Publications

Publications

81. Chowdhury A, Yu M, Lemke EA. Phase Separation Comes of Age: From Phenomenology to Single Molecules. Mol Cell. (2019) May 2;74(3):413-415. doi: 10.1016/j.molcel.2019.04.016.

80. Lu M, Ma X, Castillo-Menendez LR, Gorman J, Alsahafi N, Ermel U, Terry DS, Chambers M, Peng D, Zhang B, Zhou T, Reichard N, Wang K, Grover JR, Carman BP, Gardner MR, Nikić-Spiegel I, Sugawara A, Arthos J, Lemke EA*, Smith AB 3rd, Farzan M, Abrams C, Munro JB, McDermott AB, Finzi A, Kwong PD, Blanchard SC, Sodroski JG, Mothes W. Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET. Nature. (2019) Apr;568(7752):415-419. doi: 10.1038/s41586-019-1101-y.

79. Reinkemeier CD, Girona GE, Lemke EA. Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science. (2019) Mar 29;363(6434). pii: eaaw2644. doi: 10.1126/science.aaw2644.

78. Chowdhury A, Kovalenko SA, Aramburu IV, Tan PS, Ernsting NP, Lemke EA. Mechanism-Dependent Modulation of Ultrafast Interfacial Water Dynamics in Intrinsically Disordered Protein Complexes. Angew Chem Int Ed Engl. (2019) Mar 26;58(14):4720-4724. doi: 10.1002/anie.201813354.

77. Tan PS, Lemke EA. Probing Differential Binding Mechanisms of Phenylalanine-Glycine-Rich Nucleoporins by Single-Molecule FRET. Methods Enzymol. (2018) ;611:327-346. doi: 10.1016/bs.mie.2018.08.034.

76. Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Rezaei Adariani S, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA*, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD, Hugel T. Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nat Methods. (2018) Sep;15(9):669-676. doi: 10.1038/s41592-018-0085-0.

75. Fuertes G, Banterle N, Ruff KM, Chowdhury A, Pappu RV, Svergun DI, Lemke EA*. Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”. Science (2018) Aug 31;361(6405). pii: eaau8230. doi: 10.1126/science.aau8230.

74. Das DK, Govindan R, Nikić-Spiegel I, Krammer F, Lemke EA, Munro JB. Direct Visualization of the Conformational Dynamics of Single Influenza Hemagglutinin Trimers. Cell (2018) Aug 9;174(4):926-937.e12. doi: 10.1016/j.cell.2018.05.050.

73. Mikhaleva S, Lemke EA. Beyond the Transport Function of Import Receptors: What’s All the FUS about? Cell (2018) Apr 19;173(3):549-553. doi: 10.1016/j.cell.2018.04.002.

72. Kormos A, Koehler C, Fodor EA, Rutkai ZR, Martin ME, Mező G, Lemke EA, Kele P. Bistetrazine-Cyanines as Double-Clicking Fluorogenic Two-Point Binder or Crosslinker Probes. Chemistry (2018) Jun 21;24(35):8841-8847. doi: 10.1002/chem.201800910.

71. Tan, P.S. , Aramburu IV Mercadante D, Tyagi S, Chowdhury A, Spitz, Shammas S, Gräter F*, Lemke EA*. Two differential binding mechanisms of FG-Nucleoporins and Nuclear Transport Receptors, Cell Reports (2018), 22, 1-12 March 27

70. Kozma E, Paci G, Estrada Girona G, Lemke EA, Kele P. Fluorogenic Tetrazine-Siliconrhodamine Probe for the Labeling of Noncanonical Amino Acid Tagged Proteins. Methods Mol Biol. (2018);1728:337-363.

69. Koehler C, Lemke EA. MultiBacTAG-Genetic Code Expansion Using the Baculovirus Expression System in Sf21 Cells. Methods Mol Biol. (2018);1728:297-311

68. Brabham RL, Spears RJ, Walton J, Tyagi S, Lemke EA, Fascione MA. Palladium-unleashed proteins: gentle aldehyde decaging for site-selective protein modification. Chem Commun (Camb). (2018) Feb 11;54(12):1501-1504.

67. Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I. Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. Elife. (2017) Nov 7;6. pii: e30395

66. Warner JB 4th, Ruff KM, Tan PS, Lemke EA, Pappu RV, Lashuel HA. Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths.  J Am Chem Soc. (2017) Oct 18;139(41):14456-14469.

65. Mercadante D, Wagner JA, Aramburu IV, Lemke EA, Gräter F. Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins. J Chem Theory Comput (2017) Sep 12;13(9):3964-3974.

64. Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV*, Svergun DI*, Lemke EA*. Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proc Natl Acad Sci U S A. (2017) Aug 1;114(31):E6342-E6351.

63. Aramburu IV, Lemke EA*. Floppy but not sloppy: Interaction mechanism of FG-nucleoporins and nuclear transport receptors. Semin Cell Dev Biol. (2017) Aug;68:34-41

62. Kozma E, Estrada Girona G, Paci G, Lemke EA, Kele P. Bioorthogonal double-fluorogenic siliconrhodamine probes for intracellular super-resolution microscopy. Chem Commun (Camb). (2017) Jun 20;53(50):6696-669

61. Sakin V, Hanne J, Dunder J, Anders-Össwein M, Laketa V, Nikić I, Kräusslich HG, Lemke EA, Müller B. A Versatile Tool for Live-Cell Imaging and Super-Resolution Nanoscopy Studies of HIV-1 Env Distribution and Mobility. Cell Chem Biol.(2017) May 18;24(5):635-645.e5.

60. Demeter O, Kormos A, Koehler C, Mezõ G, Németh K, Kozma E, Takacs L, Lemke EA, Kele P*. Bisazide Cyanine Dyes as Fluorogenic Probes for Bis-Cyclooctynylated Peptide Tags and as Fluorogenic Cross-Linkers of Cyclooctynylated Proteins. Bioconjug Chem. (2017) Apr 25. doi: 10.1021/acs.bioconjchem.7b00178.

59. Sakin V, Hanne J, Dunder J, Anders-Osswein M, Laketa V, Nikic I, Krausslich H-G, Lemke EA, Muller B*, A Versatile Tool for Live-Cell Imaging and Super-Resolution Nanoscopy Studies of HIV-1 Env Distribution and Mobility. Cell Chemical Biology (2017), May 18;24(5):635-645.e5.

58. Paci G, Lemke EA*. Shining a Light on Phase Separation in the Cell. Cell (2017) Jan 12;168(1-2):11-13.

57. Kucher S, Korneev S, Tyagi S, Apfelbaum R, Grohmann D, Lemke EA, Klare JP, Steinhoff HJ*, Klose D*. Orthogonal spin labeling using click chemistry for in vitro and in vivo applications. J Magn Reson. (2017) Feb;275:38-45.

56. Kipper K, Lundius EG, Ćurić V, Nikić I, Wiessler M, Lemke EA, Elf J. Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli. ACS Synth Biol. (2017) Feb 17;6(2):233-255.

55. Nikić I, Estrada Girona G, Kang JH, Paci G, rei S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA*, Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy. Angew Chem Int Ed Engl. (2016) Dec 23;55(52):16172-16176

54. Koehler C, Sauter PF, Wawryszyn M, Estrada Girona G, Gupta K, Landry JJM, Hsi‐Yang Fritz M, Radic K, Hoffmann J-E, Chen ZA, Zou J, Tan PS, Galik B, Junttila S, Stolt‐Bergner P, Pruneri G, Gyenesei A, Schultz C, Biskup MB, Besir H, Benes V, Rappsilber J, Jechlinger M, Korbel JO, Berger I, Braese S, Lemke EA*. Genetic code expansion for multiprotein complex engineering. Nature Methods (2016) 2016 Dec;13(12):997-1000

53. Kozma E, Nikic I, Varga BR, Aramburu IV, Kang JH, Fackler OT, Lemke EA*, Kele P*. Hydrophilic trans-Cyclooctenylated Non-Canonical Amino Acids for Fast Intracellular Protein Labeling. Chembiochem
(2016) May 25. doi: 10.1002/cbic.201600284

52. Knorr A, Kozma E, Lemke EA, Kele P*. New, red-emitting tetrazine-phenoxazone fluorogenic labels for intracellular bioorthogonal labeling schemes. Chemistry (2016), doi: 10.1002/chem.201600590

51. Sakin V, Paci G, Lemke EA, Müller B*. Labeling of virus components for advanced, quantitative imaging analyses. FEBS Lett. (2016) Mar 14. doi: 10.1002/1873-3468.12131.

50. Banterle N, Lemke EA*, Nanoscale devices for linkerless long-term single-molecule observation, Current Opinion in Biotechnology, COBIOT_COBIOT-D-15-00108 (2016, in press)

49. Lemke EA*. The Multiple Faces of Disordered Nucleoporins. J Mol Biol. Jan 11. pii: S0022-2836(16)00021-8. doi: 10.1016/j.jmb.2016.01.002. (2016)

48. Vreja IC, Nikić I, Göttfert F, Bates M, Kröhnert K, Outeiro TF, Hell SW, Lemke EA, Rizzoli SO*. Super-resolution Microscopy of Clickable Amino Acids Reveals the Effects of Fluorescent Protein Tagging on Protein Assemblies. ACS Nano.(2015) Oct 28.

47. Milles S, Mercadante D, Aramburu IV, Jensen MR, Banterle N, Koehler C, Tyagi S, Clarke J, Shammas S, Blackledge M*, Gräter F*, Lemke EA*. Plasticity of an ultrafast interaction between nucleoporin and transport receptors. Cell (2015) 10.1016/j.cell.2015.09.047

46. Delaforge E, Milles S, Bouvignies G, Bouvier D, Boivin S, Salvi N, Maurin D, Martel A, Round A, Lemke EA, Jensen MR, Hart D, Blackledge M. Large Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α. J Am Chem Soc. (2015) Oct 1.

45. Appen A, Kosinski J, Sparks L, Ori A, Di Guilio AL, Vollmer B, Mackmull MT, Banterle B, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH*, Beck M*. In situ structural analysis of the human nuclear pore complex. Nature (2015) Oct 1;526(7571):140-3 

44. Nikić I, Lemke EA*, Genetic code expansion enabled site-specific dual-color protein labeling: superresolution microscopy and beyond. Curr Opin Chem Biol. (2015) Aug 22;28:164-173. doi: 10.1016/j.cbpa.2015.07.021.

43. Wagner JA, Mercadante D, Nikić I, Lemke EA, Gräter F*, Origin of Orthogonality of Strain-Promoted Click Reactions. Chemistry (2015) Aug 24;21(35):12431-12435. doi: 10.1002/chem.201501727.

42. Hoffmann JE, Plass T, Nikic I, Aramburu, IV, Koehler C, Lemke EA, Schultz C*. Highly stable trans-cyclooctene amino acids for live cell labeling, Chemistry (2015) Aug 24;21(35). doi: 10.1002/chem.201583561

41. Mercadante D, Milles S, Fuertes G, Svergun DI, Lemke EA, Gräter F*. Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields. J Phys Chem B. (2015) Jun 25;119(25):7975-84. doi: 10.1021/acs.jpcb.5b03440

40. Nikić I, Estrada Girona G, Kang JH, Aramburu IV, Lemke EA* Membrane protein labeling of live mammalian cells using click chemistry. Nature Protocols (2015) May;10(5):780-91 .

39. Tyagi S, Lemke EA*. (2015) Single-molecule FRET and crosslinking studies in structural biology enabled by noncanonical amino acids. Curr Opin Struct Biol. (2015) Mar 7;32:66-73. doi: 10.1016/j.sbi.2015.02.009.

38. Lemke EA*.The exploding genetic code. Chembiochem. (2014, editorial)  Aug 18;15(12):1691-4.

37. Dunne M, Mertens HD, Garefalaki V, Jeffries CM, Thompson A, Lemke EA, Svergun DI, Mayer MJ, Narbad A, Meijers R.The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. PLoS Pathog. (2014) Jul 24;10(7):e1004228. doi: 10.1371/journal.ppat.1004228

36. Herner A, Estrada Girona G, Nikić I, Kállay M, Lemke EA, Kele P.New generation of bioorthogonally applicable fluorogenic dyes with visible excitations and large stokes shifts. Bioconjug Chem. (2014) Jul 16;25(7):1370-4.

35. Milles S, Lemke EA*. Mapping multivalency and differential affinities within large intrinsically disordered protein complexes with segmental motion analysis. Angew Chem Int Ed Engl. (2014) Jul 7;53(28):7364-7

34. Pavic K, Rios P, Dzeyk K, Koehler C, Lemke EA, Köhn M*. Unnatural Amino Acid Mutagenesis Reveals Dimerization As a Negative Regulatory Mechanism of VHR’s Phosphatase Activity. ACS Chem Biol. (2014) Jul 18;9(7):1451-9

33. Tyagi S, VanDelinder V, Banterle N, Fuertes G, Milles S, Agez M, Lemke EA*. Continuous throughput and long-term observation of single-molecule FRET without immobilization. Nature Methods (2014) Mar;11(3):297-300

32. Nikic I, Plass T, Schraidt O, Szymanski J, Briggs JA, Schultz C, Lemke EA*. Dual-color super-resolution microscopy via genetic code expansion technology and tuned click reactions. Angew Chem Int Ed Engl. (2014) 2014, Feb, 53(8), 2245-2249

31. Banterle N, Bui HK, Lemke EA*, Beck M*. Fourier ring correlation as a resolution criterion for super resolution microscopy. J Struct Bio. (2013) Sep;183(3):363-7

30. Herner A, Nikic I, Kallay M, Lemke EA, Kele P A new family of bioorthogonally applicable Fluorogenic labels. Org Biomol Chem. (2013) 11(20):3297-306

29. Ori A, Banterle N, Iskar M, Andres-Pons A, Escher C, Bui HK, Sparks L, Mezarino VMS, Rinner O, Bork P*, Lemke EA* and Beck M*. Cell-type specific nuclear pore complexes: A case in point for context-dependent stoichiometry of molecular machines. Molecular System Biology (2013) 9:648

28. Lukinavicius G, Umezawa K, Olivier N, Honigmann A, Yang G, Plass T, Müller V, Reymond L, Corrêa Jr. I, Luo ZG, Schultz C, Lemke EA, Heppenstall P, Eggeling C, Manley S. A near-infrared fluorophore for live-cell superresolution microscopy of cellular proteins. Nature Chemistry (2013) 5(2):132-9

27. Milles S, Bui H, Koehler C, Beck M*, Lemke EA*. Facilitated aggregation propensity of FG Nucleoporins under molecular crowding conditions. EMBO Reports (2013) Dec 14

26. Tyagi S, Lemke EA*. Genetically encoded click chemistry for single molecule FRET of proteins. In Methods in Cell Biology (2013) 113:169-87 

25. Milles S, Lemke EA*. At the crossroads of Nano-resolved Single Molecule Sciences and Precision-Protein-Tuning. Bioassays (2013) 35(1):65-74

24. Borrmann A#, Milles S#, Plass T, Dommerholt J, Verkade JMM, Wießler M, Schultz, C., van Hest JCM, van Delft FL*, Lemke EA*. Genetic encoding of a bicyclononyne-charged amino acid enables fast cellular protein imaging by metal-free ligation. ChemBioChem (2012) 24;13(14)2094-9

23. Krishnan R, Goodman JL, Mukhopadhyay S, Pacheco CD, Lemke EA, Deniz AA, Lindquist S. Conserved features of intermediates in amyloid assembly determine their benign or toxic states. Proc Natl Acad Sci USA (2012) 109, 11172-7

22. Milles S, Koehler C, Gambin Y, Deniz AA* Lemke EA*. Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range. Mol Biosyst (2012) Jun 27

21. Plass T, Milles S, Koehler C, Szymanski J. Mueller R, Wieβler M, Schultz C*, Lemke EA*. Amino Acids for Diels-Alder Reactions in Living Cells. Angew Chem Int Ed Engl.(2012) 23;51(17):4166-70.

20. Milles S, Tyagi S, Banterke N, Koehler C, VanDelinder V, Neal AP, Lemke EA*. Click Strategies for Single-Molecule Protein Fluorescence. J Am Chem Soc (2012) 134, 5187-95

19. Milles S, Lemke EA*. Single molecule study of the intrinsically disordered FG-repeat Nucleoporin 153. Biophys J (2011) 101(7):1710-9 

18. Lemke EA*, Schultz C*; Principles for designing fluorescent sensors and reporters. Nature Chem Biol. (2011) 18;7(8)

17. Lemke EA*. Site-specific labeling of proteins for single-molecule FRET measurements using genetically encoded ketone functionalities. In Methods Mol Biol (2011) 751:3-15.

16. Plass T, Milles S, Koehler C, Schultz C*, Lemke EA*. Genetically encoded copper-free click chemistry. Angew Chem Int Ed Engl.(2011) 18;50(17):3878-81.

15. Gambin Y, VanDelinder V, Ferreon AC, Lemke EA, Groisman A, Deniz AA. Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nature Methods (2011) 8(3):239-41

14. Lemke EA*. Precision Control of Cellular Pathways with Light. ChemBioChem (2010) 11,1825-7 

13. Lemke EA, Gambin, Y, Vandelinder V, Brustad EM, Liu H-W, Schultz PG, Groisman A, Deniz AA. Microfluidic Device for Single-Molecule Experiments with Enhanced Photostability. J Am Chem Soc (2009) 38, 13 610-2

12. Lee HS, Guo J, Lemke EA, Dimla RD, Schultz PG. Genetic Incorporation of a Small, Environmentally Sensitive, Fluorescent Probe into Proteins in Saccharomyces cerevisiae. J Am  Chem Soc (2009) 36, 12921-3

11. Gambin Y, Schug A, Lemke EA, Lavinder JJ, Ferreon ACM, Magliery TJ, Onuchic JN, Deniz AA. The struggle for conformational dominance: Direct single-molecule observation of a protein dynamically switching between two alternate native structures. Proc Natl Acad Sci USA (2009) 106, 10153-8

10. Ferreon ACM, Gambin Y, Lemke EA, Deniz AA. Single-molecule Fluorescence illuminates a-synuclein structural plasticity and membrane binding. Proc Natl Acad Sci USA (2009) 106, 5645-50

9. Brustad EM, Lemke EA, Schultz PG, Deniz AA. A General and Efficient Method for the Site-Specific  Dual-Labeling of Proteins for Single Molecule Fluorescence Resonance Energy Transfer. J Am Chem Soc (2008) 52,17664-5 

8. Deniz AA, Mukhopadhyay S, Lemke EA. Single-molecule biophysics: at the interface of biology, physics and chemistry. J R Soc Interface (2008) 5(18), 15-45 (review article)

7. Lemke EA#, Summerer D#, Geierstanger B, Brittain S, Schultz PG. Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nature Chem Biol (2007) 3, 769-772

6. Mukhopadhyay S, Krishnan R, Lemke EA, Lindquist S, Deniz AA. A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proc Natl Acad Sci USA (2007) 104, 2649-2654

5. Henkel AW, Dittrich PS, Groemer TW, Lemke EA, Klingauf J, Klafki HW, Lewczuk P, Esselmann H, Schwille P, Kornhuber J, Wiltfang J. Immune complexes of auto-antibodies against A beta 1-42 peptides patrol cerebrospinal fluid of non-Alzheimer’s patients. Mol Psychiatry (2007) 12, 601-610

4. Takamori S, Holt M, Stenius K, Lemke EA, Gronborg M, Riedel D, Urlaub H, Schenck S, Brugger B, Ringler P, Muller SA, Rammner B, Grater F, Hub JS, De Groot BL, Mieskes G, Moriyama Y, Klingauf J, Grubmuller H, Heuser J, Wieland F, Jahn R. Molecular anatomy of a trafficking organelle. Cell (2006) 127, 831-846

3. Lemke EA, Klingauf J. Single synaptic vesicle tracking in individual hippocampal boutons at rest and during synaptic activity. J Neurosci (2005) 25, 11034-11044

2. Jordan R#, Lemke EA#, Klingauf J. Visualization of synaptic vesicle movement in intact synaptic boutons using fluorescence fluctuation spectroscopy. Biophys J (2005) 89, 2091-2102

1. Chakraborty R, Lemke EA, Cao Z, Klebba PE, van der Helm D. Identification and mutational studies of conserved amino acids in the outer membrane receptor protein, FepA, which affect transport but not binding of ferric-enterobactin in Escherichia coli. Biometals (2003) 16, 507-518