Publications

  • Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010, D66:213-221. [PMID: 20124702] [PMCID: PMC2815670]
  • Adams PD, Mustyakimov M, Afonine PV, Langan P: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Acta Cryst. 2009, D65:567-573. [PMID: 19465771] [PMCID: PMC2685734]
  • Adams P, Langan P: Opportunities and challenges with the growth of neutron crystallography. Acta Cryst. 2010, D66:1121-1123. [PMID: 21041924]
  • Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43:677-685. [PMID: 20648263] [PMCID: PMC2906258]
  • Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD: Towards automated crystallographic structure refinement with phenix.refine. Acta Cryst. 2012, D68:352-367 [PMID: 22505256] [PMCID: PMC3322595]
  • Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD: Joint X-ray and neutron refinement with phenix.refine. Acta Cryst. 2010, D66:1153-1163. [PMID: 21041930] [PMCID: PMC2967420]
  • Chen JCH, Fisher SZ, Kovalevsky AY, Mustyakimov M, Hanson LB, Zhurov V, Langan P: Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin. Acta Crystallographica Section F-Structural Biology and Crystallization Communications, 2012. 68: p. 119-123. [PMID: 22297981] [PMCID: PMC3274385]
  • Chen JCH, Fisher Z, Hanson LB, Langan P, Kovalevsky AY: Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography. Proceedings of the National Academy of Sciences of the United States of America, 2012. 109(38): p. 15301-15306. [PMID: 22949690] [PMCID: PMC3458323]
  • Fenn TD, Schnieders MJ, Mustyakimov M, Wu C, Langan P, Pande VS, Brunger AT: Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration. Structure. 2011. 19:523-33. [PMID: 21481775] [PMCID: PMC3083928]
  • Fisher SZ, Kovalevsky AY, Domsic JF, Mustyakimov M, Silverman DN, McKenna R, Langan P: Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer. Biochemistry, 2010. 49(3): p. 415-421. [PMID: 20025241] [PMCID: PMC2893723]
  • Fisher Z, Kovalevsky AY, Mustyakimov M, Silverman DN, McKenna R, Langan P: Neutron Structure of Human Carbonic Anhydrase II: A Hydrogen-Bonded Water Network "Switch" Is Observed between pH 7.8 and 10.0. Biochemistry, 2011. 50(44): p. 9421-9423. [PMID: 21988105] [PMCID: PMC3371383]
  • Fisher SZ, Aggarwal M, Kovalevsky AY, Silverman DN, McKenna R: Neutron Diffraction of Acetazolamide-Bound Human Carbonic Anhydrase II Reveals Atomic Details of Drug Binding. Journal of the American Chemical Society, 2012. 134(36): p. 14726-14729. [PMID: 22928733] [PMCID: PMC3524527]
  • Fisher Z: Neutron Crystallography Contributes to Drug Design. American Laboratory, 2013. 45(3): p. 28-31. [PMID: ] [PMCID: ]
  • Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams PD: Exact direct-space asymmetric units for the 230 crystallographic space groups. Acta Cryst. 2011, A67: [PMID: 21487185] [PMCID: PMC3082335]
  • Langan P, Chen JCH: Seeing the chemistry in biology with neutron crystallography. Physical Chemistry Chemical Physics, 2013. 15(33): p. 13705-13712. [PMID: 23852376] [PMCID: ]
  • Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD: Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Acta Crystallographica Section D-Structural biology, 2018. 74: p. 800-318. doi:10.1107/S2059798318004588.
  • Michalczyk R, Unkefer CJ, Bacik JP, Schrader TE, Ostermann A, Kovalevsky AY, McKenna R, Fisher SZ. Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(18):5673-8. doi: 10.1073/pnas.1502255112. PubMed PMID: WOS:000353953800049.
  • Schuman B, Fisher SZ, Borisova S, Kovalevsky A, Palcic MM, Coates LC, Langan P, Evans SV: Preliminary joint neutron time-of-flight and X-ray crystallographic study of human ABO(H) blood group A glycosyltransferase. Acta Crystallographica Section F-Structural Biology and Crystallization Communications, 2011. 67: p. 258-262. [PMID: 21301100] [PMCID: PMC3034622]
  • Schuman B, Fisher SZ, Borisova S, Coates LC, Langan P, Evans SV: Neutron Structure of Retaining Glycosyltransferase GTA. Glycobiology, 2011. 21(11): p. 1469-1469. [PMID: ] [PMCID: ]
  • Sullivan B, Archibald R, Langan PS, Dobbek H, Bommer M, McFeeters RL, Coates L, Wang X, Gallmeier F, Carpenter JM, Lynch VE, Langan P: Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space. Acta Crystallographica Section D-Biological Crystallography. 2018;74:1085-1095. doi: 10.1107/S2059798318013347.
  • Wan Q, Bennett BC, Wilson MA, Kovalevsky A, Langan P, Howell EE, 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. 2014;111(51):18225-30. doi: 10.1073/pnas.1415856111. PubMed PMID: WOS:000346767200046.
  • Wan Q, Kovalevsky AY, Wilson MA, Bennett BC, Langan P, Dealwis C. Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+. Acta Crystallographica Section F. 2014;70(6):814-8. doi:10.1107/S2053230X1400942X.

    • Publications Using the Software tools

  • Casadei CM, Gumiero A, Metcalfe CL, Murphy EJ, Basran J, Concilio MG, Teixeira SCM, Schrader TE, Fielding AJ, Ostermann A, Blakeley MP, Raven EL, Moody PCE: Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase. Science. 2014;345(6193):193-7. doi: 10.1126/science.1254398. PubMed PMID: WOS:000339409900048.
  • Harp JM, Coates L, Sullivan B, Egli M: Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG). Acta Crystallographica F. 2018; F74: 603-609. doi: 10.1107/S2053230X1801066X.
  • Haupt M, Blakeley MP, Fisher SJ, Mason SA, Cooper JB, Mitchell EP, Forsyth VT: Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. Iucrj. 2014;1:429-38. doi: 10.1107/s2052252514021113. PubMed PMID: WOS:000356865600007.
  • Huang GY, Gerlits OO, Blakeley MP, Sankaran B, Kovalevsky AY, Kim C: Neutron Diffraction Reveals Hydrogen Bonds Critical for cGMP-Selective Activation: Insights for cGMP-Dependent Protein Kinase Agonist Design. Biochemistry. 2014;53(43):6725-7. doi: 10.1021/bi501012v. PubMed PMID: WOS:000344510300001.
  • Hughes RC, Coates L, Blakeley MP, Tomanicek SJ, Langan P, Kovalevsky AY, Garcia-Ruize JM, Ng JD: Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction. Acta Cryst. 2012, F68: 1482-1487.
  • Laulumaa S, Blakeley MP, Raasakka A, Moulin M, Hartlein M, Kursula P: Production, crystallization and neutron diffraction of fully deuterated human myelin peripheral membrane protein P2. Acta Crystallographica F. 2015. 71:1391-1395.
  • Ohlin M, von Schantz L, Schrader TE, Ostermann A, Logan DT, Fisher SZ: Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase. Acta Crystallographica Section F-Structural Biology Communications. 2015;71:1072-7. doi: 10.1107/s2053230x15011383. PubMed PMID: WOS:000359352700026.
  • Ohnishi Y, Yamada T, Kurihara K, Tanaka I, Sakiyama F, Masaki T, Niimura N: Neutron and X-ray crystallographic analysis of Achromobacter protease I at pD 8.0: Protonation states and hydration structure in the free-form. Biochimica Et Biophysica Acta-Proteins and Proteomics 2013, 1834(8): 1642-1647.
  • Oksanen E, Blakeley MP, El-Hajji M, Ryde U, Budayova-Spano M: The Neutron Structure of Urate Oxidase Resolves a Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation. Plos One 2014. 9(1).
  • Tomanicek SJ, Standaert RF, Weiss KL, Ostermann A, Schrader TE, Ng JD, Coates LC: Neutron and X-ray Crystal Structures of a Perdeuterated Enzyme Inhibitor Complex Reveal the Catalytic Proton Network of the Toho-1 beta-Lactamase for the Acylation Reaction. Journal of Biological Chemistry 2013, 288(7): 4715-4722.
  • Waltman MJ, Yang ZK, Langan P, Graham DE, Kovalevsky A. Engineering acidic Streptomyces rubiginosus d-xylose isomerase by rational enzyme design. Protein Engineering Design and Selection. 2014;27(2):59-64. doi: 10.1093/protein/gzt062
  • Wan Q, Parks JM, Hanson BF, Fisher Z, Ostermann A, Schrader T, Graham DE, Coates L, Langan P, Kovalevsky A: On the protonation states, hydrogen bonding and catalytic mechanism of family 11 glycosidases: Direct visualization with neutrons” on-line for Proceedings of the National Academy of Sciences, 2015.
  • Weber IT, Waltman MJ, Mustyakimov M, Blakeley MP, Keen DA, Ghosh AK, Langan P, Kovalevsky AY: Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design. Journal of Medicinal Chemistry 2013. 56(13): 5631-5635.
  • Yamada T, Kurihara K, Ohnishi Y, Tamada T, Tomoyori K, Masumi K, Tanaka I, Kuroki R, Niiumra N: Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: Protonation states and hydration structure of the enzyme-product complex. Biochimica Et Biophysica Acta-Proteins and Proteomics 2013, 1834(8): 1532-1538.
  • Yokoyama T, Mizuguchi M, Nabeshima Y, Kusaka K, Yamada T, Hosoya T, Ohhara T, Kurihara K, Tanaka I, Nobuo N: Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin. Journal of Structural Biology 2012, 177(2): 283-290.
  • Yokoyama T, Mizuguchi M, Ostermann A, Kusaka K, Niimura N, Schrader TE, Tanaka I. Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase. Journal of Medicinal Chemistry. 2015;58(18):7549-56. doi: 10.1021/acs.jmedchem.5b01147. PubMed PMID: WOS:000361921800033.