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: ]
  • 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: ]
  • 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.
  • 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: doi:10.1107/S2053230X1400942X.
  • Publications Using the Software tools

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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