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Items: 1 to 50 of 122

1.

Interactions between Atorvastatin and the Farnesoid X Receptor Impair Insulinotropic Effects of Bile Acids and Modulate Diabetogenic Risk.

Hoffmeister T, Kaiser J, Lüdtke S, Drews G, Düfer M.

Mol Pharmacol. 2020 Mar;97(3):202-211. doi: 10.1124/mol.119.118083. Epub 2020 Jan 7.

PMID:
31911428
2.

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions.

Li S, Su Z, Lehmann J, Stamatopoulou V, Giarimoglou N, Henderson FE, Fan L, Pintilie GD, Zhang K, Chen M, Ludtke SJ, Wang YX, Stathopoulos C, Chiu W, Zhang J.

Nat Struct Mol Biol. 2019 Dec;26(12):1094-1105. doi: 10.1038/s41594-019-0326-7. Epub 2019 Nov 18.

PMID:
31740854
3.

A complete data processing workflow for cryo-ET and subtomogram averaging.

Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ.

Nat Methods. 2019 Nov;16(11):1161-1168. doi: 10.1038/s41592-019-0591-8. Epub 2019 Oct 14.

PMID:
31611690
4.

Cool Farm Tool Water: A global on-line tool to assess water use in crop production.

Kayatz B, Baroni G, Hillier J, Lüdtke S, Heathcote R, Malin D, van Tonder C, Kuster B, Freese D, Hüttl R, Wattenbach M.

J Clean Prod. 2019 Jan 10;207:1163-1179. doi: 10.1016/j.jclepro.2018.09.160.

5.

Structural and functional analyses of photosystem II in the marine diatom Phaeodactylum tricornutum.

Levitan O, Chen M, Kuang X, Cheong KY, Jiang J, Banal M, Nambiar N, Gorbunov MY, Ludtke SJ, Falkowski PG, Dai W.

Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17316-17322. doi: 10.1073/pnas.1906726116. Epub 2019 Aug 13.

6.

In situ structure and assembly of the multidrug efflux pump AcrAB-TolC.

Shi X, Chen M, Yu Z, Bell JM, Wang H, Forrester I, Villarreal H, Jakana J, Du D, Luisi BF, Ludtke SJ, Wang Z.

Nat Commun. 2019 Jun 14;10(1):2635. doi: 10.1038/s41467-019-10512-6.

7.

Analysing Cooking Behaviour in Home Settings: Towards Health Monitoring.

Yordanova K, Lüdtke S, Whitehouse S, Krüger F, Paiement A, Mirmehdi M, Craddock I, Kirste T.

Sensors (Basel). 2019 Feb 4;19(3). pii: E646. doi: 10.3390/s19030646.

8.

Cryo-EM reveals ligand induced allostery underlying InsP3R channel gating.

Fan G, Baker MR, Wang Z, Seryshev AB, Ludtke SJ, Baker ML, Serysheva II.

Cell Res. 2018 Dec;28(12):1158-1170. doi: 10.1038/s41422-018-0108-5. Epub 2018 Nov 23.

9.

New software tools in EMAN2 inspired by EMDatabank map challenge.

Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ.

J Struct Biol. 2018 Nov;204(2):283-290. doi: 10.1016/j.jsb.2018.09.002. Epub 2018 Sep 4.

10.

Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography.

Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W.

J Mol Biol. 2018 Oct 19;430(21):4156-4167. doi: 10.1016/j.jmb.2018.08.013. Epub 2018 Aug 20.

11.

Integrative structure and functional anatomy of a nuclear pore complex.

Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP.

Nature. 2018 Mar 22;555(7697):475-482. doi: 10.1038/nature26003. Epub 2018 Mar 14.

12.

Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

Zhang K, Keane SC, Su Z, Irobalieva RN, Chen M, Van V, Sciandra CA, Marchant J, Heng X, Schmid MF, Case DA, Ludtke SJ, Summers MF, Chiu W.

Structure. 2018 Mar 6;26(3):490-498.e3. doi: 10.1016/j.str.2018.01.001. Epub 2018 Feb 2.

13.

Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.

Chen M, Dai W, Sun SY, Jonasch D, He CY, Schmid MF, Chiu W, Ludtke SJ.

Nat Methods. 2017 Oct;14(10):983-985. doi: 10.1038/nmeth.4405. Epub 2017 Aug 28.

14.

Structural and Functional Impacts of ER Coactivator Sequential Recruitment.

Yi P, Wang Z, Feng Q, Chou CK, Pintilie GD, Shen H, Foulds CE, Fan G, Serysheva I, Ludtke SJ, Schmid MF, Hung MC, Chiu W, O'Malley BW.

Mol Cell. 2017 Sep 7;67(5):733-743.e4. doi: 10.1016/j.molcel.2017.07.026. Epub 2017 Aug 24.

15.

The advent of structural biology in situ by single particle cryo-electron tomography.

Galaz-Montoya JG, Ludtke SJ.

Biophys Rep. 2017;3(1):17-35. doi: 10.1007/s41048-017-0040-0. Epub 2017 May 29.

16.

A Near-Atomic Structure of the Dark Apoptosome Provides Insight into Assembly and Activation.

Cheng TC, Akey IV, Yuan S, Yu Z, Ludtke SJ, Akey CW.

Structure. 2017 Jan 3;25(1):40-52. doi: 10.1016/j.str.2016.11.002. Epub 2016 Dec 1.

17.

Single-Particle Refinement and Variability Analysis in EMAN2.1.

Ludtke SJ.

Methods Enzymol. 2016;579:159-89. doi: 10.1016/bs.mie.2016.05.001. Epub 2016 Jul 1. Review.

18.

De Novo modeling in cryo-EM density maps with Pathwalking.

Chen M, Baldwin PR, Ludtke SJ, Baker ML.

J Struct Biol. 2016 Dec;196(3):289-298. doi: 10.1016/j.jsb.2016.06.004. Epub 2016 Jul 17.

19.

Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.

Galaz-Montoya JG, Hecksel CW, Baldwin PR, Wang E, Weaver SC, Schmid MF, Ludtke SJ, Chiu W.

J Struct Biol. 2016 Jun;194(3):383-94. doi: 10.1016/j.jsb.2016.03.018. Epub 2016 Mar 22.

20.

High resolution single particle refinement in EMAN2.1.

Bell JM, Chen M, Baldwin PR, Ludtke SJ.

Methods. 2016 May 1;100:25-34. doi: 10.1016/j.ymeth.2016.02.018. Epub 2016 Feb 27.

21.

The Electron Microscopy eXchange (EMX) initiative.

Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM.

J Struct Biol. 2016 May;194(2):156-63. doi: 10.1016/j.jsb.2016.02.008. Epub 2016 Feb 9.

22.

Direct Measurement of the Structure of Reconstituted High-Density Lipoproteins by Cryo-EM.

Murray SC, Gillard BK, Ludtke SJ, Pownall HJ.

Biophys J. 2016 Feb 23;110(4):810-6. doi: 10.1016/j.bpj.2015.10.028. Epub 2015 Dec 30.

23.

EMDataBank unified data resource for 3DEM.

Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W.

Nucleic Acids Res. 2016 Jan 4;44(D1):D396-403. doi: 10.1093/nar/gkv1126. Epub 2015 Nov 17.

24.

Erratum: Structural diversity of supercoiled DNA.

Irobalieva RN, Fogg JM, Catanese DJ Jr, Sutthibutpong T, Chen M, Barker AK, Ludtke SJ, Harris SA, Schmid MF, Chiu W, Zechiedrich L.

Nat Commun. 2015 Oct 29;6:8851. doi: 10.1038/ncomms9851. No abstract available.

PMID:
26511109
25.

Gating machinery of InsP3R channels revealed by electron cryomicroscopy.

Fan G, Baker ML, Wang Z, Baker MR, Sinyagovskiy PA, Chiu W, Ludtke SJ, Serysheva II.

Nature. 2015 Nov 19;527(7578):336-41. doi: 10.1038/nature15249. Epub 2015 Oct 12.

26.

Structural diversity of supercoiled DNA.

Irobalieva RN, Fogg JM, Catanese DJ Jr, Sutthibutpong T, Chen M, Barker AK, Ludtke SJ, Harris SA, Schmid MF, Chiu W, Zechiedrich L.

Nat Commun. 2015 Oct 12;6:8440. doi: 10.1038/ncomms9440. Erratum in: Nat Commun. 2015;6:8851. Catanese, Daniel J [Corrected to Catanese, Daniel J Jr].

27.

Single particle tomography in EMAN2.

Galaz-Montoya JG, Flanagan J, Schmid MF, Ludtke SJ.

J Struct Biol. 2015 Jun;190(3):279-90. doi: 10.1016/j.jsb.2015.04.016. Epub 2015 May 5.

28.

CTF Challenge: Result summary.

Marabini R, Carragher B, Chen S, Chen J, Cheng A, Downing KH, Frank J, Grassucci RA, Bernard Heymann J, Jiang W, Jonic S, Liao HY, Ludtke SJ, Patwari S, Piotrowski AL, Quintana A, Sorzano CO, Stahlberg H, Vargas J, Voss NR, Chiu W, Carazo JM.

J Struct Biol. 2015 Jun;190(3):348-59. doi: 10.1016/j.jsb.2015.04.003. Epub 2015 Apr 23.

29.

MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography.

Cheng A, Henderson R, Mastronarde D, Ludtke SJ, Schoenmakers RH, Short J, Marabini R, Dallakyan S, Agard D, Winn M.

J Struct Biol. 2015 Nov;192(2):146-50. doi: 10.1016/j.jsb.2015.04.002. Epub 2015 Apr 13.

30.

Structure of a biologically active estrogen receptor-coactivator complex on DNA.

Yi P, Wang Z, Feng Q, Pintilie GD, Foulds CE, Lanz RB, Ludtke SJ, Schmid MF, Chiu W, O'Malley BW.

Mol Cell. 2015 Mar 19;57(6):1047-1058. doi: 10.1016/j.molcel.2015.01.025. Epub 2015 Feb 26.

31.

Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages.

Dai W, Fu C, Khant HA, Ludtke SJ, Schmid MF, Chiu W.

Nat Protoc. 2014 Nov;9(11):2630-42. doi: 10.1038/nprot.2014.176. Epub 2014 Oct 16.

32.

An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W.

Nat Commun. 2014 Sep 4;5:4808. doi: 10.1038/ncomms5808.

33.

Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor.

Chen Z, Fischer ER, Kouiavskaia D, Hansen BT, Ludtke SJ, Bidzhieva B, Makiya M, Agulto L, Purcell RH, Chumakov K.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20242-7. doi: 10.1073/pnas.1320041110. Epub 2013 Nov 25.

34.

Structure of the SecY channel during initiation of protein translocation.

Park E, Ménétret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW.

Nature. 2014 Feb 6;506(7486):102-6. doi: 10.1038/nature12720. Epub 2013 Oct 23.

35.

Visualizing virus assembly intermediates inside marine cyanobacteria.

Dai W, Fu C, Raytcheva D, Flanagan J, Khant HA, Liu X, Rochat RH, Haase-Pettingell C, Piret J, Ludtke SJ, Nagayama K, Schmid MF, King JA, Chiu W.

Nature. 2013 Oct 31;502(7473):707-10. doi: 10.1038/nature12604. Epub 2013 Oct 9.

36.

Sub-ångström-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate.

Lüdtke S, Neumann P, Erixon KM, Leeper F, Kluger R, Ficner R, Tittmann K.

Nat Chem. 2013 Sep;5(9):762-7. doi: 10.1038/nchem.1728. Epub 2013 Aug 18.

PMID:
23965678
37.

TRiC's tricks inhibit huntingtin aggregation.

Shahmoradian SH, Galaz-Montoya JG, Schmid MF, Cong Y, Ma B, Spiess C, Frydman J, Ludtke SJ, Chiu W.

Elife. 2013 Jul 9;2:e00710. doi: 10.7554/eLife.00710.

38.

Single-particle cryo-EM of calcium release channels: structural validation.

Ludtke SJ, Serysheva II.

Curr Opin Struct Biol. 2013 Oct;23(5):755-62. doi: 10.1016/j.sbi.2013.06.003. Epub 2013 Jul 5. Review.

39.

Validation of cryo-EM structure of IP₃R1 channel.

Murray SC, Flanagan J, Popova OB, Chiu W, Ludtke SJ, Serysheva II.

Structure. 2013 Jun 4;21(6):900-9. doi: 10.1016/j.str.2013.04.016. Epub 2013 May 23.

40.

Domain organization of membrane-bound factor VIII.

Stoilova-McPhie S, Lynch GC, Ludtke S, Pettitt BM.

Biopolymers. 2013 Jul;99(7):448-59. doi: 10.1002/bip.22199.

41.

Human CCT4 and CCT5 chaperonin subunits expressed in Escherichia coli form biologically active homo-oligomers.

Sergeeva OA, Chen B, Haase-Pettingell C, Ludtke SJ, Chiu W, King JA.

J Biol Chem. 2013 Jun 14;288(24):17734-44. doi: 10.1074/jbc.M112.443929. Epub 2013 Apr 23.

42.

Details of ssDNA annealing revealed by an HSV-1 ICP8-ssDNA binary complex.

Tolun G, Makhov AM, Ludtke SJ, Griffith JD.

Nucleic Acids Res. 2013 Jun;41(11):5927-37. doi: 10.1093/nar/gkt266. Epub 2013 Apr 19.

43.

Cryo-EM structure of a molluscan hemocyanin suggests its allosteric mechanism.

Zhang Q, Dai X, Cong Y, Zhang J, Chen DH, Dougherty MT, Wang J, Ludtke SJ, Schmid MF, Chiu W.

Structure. 2013 Apr 2;21(4):604-13.

44.

EMEN2: an object oriented database and electronic lab notebook.

Rees I, Langley E, Chiu W, Ludtke SJ.

Microsc Microanal. 2013 Feb;19(1):1-10. doi: 10.1017/S1431927612014043. Epub 2013 Jan 29.

45.

Data management challenges in three-dimensional EM.

Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ.

Nat Struct Mol Biol. 2012 Dec;19(12):1203-7. doi: 10.1038/nsmb.2426. No abstract available.

46.

A δ38 deletion variant of human transketolase as a model of transketolase-like protein 1 exhibits no enzymatic activity.

Schneider S, Lüdtke S, Schröder-Tittmann K, Wechsler C, Meyer D, Tittmann K.

PLoS One. 2012;7(10):e48321. doi: 10.1371/journal.pone.0048321. Epub 2012 Oct 31.

47.

Updates from the EBF DBS--microsampling consortium.

Timmerman P, White S, Cobb Z, de Vries R, Thomas E, van Baar B, Smith C, Zimmer D, Delrat P, Smeraglia J, Lüdtke S.

Bioanalysis. 2012 Aug;4(16):1969-70. doi: 10.4155/bio.12.182. No abstract available.

48.

Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin.

Meyer D, Neumann P, Koers E, Sjuts H, Lüdtke S, Sheldrick GM, Ficner R, Tittmann K.

Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10867-72. doi: 10.1073/pnas.1201280109. Epub 2012 Jun 22.

49.

The 2010 cryo-EM modeling challenge.

Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W.

Biopolymers. 2012 Sep;97(9):651-4. doi: 10.1002/bip.22081. No abstract available.

PMID:
22696402
50.

The molecular architecture of the eukaryotic chaperonin TRiC/CCT.

Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J.

Structure. 2012 May 9;20(5):814-25. doi: 10.1016/j.str.2012.03.007. Epub 2012 Apr 12.

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