[62] Ausserwoeger H, Scrutton R, Fischer CM, Sneideris T, Qian D, de Csilléry E, Baronaitė I, Saar KL, Białek AZ, Oeller M, Krainer G, Franzmann TM, Wittmann S, Iglesias-Artola JM, Invernizzi G, Hyman AA, Alberti S, Lorenzen N, Knowles TPJ. Biomolecular condensates sustain pH gradients at equilibrium through charge neutralization. Nat Chem 2026, 18, 246. DOI: doi.org/10.1038/s41557-025-02039-9
[61] Hohenester U, Hitzelhammer F, Krainer G, Banzer P, Juffmann T. Optimizing the localization precision in coherent scattering microscopy using structured light. Nanophotonics 2025. DOI: doi.org/10.1515/nanoph-2025-0435
[60] Agarwal T, Sneideris T, Svara F, Jermakovs K, Coyle H, Qamar S, Kava E, Scrutton R, Pleschka N, Peres Priyanka, Cereghetti G, Andrzejewska E, Diaz-Barreiro A, Palmer G, Costa-Filho AJ, Krainer G, Knowles TPJ, Nixon-Abell J. Mapping high resolution, multidimensional phase diagrams of physiological protein condensates. BioRxiv 2025. [co-corresponding author] DOI: doi.org/10.1101/2025.11.24.690258
[59] Ausserwoeger H, de Csilléry E, Qian D, Krainer G, Welsh TJ, Sneideris T, Franzmann TM, Qamar SS, Erkamp NA, Nixon-Abell J, Kar M, St George-Hyslop P, Hyman AA, Alberti S, Pappu RV, Knowles TPJ. Quantifying collective interactions in biomolecular phase separation. Nat Commun 2025, 16, 7724. [co-first author] DOI: doi.org/10.1038/s41467-025-62437-y
[58] Agbadaola MT, Hilger D, Keller S, Krainer G. Unravelling allosteric signaling of G protein-coupled receptors (GPCRs) by single-molecule fluorescence. Biophys Rev 2025. DOI: doi.org/10.1007/s12551-025-01361-3
[57] Schneider M, Knowles TPJ, Keller S, Krainer G. Microfluidics for Protein Interaction Studies: Current Methods, Challenges, and Future Perspectives. European Biophys J 2025. DOI: doi.org/10.1007/s00249-025-01763-x
[56] Krainer G, Jacquat RPB, Schneider MM, Welsh TJ, Fan J, Peter QAE, Andrzejewska EA, Šneiderienė G, Czekalska MA, Ausserwoeger H, Chai L, Arter WE, Saar KL, Herling TW, Franzmann TM, Kosmoliaptsis V, Alberti S, Hartl F-U, Lee SF, Knowles TPJ. Single-molecule digital sizing of proteins in solution. Nat Commun 2024, 15, 7740. [co-corresponding author] DOI: doi.org/10.1038/s41467-024-50825-9
[55] Xu CK, Meisl G, Andrzejewska E, Krainer G, Dear AJ, Castellana Cruz M, Turi S, Edu IA, Vivacqua G, Jacquat R, Arter WE, Spillantini MG, Vendruscolo M, Linse S, Knowles TPJ. α-Synuclein oligomers form predominantly by secondary nucleation. Nat Commun 2024, 15, 7083. DOI: doi.org/10.1038/s41467-024-50692-4
[54] Ghosh D, Torres F, Schneider MM, Ashkinadze D, Kadavath H, Fleischmann Y, Mergenthal S, Güntert P, Krainer G, Andrzejewska EA, Lin L, Wei J, Klotzsch E, Knowles T, Riek R. The inhibitory action of the chaperone BRICHOS against the α-Synuclein secondary nucleation pathway. Nat Commun 2024, 15, 10038. DOI: doi.org/10.1038/s41467-024-54212-2
[53] Nielsen J, Lauritsen J, Pedersen J, Nowak J, Bendtsen M, Kleijwegt G, Lusser K, Pitarch LC, Moreno JV, Schneider M, Krainer G, Goksøyr L, Khalifé P, Kaalund S, Aznar S, Kjærgaard M, Sereikaité V, Strømgaard K, Knowles TPJ, Nielsen M, Sander F, Romero-Ramos M, Otzen D. Molecular properties and diagnostic potential of monoclonal antibodies targeting cytotoxic α-synuclein oligomers. NPJ Parkinsons Dis 2024, 10, 139. DOI: doi.org/10.1038/s41531-024-00747-6
[52] Sneideriene G, Czekalska MA, Xu CK, Jayaram A, Krainer G, Arter WE, Peter Q, Castellana-Cruz M, Saar KL, Levin A, Mueller T, Fiedler S, Devenish SRA, Fiegler H, Kumita JR, Knowles TPJ. Alpha-synuclein oligomers displace monomeric alpha-synuclein from lipid membranes. Nano Lett 2024, 18, 17469. DOI: doi.org/10.1021/acsnano.3c10889
[51] Bauernhofer L, Glueck D, Krainer G, Keller S. Mikrofluidische Partikelgrößenbestimmung BIOspektrum 2024, 30, 180. DOI: doi.org/10.1007/s12268-024-2133-x
[50] Sneideris T, Erkamp NA, Ausserwöger H, Saar KL, Welsh TJ, Qian D, Katsuya-Gaviria K, Johncock MLLY, Krainer G, Borodavka A, Knowles TPJ. Targeting nucleic acid phase transitions as a mechanism of action for antimicrobial peptides. Nat Commun 2023, 14, 7170. DOI: doi.org/10.1038/s41467-023-42374-4
[49] Hartmann A, Sreenivasa K, Schenkel M, Chamachi N, Schake P, Krainer G, Schlierf M. An automated single-molecule FRET platform for high-content, multiwell plate screening of biomolecular conformations and dynamics. Nat Commun 2023, 14, 6511. DOI: doi.org/10.1038/s41467-023-42232-3
[48] Ausserwöger H, Krainer G, Welsh TJ, Thorsteinson N, de Csilléry E, Šneideris T, Schneider MM, Egebjerg T, Invernizzi G, Herling TW, Lorenzen N, Knowles TPJ. Surface patches induce nonspecific binding and phase separation of antibodies. Proc Natl Acad Sci2023, 120, e2210332120. DOI: doi.org/10.1073/pnas.2210332120
[47] Agam G, Gebhardt C, Popara M, Maechtel R, Folz J, Ambrose B, Chamachi N, Chung SY, Craggs TD, de Boer M, Grohmann D, Ha T, Hartmann A, Hendrix J, Hirschfeld V, Huebner CG, Hugel T, Kammerer D, Kang HS, Kapanidis A, Krainer G, Kramm K, Lemke E, Lerner E, Margeat E, Martens K, Michaelis J, Mitra J, Moya Munoz GG, Quast R, Robb N, Sattler M, Schlierf M, Schneider J, Schroeder T, Sefer A, Tan PS, Thurn J, Tinnefeld P, van Noort J, Weiss S, Wendler N, Barth A, Seidel CAM, Lamb DC, Cordes T. Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nat Meth 2023, 20, 523–535. DOI: doi.org/10.1038/s41592-023-01807-0
[46] Jacquat RPB, Krainer G, Peter Q, Babar AN, Vanderpoorten O, Xu CK, Kaminski CF, Keyser UF, Baumberg JJ, Knowles TPJ. Single-molecule sizing through nanocavity confinement. Nano Lett 2023, 23, 1629–1636. [co-first author] DOI: doi.org/10.1021/acs.nanolett.1c04830
[45] Krainer G, Saar KL, Arter WE, Welsh TJ, Czekalska MA, Jacquat RPB, Peter Q, Traberg WC, Pujari A, Jayaram AK, Challa P, Taylor CG, van der Linden L-M, Franzmann T, Owens RM, Alberti S, Klenerman D, Knowles TPJ. Direct digital sensing of protein biomarkers in solution. Nat Commun 2023, 14, 653. DOI: doi.org/10.1038/s41467-023-35792-x
[44] Zhu H, Narita M, Joseph JA, Krainer G, Arter WE, Olan I, Saar KL, Ermann N, Espinosa JR, Shen Y, Kuri MA, Qi R, Welsh TJ, Xu Y, Collepardo-Guevara R, Narita M, Knowles TPJ. The chromatin regulator HMGA1a undergoes phase separation in the nucleus. ChemBioChem 2023, 24, e202200450. [co-first author] DOI: doi.org/10.1016/j.bbamem.2022.184078
[43] Schenkel M, Ravamehr-Lake D, Czerniak T, Saenz JP, Krainer G, Schlierf M, Deber CM. Impact of cholesterol and Lumacaftor on the folding of CFTR helical hairpins. Biochim Biophys Acta Biomembr 2023, 1865, 184078. [co-corresponding author] DOI: doi.org/10.1038/s41467-022-35265-7
[42] Arter W, Qi R, Erkamp NA, Krainer G, Didi K, Welsh TJ, Acker J, Nixon-Abell J, Qamar S, Guillén-Boixet J, Franzmann TM, Kuster D, Hyman AA, Borodavka A, St George-Hyslop P, Alberti S, Knowles TPJ. High resolution biomolecular condensate phase diagrams with a combinatorial microdroplet platform. Nat Commun 2022, 13, 7845. [co-first author]
[41] Qian D, Welsh TJ, Erkamp NA, Qamar S, Nixon-Abell J, Krainer G, St George-Hyslop P, Michaels TCT, Knowles TPJ. Tie-lines reveal interactions driving heteromolecular condensate formation. Phys Rev X 2023, 12, 041038. DOI: doi.org/10.1103/PhysRevX.12.041038
[40] Kar M, Dar F, Welsh TJ, Vogel L, Kühnemuth R, Majumdar A, Krainer G, Franzmann TM, Alberti A, Seidel CAM, Knowles TPJ, Hyman AA, Pappu RV.Phase separating RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions. Proc Natl Acad Sci 2022, 119, e2202222119. DOI: doi.org/10.1073/pnas.2202222119
[39] Garaizar A, Espinosa JR, Joseph JA, Krainer G, Shen Y, Knowles TPJ, Collepardo-Guevara R. Aging can transform single-component protein condensates into multiphase architectures. Proc Natl Acad Sci 2022, 119, e2119800119. DOI: doi.org/10.1073/pnas.211980011
[38] Chamachi N, Hartmann A, Ma MQ, Krainer G, Schlierf M. Chaperones Skp and SurA dynamically expand unfolded outer membrane protein X and synergistically disassemble oligomeric aggregates Proc Natl Acad Sci 2022, 119, e2118919119. [co-corresponding author] DOI: doi.org/10.1073/pnas.211891911
[37] Vanderpoorten O, Babar AN, Krainer G, Jacquat RPB, Challa PK, Peter Q, Toprakcioglu Z, Xu CK, Keyser UF, Baumberg J, Kaminski CF, Knowles TPJ. Nanofluidic traps by two-photon fabrication for extended detection of single macromolecules and colloids in solution. ACS Appl Nano Mater 2022, 5, 2, 1995. [co-first author] DOI: doi.org/10.1021/acsanm.1c03691
[36] Welsh TJ, Krainer G, Espinosa JR, Joseph JA, Sridhar A, Jahnel M, Arter WE, Saar KL, Alberti S, Collepardo-Guevara R, Knowles TPJ. Surface electrostatics govern the emulsion stability of biomolecular condensates. Nano Lett 2022, 22, 612. [co-first author] DOI: doi.org/10.1021/acs.nanolett.1c03138
[35] Geiger F, Acker J, Papa G, Wang X, Arter WE, Saar KL, Erkamp NA, Qi R, Bravo JPK, Strauss S, Krainer G, Burrone OR, Jungmann R, Knowles TPJ, Engelke H, Borodavka. A Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. EMBO J 2021, 40:e107711 2020. DOI: doi.org/10.15252/embj.2021107711
[34] Schneider MM, Gautam S, Herling TW, Andrzejwska E, Krainer G, Miller AM, Trinkhaus VA, Peter QAE, Ruggeri FS, Vendruscolo M, Bracher A, Dobson CM, Hartl F-U, Knowles TPJ. The Hsc70 disaggregation machinery removes monomer units directly from α-synuclein fibril ends. Nat Commun 2021, 12, 5999. [co-first author] DOI: doi.org/10.1038/s41467-021-25966-w
[33] Schenkel M, Treff A, Deber CM, Krainer G, Schlierf M. Heat treatment of thioredoxin fusions increases the purity of α-helical transmembrane protein constructs. Prot Sci 2021, 30, 1974. [co-corresponding author] DOI: doi.org/10.1002/pro.4150
[32] Wen J, Hong L, Krainer G, Yao Q-Q, Knowles TPJ, Wu S, Perrett S. Conformational expansion of Tau in condensates promotes irreversible aggregation. J Am Chem Soc 2021, 143, 13056. DOI: doi.org/10.1021/jacs.1c03078
[31] Xu Y, Qi R, Zhu H, Li B, Shen Y, Krainer G, Klenerman D, Knowles TPJ. Liquid–liquid phase-separated systems from reversible gel–sol transition of protein microgels. Adv Mater 2021, 33, 2008670. DOI: https://doi.org/10.1002/adma.202008670
[30] Paketurytė V, Petrauskas V, Zubrienė A, Abian O, Bastos M, Chen W-Y, Moreno MJ, Krainer G, Linkuvienė V, Sedivy A, Velazquez-Campoy A, Williams MA, Matulis D. Uncertainty in protein–ligand binding constants: asymmetric confidence intervals versus standard errors. Eur Biophys J 2021, 50, 661. DOI: doi.org/10.1007/s00249-021-01518-4
[29] Saar KL, Morgunov AS, Qi R, Arter WE, Krainer G, Lee AA, Knowles TPJ. Learning the molecular grammar of protein condensates from sequence determinants and embeddings. Proc Natl Acad Sci 2021, 118, e2019053118. DOI: doi.org/10.1073/pnas.2019053118
[28] Musteikytė G, Jayaram AK, Xu CK, Vendruscolo M, Krainer G, Knowles TPJ. Interactions of α-synuclein oligomers with lipid membranes. Biochim Biophys Acta Biomembr 2021, 1863, 183536. [co-corresponding author] DOI: doi.org/10.1016/j.bbamem.2020.183536
[27] Krainer G, Welsh TJ, Joseph JA, Espinosa JR, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska M, Arter WE, Guillén-Boixet J, Franzmann TM, Qamar S, St George-Hyslop P, Hyman AA, Collepardo-Guevara R, Alberti S, Knowles TPJ. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021, 12, 1085. DOI: doi.org/10.1038/s41467-021-21181-9
[26] Krainer G, Hartmann A, Bogatyr V, Nielsen J, Schlierf M, Otzen D. SDS-induced multi-stage unfolding of a small globular protein through different denatured states revealed by single-molecule fluorescence. Chem Sci 2020, 11, 9141. [co-corresponding author] DOI: doi.org/10.1039/D0SC02100H
[25] Arter WE, Xu CK, Castellana-Cruz M, Herling TW, Krainer G, Saar KL, Kumita JR, Dobson CM, Knowles TPJ. Rapid fractionation and characterisation of α-synuclein oligomers in solution. Nano Lett 2020, 20, 8163. DOI: doi.org/10.1021/acs.nanolett.0c03260
[24] Arter WE, Levin A, Krainer G, Knowles TPJ. Microfluidic approaches for the analysis of protein-protein interactions in solution. Biophys Rev 2020, 12, 575. DOI: doi.org/10.1007/s12551-020-00679-4
[23] Bose SJ, Krainer G, Ng DRS, Schenkel M, Shishido H, Yoon J S, Haggie PM, Schlierf M, Sheppard DN, Skach WR. Towards next generation therapies for cystic fibrosis: Folding function and pharmacology of CFTR. J Cyst Fibros 2020, 19, S25. [co-first author] DOI: doi.org/10.1016/j.jcf.2019.12.009
[22] Krainer G, Schenkel M, Hartmann A, Ravamehr-Lake D, Deber CM, Schlierf M. CFTR transmembrane segments are impaired in their conformational adaptability by a pathogenic loop mutation and dynamically stabilized by Lumacaftor. J Biol Chem 2020, 295, 1985. [co-corresponding author] DOI: doi.org/10.1074/jbc.AC119.011360
[21] Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019, 58, 124. [co-corresponding author] DOI: doi.org/10.1016/j.sbi.2019.05.025
[20] Ramakrishnan S, Schärfen L, Hunold K, Fricke S, Grundmeier G, Schlierf M, Keller A, Krainer G. Enhancing the stability of DNA origami nanostructures: staple strand redesign versus enzymatic ligation. Nanoscale 2019, 11, 16270. [co-corresponding author] DOI: doi.org/10.1039/C9NR04460D
[19] Krainer G, Treff A, Hartmann A, Stone T, Schenkel M, Keller S, Deber CM Schlierf M. A minimal helical-hairpin motif provides molecular-level insights into misfolding and pharmacological rescue of CFTR. Commun Biol 2018, 1, 154. [co-corresponding author] DOI: doi.org/10.1038/s42003-018-0153-0
[18] Frotscher E, Krainer G, Hartmann A, Schlierf M, Keller S. Conformational Dynamics Govern the Free-Energy Landscape of a Membrane-Interacting Protein. ACS Omega 2018, 3, 12026. [co-first author] DOI: doi.org/10.1021/acsomega.8b01609
[17] Ruer M, Krainer G, Gröger P, Schlierf M. ATPase and protease domain movements in the bacterial AAA+ protease FtsH are driven by thermal fluctuations. J Mol Biol 2018, 430, 4592. [co-first author] DOI: doi.org/10.1016/j.jmb.2018.07.023
[16] Paketurytė V, Linkuvienė V, Krainer G, Chen WY, Matulis D. Repeatability precision and accuracy of the enthalpies and Gibbs energies of a protein-ligand binding reaction measured by isothermal titration calorimetry. Eur Biophys J 2018, 48, 139. DOI: doi.org/10.1007/s00249-018-1341-z
[15] 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, Hübner CG, Kallis E, Kapanidis AN, Kim J-Y, 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 Meth 2018, 15, 669. DOI: doi.org/10.1038/s41592-018-0085-0
[14] Frotscher E, Krainer G, Schlierf M, Keller S. Dissecting nanosecond dynamics in membrane proteins with dipolar relaxation upon tryptophan photoexcitation. J Phys Chem Lett 2018, 17, 2241. DOI: doi.org/10.1021/acs.jpclett.8b00834
[13] Hartmann A, Berndt F, Ollmann S, Krainer G, Schlierf M. In situ temperature monitoring in single-molecule FRET experiments. J Chem Phys 2018, 148, 123330. DOI: doi.org/10.1063/1.5008966
[12] Krainer G, Hartmann A, Anandamurugan A, Gracia P, Keller S, Schlierf M. Ultrafast protein folding through polar interactions in membrane-mimetic environments. J Mol Biol 2018, 430, 554. [co-corresponding author] DOI: doi.org/10.1016/j.jmb.2017.10.031
[11] Ramakrishnan S, Krainer G, Grundmeier G, Schlierf M, Keller A. Cation-Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride. Small 2017, 13, 1702100. DOI: doi.org/10.1002/smll.201702100
[10] Krainer G, Gracia P, Frotscher E, Hartmann A, Gröger P, Keller S, Schlierf M. Slow Interconversion in a Heterogeneous Unfolded-State Ensemble of Outer-Membrane Phospholipase A. Biophys J 2017, 113, 1280. DOI: doi.org/10.1016/j.bpj.2017.05.037
[9] Linkuvienė V, Krainer G, Chen W, Matulis D. Isothermal Titration Calorimetry for Drug Design: Precision of the Enthalpy and Binding Constant Measurements and Comparison of the Instrument. Anal Biochem 2016, 515, 61. DOI: doi.org/10.1016/j.ab.2016.10.005
[8] Ramakrishnan S, Krainer G, Grundmeier G, Schlierf M, Keller A. Structural Stability of DNA Origami Nanostructures in the Presence of Chaotropic Agents. Nanoscale 2016, 8, 10398. [co-first author] DOI: doi.org/10.1039/C6NR00835F
[7] Hartmann A, Krainer G, Keller S, Schlierf M. Quantification of Millisecond Protein-Folding Dynamics in Membrane-Mimetic Environments by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Anal Chem 2015, 87, 11224. [co-first author] DOI: doi.org/10.1021/acs.analchem.5b03207
[6] Krainer G, Hartmann A, Schlierf M. farFRET: Extending the Range in Single-Molecule FRET Experiments beyond 10 nm. Nano Lett 2015, 15, 5826. [co-corresponding author] DOI: doi.org/10.1021/acs.nanolett.5b01878
[5] Krainer G, Keller, S. Single-Experiment Displacement Assay for Quantifying High-Affinity Binding by Isothermal Titration Calorimetry. Methods 2015, 76, 116. DOI: doi.org/10.1016/j.ymeth.2014.10.034
[4] Hartmann A, Krainer G, Schlierf M. Different Fluorophore Labeling Strategies and Designs Affect Millisecond Kinetics of DNA Hairpins. Molecules 2014, 19, 13735. [co-first author] DOI: doi.org/10.3390/molecules190913735
[3] Krainer G, Broecker J, Vargas C, Fanghänel J, Keller S. Quantifying High-Affinity Binding of Hydrophobic Ligands by Isothermal Titration Calorimetry. Anal Chem 2012, 84, 10715. DOI: doi.org/10.1021/ac3025575
[2] Pechstein A, Bacetic J, Vahedi-Faridi A, Gromova K, Sundborger A, Tomlin N, Krainer G, Vorontsova O, Schäfer JG, Owe SG, Cousin MA, Saenger W, Shupliakov O, Haucke V. Regulation of Synaptic Vesicle Recycling by Complex Formation Between Intersectin 1 and the Clathrin Adaptor Complex AP2. Proc Natl Acad Sci 2010, 107, 4206. doi.org/10.1073/pnas.0911073107
[1] Kahlfeldt N, Vahedi-Faridi A, Koo SJ, Schäfer JG, Krainer G, Keller S, Saenger W, Krauss M, Haucke V. Molecular Basis for Association of PIPKIγ-p90 with Clathrin Adaptor AP-2. J Biol Chem 2010, 285, 2734. DOI: https://doi.org/10.1074/jbc.M109.074906