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Department of Biochemistry

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Publications of Daniel Nettels

2021
König, I., Soranno, A., Nettels, D. & Schuler, B. Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 60, 10724-10729 (2021). PMID: 33587794.

Lerner, E., Barth, A., Hendrix, J., Ambrose, B., Birkedal, V., Blanchard, SC., Börner, R., Sung Chung, H., Cordes, T., Craggs, TD., Deniz, AA., Diao, J., Fei, J., Gonzalez, RL., Gopich, IV., Ha, T., Hanke, CA., Haran, G., Hatzakis, NS., Hohng, S., Hong, SC., Hugel, T., Ingargiola, A., Joo, C., Kapanidis, AN., Kim, HD., Laurence, T., Lee, NK., Lee, TH., Lemke, EA., Margeat, E., Michaelis, J., Michalet, X., Myong, S., Nettels, D., Peulen, TO., Ploetz, E., Razvag, Y., Robb, NC., Schuler, B., Soleimaninejad, H., Tang, C., Vafabakhsh, R., Lamb, DC., Seidel, CA. & Weiss, S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife 10, (2021). PMID: 33779550.

2020
Ernst, P., Zosel, F., Reichen, C., Nettels, D., Schuler, B. & Plückthun, A. Structure-Guided Design of a Peptide Lock for Modular Peptide Binders. ACS Chem Biol 15, 457-468 (2020). PMID: 31985201.

Schuler, B., Borgia, A., Borgia, MB., Heidarsson, PO., Holmstrom, ED., Nettels, D. & Sottini, A. Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Curr Opin Struct Biol 60, 66-76 (2020). PMID: 31874413.

Sottini, A., Borgia, A., Borgia, MB., Bugge, K., Nettels, D., Chowdhury, A., Heidarsson, PO., Zosel, F., Best, RB., Kragelund, BB. & Schuler, B. Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nat Commun 11, 5736 (2020). PMID: 33184256.

Zijlstra, N., Nettels, D., Satija, R., Makarov, DE. & Schuler, B. Transition Path Dynamics of a Dielectric Particle in a Bistable Optical Trap. Phys Rev Lett 125, 146001 (2020). PMID: 33064519.

Zosel, F., Soranno, A., Buholzer, KJ., Nettels, D. & Schuler, B. Depletion interactions modulate the binding between disordered proteins in crowded environments. Proc Natl Acad Sci U S A 117, 13480-13489 (2020). PMID: 32487732.

2019
Holmstrom, ED., Liu, Z., Nettels, D., Best, RB. & Schuler, B. Disordered RNA chaperones can enhance nucleic acid folding via local charge screening. Nat Commun 10, 2453 (2019). PMID: 31165735.

2018
Best, RB., Zheng, W., Borgia, A., Buholzer, K., Borgia, MB., Hofmann, H., Soranno, A., Nettels, D., Gast, K., Grishaev, A. & Schuler, B. Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water". Science 361, (2018). PMID: 30166459.

Borgia, A., Borgia, MB., Bugge, K., Kissling, VM., Heidarsson, PO., Fernandes, CB., Sottini, A., Soranno, A., Buholzer, KJ., Nettels, D., Kragelund, BB., Best, RB. & Schuler, B. Extreme disorder in an ultrahigh-affinity protein complex. Nature 555, 61-66 (2018). PMID: 29466338.

Dingfelder, F., Benke, S., Nettels, D. & Schuler, B. Mapping an Equilibrium Folding Intermediate of the Cytolytic Pore Toxin ClyA with Single-Molecule FRET. J Phys Chem B 122, 11251-11261 (2018). PMID: 30156409.

Hansen, S., Ernst, P., König, SLB., Reichen, C., Ewald, C., Nettels, D., Mittl, PRE., Schuler, B. & Plückthun, A. Curvature of designed armadillo repeat proteins allows modular peptide binding. J Struct Biol 201, 108-117 (2018). PMID: 28864298.

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 15, 669-676 (2018). PMID: 30171252.

Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Adariani, SR., 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. Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nat Methods 15, 984 (2018). PMID: 30327572.

Holmstrom, ED., Holla, A., Zheng, W., Nettels, D., Best, RB. & Schuler, B. Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET. Methods Enzymol 611, 287-325 (2018). PMID: 30471690.

Holmstrom, ED., Nettels, D. & Schuler, B. Conformational Plasticity of Hepatitis C Virus Core Protein Enables RNA-Induced Formation of Nucleocapsid-like Particles. J Mol Biol 430, 2453-2467 (2018). PMID: 29045818.

Reinartz, I., Sinner, C., Nettels, D., Stucki-Buchli, B., Stockmar, F., Panek, PT., Jacob, CR., Nienhaus, GU., Schuler, B. & Schug, A. Simulation of FRET dyes allows quantitative comparison against experimental data. J Chem Phys 148, 123321 (2018). PMID: 29604831.

Sturzenegger, F., Zosel, F., Holmstrom, ED., Buholzer, KJ., Makarov, DE., Nettels, D. & Schuler, B. Transition path times of coupled folding and binding reveal the formation of an encounter complex. Nat Commun 9, 4708 (2018). PMID: 30413694.

Zosel, F., Mercadante, D., Nettels, D. & Schuler, B. A proline switch explains kinetic heterogeneity in a coupled folding and binding reaction. Nat Commun 9, 3332 (2018). PMID: 30127362.

2017
Benke, S., Nettels, D., Hofmann, H. & Schuler, B. Quantifying kinetics from time series of single-molecule Förster resonance energy transfer efficiency histograms. Nanotechnology 28, 114002 (2017). PMID: 28103588.

Dingfelder, F., Wunderlich, B., Benke, S., Zosel, F., Zijlstra, N., Nettels, D. & Schuler, B. Rapid Microfluidic Double-Jump Mixing Device for Single-Molecule Spectroscopy. J. Am. Chem. Soc. 139, 6062-6065 (2017). PMID: 28394601.

Soranno, A., Holla, A., Dingfelder, F., Nettels, D., Makarov, DE. & Schuler, B. Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations. Proc. Natl. Acad. Sci. U.S.A. 114, E1833-E1839 (2017). PMID: 28223518.

Zijlstra, N., Dingfelder, F., Wunderlich, B., Zosel, F., Benke, S., Nettels, D. & Schuler, B. Rapid Microfluidic Dilution for Single-Molecule Spectroscopy of Low-Affinity Biomolecular Complexes. Angew. Chem. Int. Ed. Engl. 56, 7126-7129 (2017). PMID: 28510311.

Zosel, F., Haenni, D., Soranno, A., Nettels, D. & Schuler, B. Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein. J Chem Phys 147, 152708 (2017). PMID: 29055320.

2016
Aznauryan, M., Delgado, L., Soranno, A., Nettels, D., Huang, JR., Labhardt, AM., Grzesiek, S. & Schuler, B. Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR and SAXS. Proc Natl Acad Sci U S A 113, E5389-98 (20169. PMID: 2756640.

Benke, S., Roderer, D., Wunderlich, B., Nettels, D., Glockshuber, R. & Schuler, B. Erratum: The assembly dynamics of the cytolytic pore toxin ClyA. Nat Commun 7, 10650 (2016). PMID: 26830972.

Borgia, A., Zheng, W., Buholzer, K., Borgia, MB., Schüler, A., Hofmann, H., Soranno, A., Nettels, D., Gast, K., Grishaev, A., Best, RB. & Schuler, B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J. Am. Chem. Soc. 138, 11714-26 (2016). PMID: 27583570.

Schuler, B., Soranno, A., Hofmann, H. & Nettels, D. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Annu Rev Biophys [Epub ahead of print] (2016). PMID: 27145874.

2015
Benke, S., Roderer, D., Wunderlich, B., Nettels, D., Glockshuber, R. & Schuler, B. The assembly dynamics of the cytolytic pore toxin ClyA. Nat Commun 6, 6198 (2015). PMID: 25652783.

Best, RB., Hofmann, H., Nettels, D. & Schuler, B. Quantitative interpretation of FRET experiments via molecular simulation: force field and validation. Biophys. J. 108, 2721-31 (2015). PMID: 26039173.

Borgia, A., Kemplen, KR., Borgia, MB., Soranno, A., Shammas, S., Wunderlich, B., Nettels, D., Best, RB., Clarke, J. & Schuler, B. Transient misfolding dominates multidomain protein folding. Nat Commun 6, 8861 (2015). PMID: 26572969.

Czar, MF., Zosel, F., König, I., Nettels, D., Wunderlich, B., Schuler, B., Zarrine-Afsar, A. & Jockusch, RA. Gas-Phase FRET Efficiency Measurements To Probe the Conformation of Mass-Selected Proteins. Anal. Chem. 87, 7559-65 (2015). PMID: 26110465.

König, I., Zarrine-Afsar, A., Aznauryan, M., Soranno, A., Wunderlich, B., Dingfelder, F., Stüber, JC., Plückthun, A., Nettels, D. & Schuler, B. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nat. Methods 12, 773-9 (2015). PMID: 26147918.

Nettels, D., Haenni, D., Maillot, S., Gueye, M., Barth, A., Hirschfeld, V., Hübner, CG., Léonard, J. & Schuler, B. Excited-state annihilation reduces power dependence of single-molecule FRET experiments. Phys Chem Chem Phys 17, 32304-15 (2015). PMID: 26584062

Yuan, H., Gaiduk, A., Siekierzycka, JR., Fujiyoshi, S., Matsushita, M., Nettels, D., Schuler, B., Seidel, CA. & Orrit, M. Temperature-cycle microscopy reveals single-molecule conformational heterogeneity. Phys Chem Chem Phys 17, 6532-44 (2015). PMID: 25659944.

2014
Hofmann, H., Hillger, F., Delley, C., Hoffmann, A., Pfeil, SH., Nettels, D., Lipman, EA. & Schuler, B. Role of denatured-state properties in chaperonin action probed by single-molecule spectroscopy. Biophys. J. 107, 2891-2902 (2014). PMID: 25517154.

Wunderlich, B., Nettels, D. & Schuler, B. Taylor dispersion and the position-to-time conversion in microfluidic mixing devices. Lab Chip 14, 219-28 (2014).

2013
Aznauryan, M., Nettels, D., Holla, A., Hofmann, H. & Schuler, B. Single-molecule spectroscopy of cold denaturation and the temperature-induced collapse of unfolded proteins. J. Am. Chem. Soc. 135, 14040-3 (2013).

Hofmann, H., Nettels, D. & Schuler, B. Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH. J Chem Phys 139, 121930 (2013).

Haenni, D., Zosel, F., Reymond, L., Nettels, D. & Schuler, B. Intramolecular distances and dynamics from the combined photon statistics of single-molecule FRET and photoinduced electron transfer. J Phys Che B. 117, 13015-1328 (2013).

Wunderlich, B., Nettels, D., Benke, S., Clark, J., Weidner, S., Hofmann, H., Pfeil, SH. & Schuler, B. Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes. Nat Protocols 8, 1459-1474 (2013).

2012
Borgia, A., Wensley, BG., Soranno, A., Nettels, D., Borgia, MB., Hoffmann, A., Pfeil, SH., Lipamn, EA., Clarke, J. & Schuler, B. Localizing internal friction along the reaction corrdinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nat Commun. 3, 1195 (2012).

Hofmann, H., Soranno, A., Borgia, A., Gast, K., Nettels, D. & Schuler, B. Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. PNAS USA 109, 16155-16160 (2012).

Nettels, D., Hoffmann, A. & Schuler, B. Corrections to "Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. J Phys Chem B. 112, 6137-6146 (2012).

Nettels, D. & Schuler B. Single-Molecule FRET of Protein Folding Dynamics. Advances in Chemical Physics 146, 23-48 (2012).

Schuler, B., Müller-Späth, S., Soranno, A. & Nettels, D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol Biol 896, 21-45 (2012).

Soranno, A., Buchli, B., Nettels, D., Cheng, RR., Müller-Späth, S., Pfeil, SH., Hoffmann, A., Lipman, EA., Makarov, DE. & Schuler, B. Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. PNAS 109, 17800-17806 (2012).

2011
Borgia, MB., Borgia, A., Best, RB., Steward, A., Nettels, D., Wunderlich, B., Schuler, B. & Clarke, J. Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature 474, 662-665 (2011).

Hoffmann, A., Nettels, D., Clark, J., Borgia, A., Radford, SE., Clarke, J. & Schuler, B. Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles. Phys Chem Chem Phys. 13, 1857-1871 (2011).

Hofmann H, Hillger F, Pfeil SH, Hoffmann A, Streich D, Haenni D, Nettels D, Lipman EA & Schuler B. Single-molecule spectroscopy of protein folding in a chaperonin cage. Proc Natl Acad Sci U S A. 107, 11793-11798 (2010).

2010
Müller-Späth, S., Soranno, A., Hirschfeld, V., Hofmann, H., Rüegger, S., Reymond, L., Nettels, D. & Schuler, B. Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci U S A. 107, 14609-14614 (2010).

2009
Gopich, IV., Nettels, D., Schuler, B. & Szabo, A. Protein dynamics from single-molecule fluorescence intensity correlation functions. J Chem Phys. 131, 095102 (2009).

Nettels, D., Müller-Späth, S., Küster, F., Hofmann, H., Haenni, D., Rüegger, S., Reymond, L., Hoffmann, A., Kubelka, J., Heinz, B., Gast, K., Best, RB. & Schuler, B. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci U S A. 106, 20740-20745 (2009)

2008
Hillger, F., Hänni, D., Nettels, D., Geister, S., Grandin, M., Textor, M. & Schuler, B. Probing Protein-Chaperone Interactions with Single-Molecule Fluorescence Spectroscopy. Angew Chem Int Ed Engl47, 6184-6188 (2008).

Nettels, D., Hoffmann, A. & Schuler, B. Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. J Phys Chem B. 112, 6137-6146 (2008).

Wahl, M., Rahn, HJ., Röhlicke, T., Kell, G., Nettels, D., Hillger, F., Schuler, B. & Erdmann, R. Scalable time-correlated photon counting system with multiple independent input channels. Rev. Sci. Instrum. 79, 123113-1 - 123113-8 (2008).

2007
Hillger, F., Nettels, D., Dorsch, S. & Schuler B. Detection and Analysis of Protein Aggregation with Confocal Single Molecule Fluorescence Spectroscopy. J. Fluoresc. 17, 759-765 (2007).

Hoffmann, A., Kane, A.,Nettels, D., Hertzog, D., Baumgärtel, P., Lengefeld, J., Reichardt, G., Horsley, D.A., Seckler, R., Bakajin, O & Schuler, B. Mapping protein collapse with single molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy. Proc. Natl. Acad. Sci. USA 104, 105-110 (2007).

Nettels, D., Gopich, I. V., Hoffmann, A. & Schuler, B. Ultrafast dynamics of protein collapse from single molecule photon statistics. Proc. Natl. Acad. Sci. USA 104, 2655-2660 (2007).

Nettels, D. & Schuler, B. Subpopulation-resolved photon statistics of single-molecule energy transfer dynamics. IEEE J. Sel. Top. Quant. Electron. 13, 990-995 (2007).

Publications in Atomic Physics:
Hofer, A., Moroshkin, P., Ulzega ,S., Nettels, D., Müller-Siebert, R. & Weis, A. 6S1/2-6P1/2 transition of Cs atoms in cubic and hexagonal solid 4He. Physical Review A 76, 22502 (2007).

Ulzega, S., Hofer, A., Moroshkin,P., Müller-Siebert, R., Nettels, D. &  Weis, A. Measurement of the forbidden electric tensor polarizability of Cs atoms trapped in solid 4He. Physical Review A 75, 42505 (2007).

Hofer, A., Moroshkin,P., Nettels,D., Ulzega, S. & Weis, A.Rb*Hen exciplexes in solid 4He. Physical Review A 74,  (2006).

Moroshkin, P.,  Hofer, A. Nettels, D., Ulzega, S. & Weis, A. CsHe exciplexes in solid He. The Journal of Chemical Physics 124, 024511 (2006).

Moroshkin, P., Nettels, D., Hofer, A.,  Ulzega, S. & Weis, A.
Laser-induced formation and spectroscopy of Cs*He exciplexes in solid He. Proceedings of SPIE 6257, 625706 (2006).

Nettels, D.,  Hofer, A.,  Moroshkin, P. , Müller-Siebert, R., Ulzega, S. & Weis,A. Discovery of Dumbbell-Shaped Cs*Hen Exciplexes in Solid 4He. Physical Review Letters 94, 63001 (2005).

Nettels,D., Müller-Siebert, R., Huang, X., Ulzega, S. & Weis, A. Magnetic and electric properties of alkali atoms in solid helium. Physica. B, Condensed matter 329, 406-407 (2003).

Nettels, D., Müller-Siebert, R.,  Ulzega, S. &  Weis, A. Multi-photon processes in the Zeeman structure of atomic Cs trapped in solid helium. Applied Physics B: Lasers and Optics 77, 563-570 (2003).

Nettels, D., Müller-Siebert, R. & Weis, A. Relaxation mechanisms of multi-quantum coherences in the Zeeman structure of atomic Cs trapped in solid He. Applied Physics B: Lasers and Optics 77, 753-764 (2003)

Weis, A., Bison, G., Nettels, D., Rasbach, U. & Mueller-Siebert, R. Resonant nonlinear magneto-optical effects of atoms in vapors, beams, and quantum crystals. Proceedings of SPIE 4748, 1 (2003).

Eichler, T., Müller-Siebert, R., Nettels, D., Kanorsky, S. & Weis, A. Optical Detection of Nonradiating Alkali Atoms in Solid Helium. Physical Review Letters 88, 123002 (2002).

Weis, A., Giel, D. & Nettels, D. Motion of Vapor Atoms Studied by Optical Magnetic Resonance Tomography. Laser Phys. 11, 470-475 (2001).

Giel, D., Hinz, G., Nettels, D. & Weis, A. Diffusion of Cs atoms in Ne buffer gas measured by optical magnetic resonance tomography. Optics Express 6, 251-256 (2000).