James Holton, PhD

Title(s)Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Address600 16th St, #S414
San Francisco CA 94158
ORCID ORCID Icon0000-0002-0596-0137 Additional info
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    Eliminating Critical Systematic Errors In Structural Biology With Next-Generation Simulation
    NIH R01GM124149Sep 1, 2017 - May 31, 2022
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature. 2024 Feb; 626(8000):905-911. 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 Kovacs G, Ozerov D, Stricker M, Weik M, Doak RB, Shoeman RL, Milne CJ, Huix-Rotllant M, Cammarata M, Schlichting I. PMID: 38355794; PMCID: PMC10881388.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    2. Author Correction: Structural evidence for intermediates during O2 formation in photosystem II. Nature. 2024 Feb; 626(7999):E12. 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 SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. PMID: 38291188; PMCID: PMC10866699.
      View in: PubMed   Mentions:    Fields:    
    3. Deep residual networks for crystallography trained on synthetic data. Acta Crystallogr D Struct Biol. 2024 Jan 01; 80(Pt 1):26-43. 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. PMID: 38164955; PMCID: PMC10833344.
      View in: PubMed   Mentions:
    4. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nat Chem. 2023 Nov; 15(11):1549-1558. 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. PMID: 37723259; PMCID: PMC10624634.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    5. Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography. J Am Chem Soc. 2023 Jul 12; 145(27):14621-14635. Doyle MD, Bhowmick A, Wych DC, Lassalle L, Simon PS, Holton J, Sauter NK, Yachandra VK, Kern JF, Yano J, Wall ME. PMID: 37369071; PMCID: PMC10347547.
      View in: PubMed   Mentions: 4     Fields:    
    6. Structural evidence for intermediates during O2 formation in photosystem II. Nature. 2023 May; 617(7961):629-636. 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 SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. PMID: 37138085; PMCID: PMC10191843.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    7. Large language models generate functional protein sequences across diverse families. Nat Biotechnol. 2023 08; 41(8):1099-1106. Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N. PMID: 36702895; PMCID: PMC10400306.
      View in: PubMed   Mentions: 77     Fields:    Translation:Cells
    8. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Sci Adv. 2022 May 27; 8(21):eabo5083. 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. PMID: 35622909; PMCID: PMC9140965.
      View in: PubMed   Mentions: 14     Fields:    
    9. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. bioRxiv. 2022 Feb 09. 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. PMID: 35169801; PMCID: PMC8845425.
      View in: PubMed   Mentions:
    10. Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition. Nat Commun. 2021 11 11; 12(1):6531. 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, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J. PMID: 34764256; PMCID: PMC8585918.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    11. Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry. J Synchrotron Radiat. 2021 Sep 01; 28(Pt 5):1333-1342. Kristensen LG, Holton JM, Rad B, Chen Y, Petzold CJ, Gupta S, Ralston CY. PMID: 34475282; PMCID: PMC8415330.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    12. 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. Proc Natl Acad Sci U S A. 2021 06 15; 118(24). 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. PMID: 34117122; PMCID: PMC8214684.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    13. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 04; 7(16). 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, 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 MR, 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, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. PMID: 33853786; PMCID: PMC8046379.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    14. Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase). J Biosci Bioeng. 2021 Jun; 131(6):605-612. Gee CL, Holton JM, McPherson A. PMID: 33814275; PMCID: PMC8187280.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    15. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv. 2020 Nov 24. 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, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Neto JB, 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, Johannes Gregor Matthias Rack, 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. PMID: 33269349; PMCID: PMC7709169.
      View in: PubMed   Mentions:
    16. Beyond integration: modeling every pixel to obtain better structure factors from stills. IUCrJ. 2020 Nov 01; 7(Pt 6):1151-1167. Mendez D, Bolotovsky R, Bhowmick A, Brewster AS, Kern J, Yano J, Holton JM, Sauter NK. PMID: 33209326; PMCID: PMC7642780.
      View in: PubMed   Mentions: 5     Fields:    
    17. Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A. 2020 06 09; 117(23):12624-12635. 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, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. PMID: 32434915; PMCID: PMC7293653.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    18. Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. Proc Natl Acad Sci U S A. 2020 02 25; 117(8):4142-4151. de la Mora E, Coquelle N, Bury CS, Rosenthal M, Holton JM, Carmichael I, Garman EF, Burghammer M, Colletier JP, Weik M. PMID: 32047034; PMCID: PMC7049125.
      View in: PubMed   Mentions: 52     Fields:    Translation:Cells
    19. Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction. Acta Crystallogr D Struct Biol. 2020 Feb 01; 76(Pt 2):176-192. Sauter NK, Kern J, Yano J, Holton JM. PMID: 32038048; PMCID: PMC7008510.
      View in: PubMed   Mentions: 7  Translation:HumansAnimals
    20. Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite. Cell Chem Biol. 2019 05 16; 26(5):674-685.e6. Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM. PMID: 30853418; PMCID: PMC7185887.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    21. Challenge data set for macromolecular multi-microcrystallography. Acta Crystallogr D Struct Biol. 2019 Feb 01; 75(Pt 2):113-122. Holton JM. PMID: 30821701; PMCID: PMC6400260.
      View in: PubMed   Mentions: 3  Translation:HumansAnimalsCells
    22. Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature. 2018 11; 563(7731):421-425. 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, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK. PMID: 30405241; PMCID: PMC6485242.
      View in: PubMed   Mentions: 120     Fields:    Translation:Cells
    23. Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Nat Struct Mol Biol. 2017 Oct; 24(10):825-833. Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA. PMID: 28892041; PMCID: PMC5961731.
      View in: PubMed   Mentions: 56     Fields:    Translation:Cells
    24. Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin. Sci Data. 2017 04 25; 4:170055. 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, Zhang L, Wakatsuki S, Boutet S, Holton JM, Hunter MS. PMID: 28440794; PMCID: PMC5404608.
      View in: PubMed   Mentions: 1     Fields:    
    25. Responses to `Atomic resolution': a badly abused term in structural biology. Acta Crystallogr D Struct Biol. 2017 04 01; 73(Pt 4):381-383. Chiu W, Holton J, Langan P, Sauter NK, Schlichting I, Terwilliger T, Martin JL, Read RJ, Wakatsuki S. PMID: 28375150.
      View in: PubMed   Mentions: 2  
    26. Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Nat Commun. 2016 11 04; 7:13388. 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, Boutet S. PMID: 27811937; PMCID: PMC5097167.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    27. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Elife. 2016 10 12; 5. Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. PMID: 27731796; PMCID: PMC5094853.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    28. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife. 2015 Sep 30; 4. 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. PMID: 26422513; PMCID: PMC4721965.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    29. Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion. Cell. 2015 Apr 23; 161(3):501-512. Rosenberg OS, Dovala D, Li X, Connolly L, Bendebury A, Finer-Moore J, Holton J, Cheng Y, Stroud RM, Cox JS. PMID: 25865481; PMCID: PMC4409929.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    30. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nat Methods. 2015 Feb; 12(2):127-30. Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC. PMID: 25532136; PMCID: PMC4312553.
      View in: PubMed   Mentions: 21     Fields:    
    31. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):17122-7. 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 B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO. PMID: 25362050; PMCID: PMC4260607.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    32. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J. 2014 Sep; 281(18):4046-60. Holton JM, Classen S, Frankel KA, Tainer JA. PMID: 25040949; PMCID: PMC4282448.
      View in: PubMed   Mentions: 48     Fields:    Translation:Cells
    33. Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC. Proc Natl Acad Sci U S A. 2014 Jun 03; 111(22):8037-42. Mavrici D, Marakalala MJ, Holton JM, Prigozhin DM, Gee CL, Zhang YJ, Rubin EJ, Alber T. PMID: 24843173; PMCID: PMC4050617.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    34. Protein structural ensembles are revealed by redefining X-ray electron density noise. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):237-42. Lang PT, Holton JM, Fraser JS, Alber T. PMID: 24363322; PMCID: PMC3890839.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    35. Predicting the X-ray lifetime of protein crystals. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20551-6. Zeldin OB, Brockhauser S, Bremridge J, Holton JM, Garman EF. PMID: 24297937; PMCID: PMC3870734.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    36. Crystallographic data processing for free-electron laser sources. Acta Crystallogr D Biol Crystallogr. 2013 Jul; 69(Pt 7):1231-40. White TA, Barty A, Stellato F, Holton JM, Kirian RA, Zatsepin NA, Chapman HN. PMID: 23793149; PMCID: PMC3689526.
      View in: PubMed   Mentions: 78     Fields:    
    37. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr. 2013 Feb 01; 46(Pt 1):1-13. Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer JA. PMID: 23396808; PMCID: PMC3547225.
      View in: PubMed   Mentions: 144  
    38. The point-spread function of fiber-coupled area detectors. J Synchrotron Radiat. 2012 Nov; 19(Pt 6):1006-11. Holton JM, Nielsen C, Frankel KA. PMID: 23093762; PMCID: PMC3480276.
      View in: PubMed   Mentions: 8     Fields:    
    39. Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt Express. 2012 Jan 30; 20(3):2706-16. 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, DePonte DP, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Fromme R, Graafsma H, Grotjohann I, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hau-Riege S, Hauser G, Hirsemann H, Holl P, Holton JM, Hömke A, Johansson L, Kimmel N, Kassemeyer S, Krasniqi F, Kühnel KU, Liang M, Lomb L, Malmerberg E, Marchesini S, Martin AV, Maia FR, Messerschmidt M, Nass K, Reich C, Neutze R, Rolles D, Rudek B, Rudenko A, Schlichting I, Schmidt C, Schmidt KE, Schulz J, Seibert MM, Shoeman RL, Sierra R, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Williams GJ, Weidenspointner G, Weierstall U, Wunderer C, Barty A, Spence JC, Chapman HN. PMID: 22330507; PMCID: PMC3413412.
      View in: PubMed   Mentions: 88     Fields:    Translation:Cells
    40. Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys Rev B Condens Matter Mater Phys. 2011 Dec 01; 84(21):214111. 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, Caleman C, Coffee R, Coppola N, Deponte DP, Doak RB, Ekeberg T, Fleckenstein H, Fromme P, Gebhardt M, Graafsma H, Gumprecht L, Hampton CY, Hartmann A, Hauser G, Hirsemann H, Holl P, Holton JM, Hunter MS, Kabsch W, Kimmel N, Kirian RA, Liang M, Maia FR, Meinhart A, Marchesini S, Martin AV, Nass K, Reich C, Schulz J, Seibert MM, Sierra R, Soltau H, Spence JC, Steinbrener J, Stellato F, Stern S, Timneanu N, Wang X, Weidenspointner G, Weierstall U, White TA, Wunderer C, Chapman HN, Ullrich J, Strüder L, Schlichting I. PMID: 24089594; PMCID: PMC3786679.
      View in: PubMed   Mentions: 59  
    41. Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci U S A. 2011 Sep 27; 108(39):16247-52. Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. PMID: 21918110; PMCID: PMC3182744.
      View in: PubMed   Mentions: 292     Fields:    Translation:Cells
    42. Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces. Proc Natl Acad Sci U S A. 2011 Aug 09; 108(32):13323-8. Chou S, Krasileva KV, Holton JM, Steinbrenner AD, Alber T, Staskawicz BJ. PMID: 21788488; PMCID: PMC3156156.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
    43. Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallogr A. 2011 Mar; 67(Pt 2):131-40. 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. PMID: 21325716; PMCID: PMC3066792.
      View in: PubMed   Mentions: 75     Fields:    Translation:Cells
    44. Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals. Opt Express. 2011 Feb 14; 19(4):2866-73. Spence JC, Kirian RA, Wang X, Weierstall U, Schmidt KE, White T, Barty A, Chapman HN, Marchesini S, Holton J. PMID: 21369108.
      View in: PubMed   Mentions: 29     Fields:    
    45. Femtosecond X-ray protein nanocrystallography. Nature. 2011 Feb 03; 470(7332):73-7. 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 R, Rolles D, Rudenko A, Foucar L, Kimmel N, Weidenspointner G, Holl P, Liang M, Barthelmess M, Caleman C, Boutet S, Bogan MJ, Krzywinski J, Bostedt C, Bajt S, Gumprecht L, Rudek B, Erk B, Schmidt C, Hömke A, Reich C, Pietschner D, Strüder L, Hauser G, Gorke H, Ullrich J, Herrmann S, Schaller G, Schopper F, Soltau H, Kühnel KU, Messerschmidt M, Bozek JD, Hau-Riege SP, Frank M, Hampton CY, Sierra RG, Starodub D, Williams GJ, Hajdu J, Timneanu N, Seibert MM, Andreasson J, Rocker A, Jönsson O, Svenda M, Stern S, Nass K, Andritschke R, Schröter CD, Krasniqi F, Bott M, Schmidt KE, Wang X, Grotjohann I, Holton JM, Barends TR, Neutze R, Marchesini S, Fromme R, Schorb S, Rupp D, Adolph M, Gorkhover T, Andersson I, Hirsemann H, Potdevin G, Graafsma H, Nilsson B, Spence JC. PMID: 21293373; PMCID: PMC3429598.
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    46. Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system. J Synchrotron Radiat. 2010 Nov; 17(6):774-81. Classen S, Rodic I, Holton J, Hura GL, Hammel M, Tainer JA. PMID: 20975223; PMCID: PMC2964114.
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    47. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci. 2010 Jul; 19(7):1420-31. Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. PMID: 20499387; PMCID: PMC2974833.
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    48. The minimum crystal size needed for a complete diffraction data set. Acta Crystallogr D Biol Crystallogr. 2010 Apr; 66(Pt 4):393-408. Holton JM, Frankel KA. PMID: 20382993; PMCID: PMC2852304.
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    49. Femtosecond protein nanocrystallography-data analysis methods. Opt Express. 2010 Mar 15; 18(6):5713-23. Kirian RA, Wang X, Weierstall U, Schmidt KE, Spence JC, Hunter M, Fromme P, White T, Chapman HN, Holton J. PMID: 20389587; PMCID: PMC4038330.
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    50. An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. J Electron Spectros Relat Phenomena. 2009 Mar 01; 170(1-3):4-12. 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. PMID: 20463854; PMCID: PMC2867487.
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    51. A beginner's guide to radiation damage. J Synchrotron Radiat. 2009 Mar; 16(Pt 2):133-42. Holton JM. PMID: 19240325; PMCID: PMC2651760.
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    52. Determination of X-ray flux using silicon pin diodes. J Synchrotron Radiat. 2009 Mar; 16(Pt 2):143-51. Owen RL, Holton JM, Schulze-Briese C, Garman EF. PMID: 19240326; PMCID: PMC2651761.
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    53. 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins. J Struct Funct Genomics. 2009 Apr; 10(2):193-208. Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W. PMID: 19148774; PMCID: PMC2705707.
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    54. Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. Nat Struct Mol Biol. 2008 Sep; 15(9):948-56. Berndsen CE, Tsubota T, Lindner SE, Lee S, Holton JM, Kaufman PD, Keck JL, Denu JM. PMID: 19172748; PMCID: PMC2678805.
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    55. Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids. Protein Sci. 2007 Oct; 16(10):2224-32. Sales M, Plecs JJ, Holton JM, Alber T. PMID: 17766380; PMCID: PMC2204136.
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    56. A steric block in translation caused by the antibiotic spectinomycin. ACS Chem Biol. 2007 Aug 17; 2(8):545-552. Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JHD. PMID: 17696316; PMCID: PMC4624401.
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    57. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol. 2007 Aug; 14(8):727-32. Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH. PMID: 17660832.
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    58. Structural insight into KCNQ (Kv7) channel assembly and channelopathy. Neuron. 2007 Mar 01; 53(5):663-75. Howard RJ, Clark KA, Holton JM, Minor DL. PMID: 17329207; PMCID: PMC3011230.
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    59. Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature. 2007 Jan 25; 445(7126):394-8. Huang DT, Hunt HW, Zhuang M, Ohi MD, Holton JM, Schulman BA. PMID: 17220875; PMCID: PMC2821831.
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    60. XANES measurements of the rate of radiation damage to selenomethionine side chains. J Synchrotron Radiat. 2007 Jan; 14(Pt 1):51-72. Holton JM. PMID: 17211072; PMCID: PMC2806430.
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    61. Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis. J Mol Biol. 2006 Sep 01; 361(5):850-63. Rho BS, Hung LW, Holton JM, Vigil D, Kim SI, Park MS, Terwilliger TC, Pédelacq JD. PMID: 16884737.
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    62. Structures of the bacterial ribosome at 3.5 A resolution. Science. 2005 Nov 04; 310(5749):827-34. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. PMID: 16272117.
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    63. Structural and mechanistic studies of VPS4 proteins. EMBO J. 2005 Oct 19; 24(20):3658-69. Scott A, Chung HY, Gonciarz-Swiatek M, Hill GC, Whitby FG, Gaspar J, Holton JM, Viswanathan R, Ghaffarian S, Hill CP, Sundquist WI. PMID: 16193069; PMCID: PMC1276703.
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    64. Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. Mol Cell. 2005 Feb 04; 17(3):341-50. Huang DT, Paydar A, Zhuang M, Waddell MB, Holton JM, Schulman BA. PMID: 15694336.
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    65. Crystal structure of PriB, a component of the Escherichia coli replication restart primosome. Structure. 2004 Nov; 12(11):1967-75. Lopper M, Holton JM, Keck JL. PMID: 15530361.
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    66. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J Synchrotron Radiat. 2004 Nov 01; 11(Pt 6):447-55. 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, Agard DA, Padmore HA. PMID: 15496731.
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    67. A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8. Nat Struct Mol Biol. 2004 Oct; 11(10):927-35. Huang DT, Miller DW, Mathew R, Cassell R, Holton JM, Roussel MF, Schulman BA. PMID: 15361859; PMCID: PMC2862556.
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    68. Ubiquitin recognition by the human TSG101 protein. Mol Cell. 2004 Mar 26; 13(6):783-9. Sundquist WI, Schubert HL, Kelly BN, Hill GC, Holton JM, Hill CP. PMID: 15053872.
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    69. Automated protein crystal structure determination using ELVES. Proc Natl Acad Sci U S A. 2004 Feb 10; 101(6):1537-42. Holton J, Alber T. PMID: 14752198; PMCID: PMC341770.
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    70. The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Mol Cell. 2003 Dec; 12(6):1427-37. Walden H, Podgorski MS, Huang DT, Miller DW, Howard RJ, Minor DL, Holton JM, Schulman BA. PMID: 14690597.
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    71. Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins. Proc Natl Acad Sci U S A. 2001 May 08; 98(10):5515-20. Lougheed JC, Holton JM, Alber T, Bazan JF, Handel TM. PMID: 11331761; PMCID: PMC33244.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    72. Crystallographic analysis of CD40 recognition and signaling by human TRAF2. Proc Natl Acad Sci U S A. 1999 Jul 20; 96(15):8408-13. McWhirter SM, Pullen SS, Holton JM, Crute JJ, Kehry MR, Alber T. PMID: 10411888; PMCID: PMC17529.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    73. Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants. Protein Sci. 1997 Aug; 6(8):1771-3. Morgan CS, Holton JM, Olafson BD, Bjorkman PJ, Mayo SL. PMID: 9260291; PMCID: PMC2143769.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
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