Publications

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Sequence determinants of protein phase separation and recognition by protein phase-separated condensates through molecular dynamics and active learning

Arya Changiarath, Aayush Arya, Vasileios A. Xenidis, Jan Padeken, and Lukas S. Stelzl

Citation Count: 3
Published: 2025

Polymers: The Hidden Heroes of Life

D. Dormann, R. Fröhlich, T. Dias, N. Belo do Couto, N. Heinss, S. Hutten, K. Küssner, A. Ceron-Noriega, L. Chargui, M. Gelléri, A. Gopalan, K. Hertäg, R. Piccinno, C. Rickert, A. Schaaf, E. Schumbera, S. Shoup, F. Stiehler, P. Turunen, M. A. Andrade-Navarro, P. Beli, P. Besenius, M. Bonn, R. Dahm, S. Dhiman, S. Gerber, M. Girard, B. Hülsmann, R. Ketting, E. Kim, J. König, K. Kremer, O. Kukharenko, K. Landfester, K. Luck, A. Methner, J. Michels, M. M. Möckel, S. Morsbach, S. Ritz, S. Schick-Nickolaus, F. Schmid, C. Schmidt, D. Schneider, S. Schweiger, T. Speck, L. Stelzl, M. te Vrugt, H. D. Ulrich, P. Virnau, A. Wachter, A. Walther, T. Weil, S. Wittmann, and E. A. Lemke

Citation Count: 0
Published: 2025

Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition

Kumar Gaurav, Virginia Busetto, Diego Javier Páez-Moscoso, Arya Changiarath, Sonya M. Hanson, Sebastian Falk, René F. Ketting, and Lukas S. Stelzl

Citation Count: 1
Published: 2025-11

A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles

Daniel B. Grabarczyk, Eric J. Aird, Vanessa Reznikow, Paul C. Kirchgatterer, Julian F. Ehrmann, Robert Kurzbauer, Lillie E. Bell, Max J. Kellner, Ritika Aggarwal, Alexander Schleiffer, Victoria Faas, Luiza Deszcz, Anton Meinhart, Gijs A. Versteeg, Josef M. Penninger, Lukas S. Stelzl, Moritz M. Gaidt, Ingrid Tessmer, Jacob E. Corn, and Tim Clausen

Citation Count: 2
Published: 2025-10

Bidirectional control of a metabolic transition by the GID ubiquitin ligase

Ka-Yiu Edwin Kong, Christian Ochs, Cécile Debarnot, Matti Myllykoski, Denís Arribas Blanco, Susmitha Shankar, Vivien A.C. Schoonenberg, Julia Kończak, Julia K. Varga, Ora Schueler-Furman, Katja Luck, Falk Butter, Jia-Xuan Chen, Lukas S. Stelzl, Thomas Arnesen, and Anton Khmelinskii

Citation Count: 1

Deciphering driving forces of biomolecular phase separation from simulations

Lars V. Schäfer, and Lukas S. Stelzl

Citation Count: 5
Published: 2025-6

Proton First: Rationalizing a Proton Transfer in a Protein‐Fragment Complex

Helge Vatheuer, Jonas Paulus, Lisa Johannknecht, Gerald Keller, Rebecca Maria Ziora, Lukas S. Stelzl, and Paul Czodrowski

Citation Count: 1
Published: 2025-10-15

Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates

Emanuele Zippo, Dorothee Dormann, Thomas Speck, and Lukas S. Stelzl

Citation Count: 8
Published: 2025-5-19

Promoter and Gene-Body RNA-Polymerase II co-exist in partial demixed condensates

Arya Changiarath, David Flores-Solis, Jasper J. Michels, Rosa Herrera Rodriguez, Sonya M. Hanson, Friederike Schmid, Markus Zweckstetter, Jan Padeken, and Lukas S. Stelzl

Citation Count: 5

Structure and Internal Dynamics of Short RNA Duplexes Determined by a Combination of Pulsed EPR Methods and MD Simulations

Maximilian Gauger, Marcel Heinz, Anna‐Lena J. Halbritter, Lukas S. Stelzl, Nicole Erlenbach, Gerhard Hummer, Snorri Th. Sigurdsson, and Thomas F. Prisner

Citation Count: 13
Published: 2024-6-3

Multi-scale Simulations of MUT-16 Scaffold Protein Phase Separation and Client Recognition

Kumar Gaurav, Virginia Busetto, Diego Javier Páez-Moscoso, Arya Changiarath, Sonya M. Hanson, Sebastian Falk, René F. Ketting, and Lukas S. Stelzl

Citation Count: 2

Hierarchical Assembly of Single-Stranded RNA

Lisa M. Pietrek, Lukas S. Stelzl, and Gerhard Hummer

Citation Count: 6
Published: 2024-3-12

Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II

David Flores-Solis, Irina P. Lushpinskaia, Anton A. Polyansky, Arya Changiarath, Marc Boehning, Milana Mirkovic, James Walshe, Lisa M. Pietrek, Patrick Cramer, Lukas S. Stelzl, Bojan Zagrovic, and Markus Zweckstetter

Citation Count: 55
Published: 2023-9-25

Structural ensembles of disordered proteins from hierarchical chain growth and simulation

Lisa M. Pietrek, Lukas S. Stelzl, and Gerhard Hummer

Citation Count: 27
Published: 2023-2

Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN

Samoil Sekulovski, Lukas Sušac, Lukas S. Stelzl, Robert Tampé, and Simon Trowitzsch

Citation Count: 21
Published: 2023-6

Single-chain and condensed-state behavior of hnRNPA1 from molecular simulations

D. Janka Bauer, Lukas S. Stelzl, and Arash Nikoubashman

Citation Count: 25
Published: 2022-10-21

Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks

Justus F. Gräf, Ivan Mikicic, Xiaofei Ping, Claudia Scalera, Katharina Mayr, Lukas S. Stelzl, Petra Beli, and Sebastian A. Wagner

Citation Count: 12
Published: 2022-9

Disease‐linked TDP‐43 hyperphosphorylation suppresses TDP‐43 condensation and aggregation

Lara A Gruijs da Silva, Francesca Simonetti, Saskia Hutten, Henrick Riemenschneider, Erin L Sternburg, Lisa M Pietrek, Jakob Gebel, Volker Dötsch, Dieter Edbauer, Gerhard Hummer, Lukas S Stelzl, and Dorothee Dormann

Citation Count: 163
Published: 2022-4-19

Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations

Karen Palacio-Rodriguez, Hadrien Vroylandt, Lukas S. Stelzl, Fabio Pietrucci, Gerhard Hummer, and Pilar Cossio

Citation Count: 23
Published: 2022-8-18

Molecular determinants of dynamic protein-protein interactions in the functional cycle of the membrane protein DsbD

Lukas S. Stelzl, Paraskevi Kritsiligkou, Ahmad Reza Mehdipour, Andrew J. Baldwin, Stuart J. Ferguson, Despoina A. I. Mavridou, Mark S. P. Sansom, and Christina Redfield

Citation Count: 0

Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

Lukas S. Stelzl, Lisa M. Pietrek, Andrea Holla, Javier Oroz, Mateusz Sikora, Jürgen Köfinger, Benjamin Schuler, Markus Zweckstetter, and Gerhard Hummer

Citation Count: 73
Published: 2022-3-28

Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model

Zakarya Benayad, Sören von Bülow, Lukas S. Stelzl, and Gerhard Hummer

Citation Count: 206
Published: 2021-1-12

Compaction of RNA Duplexes in the Cell

Alberto Collauto, Sören von Bülow, Dnyaneshwar B. Gophane, Subham Saha, Lukas S. Stelzl, Gerhard Hummer, Snorri Th. Sigurdsson, and Thomas F. Prisner

Citation Count: 0

High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label

Marcel Heinz, Nicole Erlenbach, Lukas S Stelzl, Grace Thierolf, Nilesh R Kamble, Snorri Th Sigurdsson, Thomas F Prisner, and Gerhard Hummer

Citation Count: 29
Published: 2020-1-24

Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

Lisa M. Pietrek, Lukas S. Stelzl, and Gerhard Hummer

Citation Count: 86
Published: 2020-1-14

Local frustration determines loop opening during the catalytic cycle of an oxidoreductase

Lukas S Stelzl, Despoina AI Mavridou, Emmanuel Saridakis, Diego Gonzalez, Andrew J Baldwin, Stuart J Ferguson, Mark SP Sansom, and Christina Redfield

Citation Count: 18
Published: 2020-6-22

Efficient Ensemble Refinement by Reweighting

Jürgen Köfinger, Lukas S. Stelzl, Klaus Reuter, César Allande, Katrin Reichel, and Gerhard Hummer

Citation Count: 95
Published: 2019-5-14

Orientation Selective 2D-SIFTER Experiments at X-Band Frequencies

A. M. Bowen, N. Erlenbach, P. van Os, L. S. Stelzl, S. Th. Sigurdsson, and T. F. Prisner

Citation Count: 10
Published: 2018-12

Dynamics of Nucleic Acids at Room Temperature Revealed by Pulsed EPR Spectroscopy

Markus Gränz, Nicole Erlenbach, Philipp Spindler, Dnyaneshwar B. Gophane, Lukas S. Stelzl, Snorri Th. Sigurdsson, and Thomas F. Prisner

Citation Count: 20
Published: 2018-8-13

Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments

Kara K. Grotz, Mark F. Nueesch, Erik D. Holmstrom, Marcel Heinz, Lukas S. Stelzl, Benjamin Schuler, and Gerhard Hummer

Citation Count: 35
Published: 2018-12-13

Precision DEER Distances from Spin-Label Ensemble Refinement

Katrin Reichel, Lukas S. Stelzl, Jürgen Köfinger, and Gerhard Hummer

Citation Count: 27
Published: 2018-10-4

Optimal Destabilization of DNA Double Strands by Single‐Nucleobase Caging

Patrick Seyfried, Marcel Heinz, György Pintér, Dean‐Paulos Klötzner, Yvonne Becker, Michael Bolte, Hendrik R. A. Jonker, Lukas S. Stelzl, Gerhard Hummer, Harald Schwalbe, and Alexander Heckel

Citation Count: 20
Published: 2018-11-27

Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron–Electron Double Resonance and Molecular Dynamics

Lukas S. Stelzl, Nicole Erlenbach, Marcel Heinz, Thomas F. Prisner, and Gerhard Hummer

Citation Count: 50
Published: 2017-8-30

1H, 13C and 15N resonance assignments for the oxidized and reduced states of the N-terminal domain of DsbD from Escherichia coli

Despoina A. I. Mavridou, Lukas S. Stelzl, Stuart J. Ferguson, and Christina Redfield

Citation Count: 4
Published: 2012-10

Stelzl Lab

Publications

Sequence determinants of protein phase separation and recognition by protein phase-separated condensates through molecular dynamics and active learning

Polymers: The Hidden Heroes of Life

Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition

A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles

Bidirectional control of a metabolic transition by the GID ubiquitin ligase

Deciphering driving forces of biomolecular phase separation from simulations

Proton First: Rationalizing a Proton Transfer in a Protein‐Fragment Complex

Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates

Promoter and Gene-Body RNA-Polymerase II co-exist in partial demixed condensates

Structure and Internal Dynamics of Short RNA Duplexes Determined by a Combination of Pulsed EPR Methods and MD Simulations

Multi-scale Simulations of MUT-16 Scaffold Protein Phase Separation and Client Recognition

Hierarchical Assembly of Single-Stranded RNA

Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II

Structural ensembles of disordered proteins from hierarchical chain growth and simulation

Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN

Single-chain and condensed-state behavior of hnRNPA1 from molecular simulations

Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks

Disease‐linked TDP‐43 hyperphosphorylation suppresses TDP‐43 condensation and aggregation

Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations

Molecular determinants of dynamic protein-protein interactions in the functional cycle of the membrane protein DsbD

Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model

Compaction of RNA Duplexes in the Cell

High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label

Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

Local frustration determines loop opening during the catalytic cycle of an oxidoreductase

Efficient Ensemble Refinement by Reweighting

Orientation Selective 2D-SIFTER Experiments at X-Band Frequencies

Dynamics of Nucleic Acids at Room Temperature Revealed by Pulsed EPR Spectroscopy

Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments

Precision DEER Distances from Spin-Label Ensemble Refinement

Optimal Destabilization of DNA Double Strands by Single‐Nucleobase Caging

Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron–Electron Double Resonance and Molecular Dynamics

Kinetics from Replica Exchange Molecular Dynamics Simulations

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

Structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle

Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

1H, 13C and 15N resonance assignments for the oxidized and reduced states of the N-terminal domain of DsbD from Escherichia coli