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Items: 1 to 50 of 60

1.

Ab initio structure determination from experimental fluctuation X-ray scattering data.

Pande K, Donatelli JJ, Malmerberg E, Foucar L, Bostedt C, Schlichting I, Zwart PH.

Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):11772-11777. doi: 10.1073/pnas.1812064115. Epub 2018 Oct 29.

2.

Evolutionarily Conserved Allosteric Communication in Protein Tyrosine Phosphatases.

Hjortness MK, Riccardi L, Hongdusit A, Zwart PH, Sankaran B, De Vivo M, Fox JM.

Biochemistry. 2018 Nov 13;57(45):6443-6451. doi: 10.1021/acs.biochem.8b00656. Epub 2018 Oct 26.

PMID:
30289703
3.

Free-electron laser data for multiple-particle fluctuation scattering analysis.

Pande K, Donatelli JJ, Malmerberg E, Foucar L, Poon BK, Sutter M, Botha S, Basu S, Bruce Doak R, Dörner K, Epp SW, Englert L, Fromme R, Hartmann E, Hartmann R, Hauser G, Hattne J, Hosseinizadeh A, Kassemeyer S, Lomb L, Montero SFC, Menzel A, Rolles D, Rudenko A, Seibert MM, Sierra RG, Schwander P, Ourmazd A, Fromme P, Sauter NK, Bogan M, Bozek J, Bostedt C, Schlichting I, Kerfeld CA, Zwart PH.

Sci Data. 2018 Oct 2;5:180201. doi: 10.1038/sdata.2018.201.

4.

Resonant Soft X-Ray Scattering Provides Protein Structure with Chemical Specificity.

Ye D, Le TP, Kuei B, Zhu C, Zwart PH, Wang C, Gomez ED, Gomez EW.

Structure. 2018 Nov 6;26(11):1513-1521.e3. doi: 10.1016/j.str.2018.07.018. Epub 2018 Sep 13.

PMID:
30220541
5.

Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation.

Hjortness MK, Riccardi L, Hongdusit A, Ruppe A, Zhao M, Kim EY, Zwart PH, Sankaran B, Arthanari H, Sousa MC, De Vivo M, Fox JM.

Biochemistry. 2018 Oct 9;57(40):5886-5896. doi: 10.1021/acs.biochem.8b00655. Epub 2018 Sep 14.

6.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses.

Kurta RP, Donatelli JJ, Yoon CH, Berntsen P, Bielecki J, Daurer BJ, DeMirci H, Fromme P, Hantke MF, Maia FRNC, Munke A, Nettelblad C, Pande K, Reddy HKN, Sellberg JA, Sierra RG, Svenda M, van der Schot G, Vartanyants IA, Williams GJ, Xavier PL, Aquila A, Zwart PH, Mancuso AP.

Phys Rev Lett. 2017 Oct 13;119(15):158102. doi: 10.1103/PhysRevLett.119.158102. Epub 2017 Oct 12.

7.

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase.

Donatelli JJ, Sethian JA, Zwart PH.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7222-7227. doi: 10.1073/pnas.1708217114. Epub 2017 Jun 26.

8.

Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase.

Fox JM, Kang K, Sastry M, Sherman W, Sankaran B, Zwart PH, Whitesides GM.

Angew Chem Int Ed Engl. 2017 Mar 27;56(14):3833-3837. doi: 10.1002/anie.201609409. Epub 2017 Mar 2.

9.

Principles for designing proteins with cavities formed by curved β sheets.

Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GV, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D.

Science. 2017 Jan 13;355(6321):201-206. doi: 10.1126/science.aah7389.

10.

Correction to A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle.

Asensio MA, Morella NM, Jakobson CM, Hartman EC, Glasgow JE, Sankaran B, Zwart PH, Tullman-Ercek D.

Nano Lett. 2016 Dec 14;16(12):8034. Epub 2016 Nov 10. No abstract available.

PMID:
27960505
11.

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core.

Mills JH, Sheffler W, Ener ME, Almhjell PJ, Oberdorfer G, Pereira JH, Parmeggiani F, Sankaran B, Zwart PH, Baker D.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15012-15017. doi: 10.1073/pnas.1600188113. Epub 2016 Dec 8.

12.

Structure of photosystem II and substrate binding at room temperature.

Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J.

Nature. 2016 Dec 15;540(7633):453-457. doi: 10.1038/nature20161. Epub 2016 Nov 21.

13.

A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle.

Asensio MA, Morella NM, Jakobson CM, Hartman EC, Glasgow JE, Sankaran B, Zwart PH, Tullman-Ercek D.

Nano Lett. 2016 Sep 14;16(9):5944-50. doi: 10.1021/acs.nanolett.6b02948. Epub 2016 Aug 25. Erratum in: Nano Lett. 2016 Dec 14;16(12):8034.

14.

No observable conformational changes in PSII.

Sauter NK, Echols N, Adams PD, Zwart PH, Kern J, Brewster AS, Koroidov S, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Yano J, Yachandra VK.

Nature. 2016 May 19;533(7603):E1-2. doi: 10.1038/nature17983. No abstract available.

15.

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.

Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D.

Science. 2016 May 6;352(6286):680-7. doi: 10.1126/science.aad8865. Erratum in: Science. 2016 May 20;352(6288). pii: aag1318. doi: 10.1126/science.aag1318.

16.

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal.

Terwilliger TC, Bunkóczi G, Hung LW, Zwart PH, Smith JL, Akey DL, Adams PD.

Acta Crystallogr D Struct Biol. 2016 Mar;72(Pt 3):359-74. doi: 10.1107/S2059798315019403. Epub 2016 Mar 1.

17.

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing.

Terwilliger TC, Bunkóczi G, Hung LW, Zwart PH, Smith JL, Akey DL, Adams PD.

Acta Crystallogr D Struct Biol. 2016 Mar;72(Pt 3):346-58. doi: 10.1107/S2059798315019269. Epub 2016 Mar 1.

18.

Iterative phasing for fluctuation X-ray scattering.

Donatelli JJ, Zwart PH, Sethian JA.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10286-91. doi: 10.1073/pnas.1513738112. Epub 2015 Aug 3.

19.

Operational properties of fluctuation X-ray scattering data.

Malmerberg E, Kerfeld CA, Zwart PH.

IUCrJ. 2015 Mar 20;2(Pt 3):309-16. doi: 10.1107/S2052252515002535. eCollection 2015 May 1.

20.

Simultaneous detection of electronic structure changes from two elements of a bifunctional catalyst using wavelength-dispersive X-ray emission spectroscopy and in situ electrochemistry.

Gul S, Ng JW, Alonso-Mori R, Kern J, Sokaras D, Anzenberg E, Lassalle-Kaiser B, Gorlin Y, Weng TC, Zwart PH, Zhang JZ, Bergmann U, Yachandra VK, Jaramillo TF, Yano J.

Phys Chem Chem Phys. 2015 Apr 14;17(14):8901-12. doi: 10.1039/c5cp01023c. Epub 2015 Mar 6.

21.

Improved crystal orientation and physical properties from single-shot XFEL stills.

Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3299-309. doi: 10.1107/S1399004714024134. Epub 2014 Nov 28.

22.

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK.

Nat Commun. 2014 Jul 9;5:4371. doi: 10.1038/ncomms5371.

23.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK.

Nat Methods. 2014 May;11(5):545-8. doi: 10.1038/nmeth.2887. Epub 2014 Mar 16. Erratum in: Nat Methods. 2015 Jul;12(7):692.

24.

Three-dimensional single-particle imaging using angular correlations from X-ray laser data.

Liu H, Poon BK, Saldin DK, Spence JC, Zwart PH.

Acta Crystallogr A. 2013 Jul;69(Pt 4):365-73. doi: 10.1107/S0108767313006016. Epub 2013 May 8.

PMID:
23778093
25.

Component particle structure in heterogeneous disordered ensembles extracted from high-throughput fluctuation x-ray scattering.

Chen G, Zwart PH, Li D.

Phys Rev Lett. 2013 May 10;110(19):195501. Epub 2013 May 6.

PMID:
23705716
26.

Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity.

Rajagopalan S, Teter SJ, Zwart PH, Brennan RG, Phillips KJ, Kiley PJ.

Nat Struct Mol Biol. 2013 Jun;20(6):740-7. doi: 10.1038/nsmb.2568. Epub 2013 May 5.

27.

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J.

Science. 2013 Apr 26;340(6131):491-5. doi: 10.1126/science.1234273. Epub 2013 Feb 14.

28.

Structure determination of LpxD from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.

Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jan 1;69(Pt 1):6-9. doi: 10.1107/S1744309112048890. Epub 2012 Dec 25.

29.

Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.

Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1477-81. doi: 10.1107/S174430911204571X. Epub 2012 Nov 28.

30.

Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode.

Alonso-Mori R, Kern J, Gildea RJ, Sokaras D, Weng TC, Lassalle-Kaiser B, Tran R, Hattne J, Laksmono H, Hellmich J, Glöckner C, Echols N, Sierra RG, Schafer DW, Sellberg J, Kenney C, Herbst R, Pines J, Hart P, Herrmann S, Grosse-Kunstleve RW, Latimer MJ, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Zouni A, Messinger J, Glatzel P, Sauter NK, Yachandra VK, Yano J, Bergmann U.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19103-7. doi: 10.1073/pnas.1211384109. Epub 2012 Nov 5.

31.

Nanoflow electrospinning serial femtosecond crystallography.

Sierra RG, Laksmono H, Kern J, Tran R, Hattne J, Alonso-Mori R, Lassalle-Kaiser B, Glöckner C, Hellmich J, Schafer DW, Echols N, Gildea RJ, Grosse-Kunstleve RW, Sellberg J, McQueen TA, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Hampton CY, Starodub D, Loh ND, Sokaras D, Weng TC, Zwart PH, Glatzel P, Milathianaki D, White WE, Adams PD, Williams GJ, Boutet S, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK, Bogan MJ.

Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1584-7. doi: 10.1107/S0907444912038152. Epub 2012 Oct 18.

32.

Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus.

Chacko AR, Zwart PH, Read RJ, Dodson EJ, Rao CD, Suguna K.

Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1541-8. doi: 10.1107/S090744491203836X. Epub 2012 Oct 18.

PMID:
23090403
33.

Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering.

Chen G, Modestino MA, Poon BK, Schirotzek A, Marchesini S, Segalman RA, Hexemer A, Zwart PH.

J Synchrotron Radiat. 2012 Sep;19(Pt 5):695-700. doi: 10.1107/S0909049512023801. Epub 2012 Jul 7.

PMID:
22898947
34.

Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials.

Liu H, Poon BK, Janssen AJ, Zwart PH.

Acta Crystallogr A. 2012 Sep;68(Pt 5):561-7. doi: 10.1107/S0108767312029637. Epub 2012 Aug 15.

PMID:
22893239
35.

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H, Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B, Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA, DiFiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM, Sokaras D, Weng TC, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U, Yano J, Yachandra VK.

Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):9721-6. doi: 10.1073/pnas.1204598109. Epub 2012 Jun 4.

36.

Determining pair distance distribution function from SAXS data using parametric functionals.

Liu H, Zwart PH.

J Struct Biol. 2012 Oct;180(1):226-34. doi: 10.1016/j.jsb.2012.05.011. Epub 2012 Jun 1.

PMID:
22659403
37.

Towards automated crystallographic structure refinement with phenix.refine.

Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi: 10.1107/S0907444912001308. Epub 2012 Mar 16.

38.

A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II.

Zhang Y, Zwart PH, Ealick SE.

Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):249-52. doi: 10.1107/S0907444911051699. Epub 2012 Feb 7.

PMID:
22349226
39.

Computation of small-angle scattering profiles with three-dimensional Zernike polynomials.

Liu H, Morris RJ, Hexemer A, Grandison S, Zwart PH.

Acta Crystallogr A. 2012 Mar;68(Pt 2):278-85. doi: 10.1107/S010876731104788X. Epub 2012 Feb 9.

PMID:
22338662
40.

A new generation of crystallographic validation tools for the protein data bank.

Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.

Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006.

41.

The Phenix software for automated determination of macromolecular structures.

Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.

Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.

42.

The structure of LpxD from Pseudomonas aeruginosa at 1.3 Å resolution.

Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jul 1;67(Pt 7):749-52. doi: 10.1107/S1744309111018811. Epub 2011 Jun 23.

43.

Hybrid molecular structure of the giant protease tripeptidyl peptidase II.

Chuang CK, Rockel B, Seyit G, Walian PJ, Schönegge AM, Peters J, Zwart PH, Baumeister W, Jap BK.

Nat Struct Mol Biol. 2010 Aug;17(8):990-6. doi: 10.1038/nsmb.1870. Epub 2010 Aug 1.

44.

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.

Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD.

J Appl Crystallogr. 2010 Aug 1;43(Pt 4):669-676. Epub 2010 May 22.

45.

Detection and correction of underassigned rotational symmetry prior to structure deposition.

Poon BK, Grosse-Kunstleve RW, Zwart PH, Sauter NK.

Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):503-13. doi: 10.1107/S0907444910001502. Epub 2010 Apr 21.

46.

Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria.

Wilson A, Kinney JN, Zwart PH, Punginelli C, D'Haene S, Perreau F, Klein MG, Kirilovsky D, Kerfeld CA.

J Biol Chem. 2010 Jun 11;285(24):18364-75. doi: 10.1074/jbc.M110.115709. Epub 2010 Apr 5.

47.

PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.

Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. doi: 10.1107/S0907444909052925. Epub 2010 Jan 22.

48.

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.

Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601. doi: 10.1107/S0907444909012098. Epub 2009 May 15.

49.

Autoindexing the diffraction patterns from crystals with a pseudotranslation.

Sauter NK, Zwart PH.

Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):553-9. doi: 10.1107/S0907444909010725. Epub 2009 May 15.

50.

Automated structure solution with the PHENIX suite.

Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.

Methods Mol Biol. 2008;426:419-35. doi: 10.1007/978-1-60327-058-8_28.

PMID:
18542881

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