Shoeman RL, Andreasson J, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, …
• Accessing protein conformational ensembles using room-temperature X-ray crystallography.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T
• Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Chou S, Krasileva KV, Holton JM, Steinbrenner AD, Alber T, Staskawicz BJ
• Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals.
  Acta crystallographica. Section A, Foundations of crystallography 2011 Kirian RA, White TA, Holton JM, Chapman HN, Fromme P, Barty A, Lomb L, Aquila A, Maia FR, Martin AV, Fromme R, Wang X, Hunter MS, Schmidt KE, Spence JC
• Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals.
  Optics express 2011 Spence JC, Kirian RA, Wang X, Weierstall U, Schmidt KE, White T, Barty A, Chapman HN, Marchesini S, Holton J
• Femtosecond X-ray protein nanocrystallography.
  Nature 2011 Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A, Hunter MS, Schulz J, DePonte DP, Weierstall U, Doak RB, Maia FR, Martin AV, Schlichting I, Lomb L, Coppola N, Shoeman RL, Epp SW, Hartmann…
• Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system.
  Journal of synchrotron radiation 2010 Classen S, Rodic I, Holton J, Hura GL, Hammel M, Tainer JA
• Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
  Protein science : a publication of the Protein Society 2010 Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T
• The minimum crystal size needed for a complete diffraction data set.
  Acta crystallographica. Section D, Biological crystallography 2010 Holton JM, Frankel KA
• Femtosecond protein nanocrystallography-data analysis methods.
  Optics express 2010 Kirian RA, Wang X, Weierstall U, Schmidt KE, Spence JC, Hunter M, Fromme P, White T, Chapman HN, Holton J
• An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy.
  Journal of electron spectroscopy and related phenomena 2009 Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JC, Starodub D
• A beginner's guide to radiation damage.
  Journal of synchrotron radiation 2009 Holton JM
• Determination of X-ray flux using silicon pin diodes.
  Journal of synchrotron radiation 2009 Owen RL, Holton JM, Schulze-Briese C, Garman EF
• 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins.
  Journal of structural and functional genomics 2009 Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W
• Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75.
  Nature structural & molecular biology 2008 Berndsen CE, Tsubota T, Lindner SE, Lee S, Holton JM, Kaufman PD, Keck JL, Denu JM
• Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.
  Protein science : a publication of the Protein Society 2007 Sales M, Plecs JJ, Holton JM, Alber T
• A steric block in translation caused by the antibiotic spectinomycin.
  ACS chemical biology 2007 Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JHD
• Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.
  Nature structural & molecular biology 2007 Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH
• Structural insight into KCNQ (Kv7) channel assembly and channelopathy.
  Neuron 2007 Howard RJ, Clark KA, Holton JM, Minor DL
• Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity.
  Nature 2007 Huang DT, Hunt HW, Zhuang M, Ohi MD, Holton JM, Schulman BA
• XANES measurements of the rate of radiation damage to selenomethionine side chains.
  Journal of synchrotron radiation 2006 Holton JM
• Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis.
  Journal of molecular biology 2006 Rho BS, Hung LW, Holton JM, Vigil D, Kim SI, Park MS, Terwilliger TC, Pédelacq JD
• Structures of the bacterial ribosome at 3.5 A resolution.
  Science (New York, N.Y.) 2005 Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH
• Structural and mechanistic studies of VPS4 proteins.
  The EMBO journal 2005 Scott A, Chung HY, Gonciarz-Swiatek M, Hill GC, Whitby FG, Gaspar J, Holton JM, Viswanathan R, Ghaffarian S, Hill CP, Sundquist WI
• Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1.
  Molecular cell 2005 Huang DT, Paydar A, Zhuang M, Waddell MB, Holton JM, Schulman BA
• Crystal structure of PriB, a component of the Escherichia coli replication restart primosome.
  Structure (London, England : 1993) 2004 Lopper M, Holton JM, Keck JL
• Suite of three protein crystallography beamlines with single superconducting bend magnet as the source.
  Journal of synchrotron radiation 2004 MacDowell AA, Celestre RS, Howells M, McKinney W, Krupnick J, Cambie D, Domning EE, Duarte RM, Kelez N, Plate DW, Cork CW, Earnest TN, Dickert J, Meigs G, Ralston C, Holton JM, Alber T, Berger JM, …
• A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8.
  Nature structural & molecular biology 2004 Huang DT, Miller DW, Mathew R, Cassell R, Holton JM, Roussel MF, Schulman BA
• Ubiquitin recognition by the human TSG101 protein.
  Molecular cell 2004 Sundquist WI, Schubert HL, Kelly BN, Hill GC, Holton JM, Hill CP
• Automated protein crystal structure determination using ELVES.
  Proceedings of the National Academy of Sciences of the United States of America 2004 Holton J, Alber T
• The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1.
  Molecular cell 2003 Walden H, Podgorski MS, Huang DT, Miller DW, Howard RJ, Minor DL, Holton JM, Schulman BA
• Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins.
  Proceedings of the National Academy of Sciences of the United States of America 2001 Lougheed JC, Holton JM, Alber T, Bazan JF, Handel TM
• Crystallographic analysis of CD40 recognition and signaling by human TRAF2.
  Proceedings of the National Academy of Sciences of the United States of America 1999 McWhirter SM, Pullen SS, Holton JM, Crute JJ, Kehry MR, Alber T
• Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants.
  Protein science : a publication of the Protein Society 1997 Morgan CS, Holton JM, Olafson BD, Bjorkman PJ, Mayo SL