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Intro
Schäfer LV, Stelzl LS (2025) Deciphering driving forces of biomolecular phase separation from simulations. Current Opinion in Structural Biology 92:103026. https://doi.org/10.1016/j.sbi.2025.103026
Zippo E, Dormann D, Speck T, Stelzl LS (2025) Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates. Nat Commun 16:4649. https://doi.org/10.1038/s41467-025-59676-4
Ruan H, Lemke EA (2025) Resolving Conformational Plasticity in Mammalian Cells with High-Resolution Fluorescence Tools. Annual Review of Physical Chemistry 76:103–128. https://doi.org/10.1146/annurev-physchem-082423-030632
Strom JM, Luck K (2025) Bias in, bias out - AlphaFold-Multimer und die strukturelle Komplexität von Proteinschnittstellen. Current Opinion in Structural Biology 91:103002. https://doi.org/10.1016/j.sbi.2025.103002
Yu M, Gruzinov AYu, Ruan H, et al (2024) A genetically encoded anomalous SAXS ruler to probe the dimensions of intrinsically disordered proteins. Proceedings of the National Academy of Sciences 121:e2415220121. https://doi.org/10.1073/pnas.2415220121
Brzezinski M, Argudo PG, Scheidt T, et al (2024) Protein-Specific Crowding Accelerates Agaging in Protein Condensates. Biomacromolecules. https://doi.org/10.1021/acs.biomac.4c00609
Brzezinski M, Argudo PG, Scheidt T, et al (2024) Protein-Specific Crowding Accelerates Agaging in Protein Condensates. Biomacromolecules. https://doi.org/10.1021/acs.biomac.4c00609
Bhattacharjee R, Lemke EA (2024) Potential vs Challenges of Expanding the Protein Universe With Genetic Code Expansion in Eukaryotic Cells. Journal of Molecular Biology 436:168807. https://doi.org/10.1016/j.jmb.2024.168807
Schartel L, Jann C, Wierczeiko A, et al (2024) Selective RNA pseudouridinylation in situ by circular gRNAs in designer organelles. Nat Commun 15:9177. https://doi.org/10.1038/s41467-024-53403-1
Junglas B, Kartte D, Kutzner M, et al (2024) Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies. Nat Struct Mol Biol 1-16. https://doi.org/10.1038/s41594-024-01399-z
Bhattacharjee R, Lemke EA (2024) Potential vs Challenges of Expanding the Protein Universe With Genetic Code Expansion in Eukaryotic Cells. Zeitschrift für Molekularbiologie 168807. https://doi.org/10.1016/j.jmb.2024.168807
Changiarath A, Arya A, Xenidis VA, et al (2024) Sequence determinants of protein phase separation and recognition by protein phase-separated condensates through molecular dynamics and active learning. Faraday Discuss. https://doi.org/10.1039/d4fd00099d
Jann C, Giofré S, Bhattacharjee R, Lemke EA (2024) Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 124:10281-10362. https://doi.org/10.1021/acs.chemrev.3c00878
Geist JL, Lee CY, Strom JM, et al (2024) Generation of a high confidence set of domain-domain interface types to guide protein complex structure predictions by AlphaFold. Bioinformatics btae482. https://doi.org/10.1093/bioinformatics/btae482
Junglas B, Hudina E, Schönnenbeck P, et al (2024) Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies. Nat Struct Mol Biol 1-12. https://doi.org/10.1038/s41594-024-01359-7
Emmanouilidis L, Bartalucci E, Kan Y, et al (2024) A solid beta-sheet structure is formed at the surface of FUS droplets during aging. Nat Chem Biol 20:1044-1052. https://doi.org/10.1038/s41589-024-01573-w
Sushkin ME, Jung M, Lemke EA (2024) Tuning the Functionality of Designer Translating Organelles with Orthogonal tRNA Synthetase/tRNA Pairs. Zeitschrift für Molekularbiologie 168728. https://doi.org/10.1016/j.jmb.2024.168728
Samanta A, Baranda Pellejero L, Masukawa M, Walther A (2024) DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 8:454-470. https://doi.org/10.1038/s41570-024-00606-1
Dormann D, Lemke EA (2024) Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 26:851-858. https://doi.org/10.1038/s41556-024-01423-w
Ren Y, Zhou Z, Maxeiner K, et al (2024) Supramolecular Assembly in Live Cells Mapped by Real-Time Phasor-Fluorescence Lifetime Imaging. J Am Chem Soc 146:11991-11999. https://doi.org/10.1021/jacs.4c01279
Lemke EA, Babu MM, Kriwacki RW, et al (2024) Intrinsic disorder: Ein Begriff zur Definition des spezifischen physikalisch-chemischen Merkmals der konformationellen Heterogenität von Proteinen. Molekulare Zelle 84:1188-1190. https://doi.org/10.1016/j.molcel.2024.02.024
Quarta N, Bhandari TR, Girard M, et al (2024) Monomer unfolding of a bacterial ESCRT-III superfamily member is coupled to oligomer disassembly. Protein Science 33:e5187. https://doi.org/10.1002/pro.5187
Krevert CS, Chavez D, Chatterjee S, et al (2023) Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics. J Phys Chem Lett 14:11224-11234. https://doi.org/10.1021/acs.jpclett.3c02790
Bronkhorst AW, Lee CY, Möckel MM, et al (2023) An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori. The EMBO Journal n/a:e114072. https://doi.org/10.15252/embj.2023114072
Rahmanto AS, Blum CJ, Scalera C, et al (2023) K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Molekulare Zelle 0: https://doi.org/10.1016/j.molcel.2023.10.011
Fung HKH, Hayashi Y, Salo VT, et al (2023) Genetisch kodierte multimere Tags für die subzelluläre Proteinlokalisierung in der Kryo-EM. Nat Methods 1-9. https://doi.org/10.1038/s41592-023-02053-0
Schlösser L, Sachse C, Low HH, Schneider D (2023) Conserved structures of ESCRT-III superfamily members across domains of life. Trends in Biochemical Sciences 48:993-1004. https://doi.org/10.1016/j.tibs.2023.08.009
Wierczeiko A, Pastore S, Mündnich S, et al (2023) NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis. Bioinformatics 39:btad492. https://doi.org/10.1093/bioinformatics/btad492
Schumbera E, Mier P, Andrade-Navarro MA (2023) Phase separating Rho: a widespread regulatory function of disordered regions in proteins revealed in bacteria. Sig Transduct Target Ther 8:253. https://doi.org/10.1038/s41392-023-01505-5
Roth P, Meyer R, Harley I, et al (2023) Supramolecular assembly guided by photolytic redox cycling. Nat Synth. https://doi.org/10.1038/s44160-023-00343-1
Maltseva D, Chatterjee S, Yu C-C, et al (2023) Fibril formation and ordering of disordered FUS LC driven by hydrophobic interactions. Nat Chem 1-9. https://doi.org/10.1038/s41557-023-01221-1
Yu M, Heidari M, Mikhaleva S, et al (2023) Visualizing the disordered nuclear transport machinery in situ. Nature 617:162-169. https://doi.org/10.1038/s41586-023-05990-0
Agam G, Gebhardt C, Popara M, et al (2023) Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nat Methods 1-13. https://doi.org/10.1038/s41592-023-01807-0
Ebersberger S, Hipp C, Mulorz MM, et al (2023) FUBP1 ist ein allgemeiner Spleißfaktor, der die Erkennung von 3′-Spleißstellen und das Spleißen von langen Introns erleichtert. Molecular Cell 83:2653-2672.e15. https://doi.org/10.1016/j.molcel.2023.07.002
Scheidt T, Ruan H, Yu M, Lemke EA (2023) Stressing the role of a short linear motif in ataxin-2 condensation. Molecular Cell 83:1961-1963. https://doi.org/10.1016/j.molcel.2023.05.024
Wettermann S, Datta R, Virnau P (2023) Influence of ionic conditions on knotting in a coarse-grained model for DNA. Frontiers in Chemistry 10:. https://doi.org/10.3389/fchem.2022.1096014
Gruijs da Silva LA, Simonetti F, Hutten S, et al (2022) Krankheitsbedingte TDP-43-Hyperphosphorylierung unterdrückt TDP-43-Kondensation und -Aggregation. The EMBO Journal 41:e108443. https://doi.org/10.15252/embj.2021108443
Chakraborty S, Berac CM, Urschbach M, et al (2022) Predicting the Supramolecular Assembly of Amphiphilic Peptides from Comprehensive Coarse-Grained Simulations. ACS Appl Polym Mater 4:822-831. https://doi.org/10.1021/acsapm.1c01208
Jin E, Fu S, Hanayama H, et al (2022) A Nanographen-Based Two-Dimensional Covalent Organic Framework as a Stable and Efficient Photocatalyst. Angewandte Chemie International Edition 61:e202114059. https://doi.org/10.1002/anie.202114059
Prawatborisut M, Oberländer J, Jiang S, et al (2022) Temperature-Responsive Nanoparticles Enable Specific Binding of Apolipoproteins from Human Plasma. Small 18:2103138. https://doi.org/10.1002/smll.202103138
Mosler T, Conte F, Longo GMC, et al (2021) R-loop proximity proteomics identifiziert eine Rolle von DDX41 in der Transkription-assoziierten genomischen Instabilität. Nat Commun 12:7314. https://doi.org/10.1038/s41467-021-27530-y
Zegota MM, Müller MA, Lantzberg B, et al (2021) Dual Stimuli-Responsive Dynamic Covalent Peptide Tags: Toward Sequence-Controlled Release in Tumor-like Microenvironments. J Am Chem Soc 143:17047-17058. https://doi.org/10.1021/jacs.1c06559
Varga J, Kube M, Luck K, Schick S (2021) The BAF chromatin remodeling complexes: structure, function, and synthetic lethalities. Biochemical Society Transactions 49:1489-1503. https://doi.org/10.1042/BST20190960
Jin E, Yang Q, Ju C-W, et al (2021) A Highly Luminescent Nitrogen-Doped Nanographene as an Acid- and Metal-Sensitive Fluorophore for Optical Imaging. J Am Chem Soc 143:10403-10412. https://doi.org/10.1021/jacs.1c04880
Chen C, Singh MK, Wunderlich K, et al (2021) Polymerzyklisierung für die Entstehung von hierarchischen Nanostrukturen. Nat Commun 12:3959. https://doi.org/10.1038/s41467-021-24222-5
Dietz S, Almeida MV, Nischwitz E, et al (2021) Die doppelsträngigen DNA-bindenden Proteine TEBP-1 und TEBP-2 bilden einen telomeren Komplex mit POT-1. Nat Commun 12:2668. https://doi.org/10.1038/s41467-021-22861-2
Dittrich F, Speck T, Virnau P (2021) Kritisches Verhalten in aktiven Gittermodellen der bewegungsinduzierten Phasentrennung. Eur Phys J E 44:53. https://doi.org/10.1140/epje/s10189-021-00058-1
Tubiana L, Kobayashi H, Potestio R, et al (2021) Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators. J Phys: Condens Matter 33:204003. https://doi.org/10.1088/1361-648X/abf20c
Worpenberg L, Paolantoni C, Longhi S, et al (2021) Ythdf ist ein N6-Methyladenosin-Leser, der die Fmr1-Ziel-mRNA-Auswahl moduliert und das axonale Wachstum in Drosophila einschränkt. Das EMBO Journal 40:e104975. https://doi.org/10.15252/embj.2020104975
Weißbach S, Sys S, Hewel C, et al (2021) Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines. BMC Genomics 22:62. https://doi.org/10.1186/s12864-020-07362-8