Publications | University of Tübingen

Selected Publications

M. Panfilov*, G. Mao*, J. Guo, J. Aguirre Rivera, A. Sabantsev and S. Deindl
Multiplexed single-molecule characterization at the library scale
*equal contribution
Nature Protocols 2026

A. N. Kapanidis, L. Muras, K. Sreenivasa, J. P. Hazra, J. van Noort, C. Joo and S. Deindl
From sequence to function: Bridging single-molecule kinetics and molecular diversity
Science 2026

J. Weiss, L. Vecchia, D. Domjan, S. Cavadini, A. Sabantsev, G. Kempf, G. R. Pathare, K. Brackmann, A. K. Michael, L. Kater, E. Hietter-Pfeiffer, M. Haddawi, U. P. Kuber, S. Mühlhäusser, R. S. Grand, M. B. Stadler, S. Deindl and N. H. Thomä
The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2
Molecular Cell 2026

L. Bacic, G. Gaullier, J. Mohapatra, G. Mao, K. Brackmann, M. Panfilov, G. Liszczak, A. Sabantsev, and S. Deindl
Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1
Nature Communications 2024

J. Aguirre Rivera*, G. Mao*, A. Sabantsev†, M. Panfilov†, Q. Hou, M. Lindell, C. Chanez, F. Ritort, M. Jinek, S. Deindl
Massively parallel analysis of single-molecule dynamics on next generation sequencing chips
*equal contribution
Science 2024
see also the accompanying SciLifeLab news item

A. Sabantsev, G. Mao, J. Aguirre Rivera, M. Panfilov, A. Arseniev, O. Ho, M. Khodorkovskiy, S. Deindl
Spatiotemporally controlled generation of NTPs for single-molecule studies
Nature Chemical Biology 2022
see also the accompanying News & Views article Very fast nucleotides on demand

E. Marklund, G. Mao*, J. Yan*, S. Zikrin, E. Abdurakhmanov, S. Deindl*, J. Elf*
Sequence specificity in DNA binding is mainly governed by association
*equal contribution
Science 2022

L. Bacic, G. Gaullier, A. Sabantsev, L. C. Lehmann, K. Brackmann, D. Dimakou, M. Halic, G. Hewitt, S. J. Boulton, S. Deindl
Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome
eLife 2021

I. Regadas, O. Dahlberg, R. Vaid, O. Ho, S. Belikov, G. Dixit, S. Deindl, J. Wen, M. Mannervik
A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation
Molecular Cell 2021

G. Hewitt, V. Borel, S. Segura-Bayona, T. Takaki, P. Ruis, R. Bellelli, L. C. Lehmann, L. Sommerova, A. Vancevska, A. Tomas-Loba, K. Zhu, C. Cooper, K. Fugger, H. Patel, R. Goldstone, D. Schneider-Luftman, E. Herbert, G. Stamp, R. Brough, S. Pettitt, C. J. Lord, S. C. West, I. Ahel, D. Ahel, J. R. Chapman, S. Deindl , S. J. Boulton
Defective ALC1 nucleosome remodeling confers PARPi sensitization and synthetic lethality with HRD
Molecular Cell 2021

E. Marklund, B. van Oosten, G. Mao, E. Amselem, K. Kipper, A. Sabantsev, A. Emmerich, D. Globisch, X. Zheng, L. C. Lehmann, O. Berg, M. Johansson, J. Elf, S. Deindl
DNA surface exploration and operator bypassing during target search
Nature 2020

L. Bacic, A. Sabantsev, and S. Deindl
Recent advances in single-molecule fluorescence microscopy render structural biology dynamic
Current Opinion in Structural Biology 2020

G. Bowman and S. Deindl
Remodeling the genome with DNA twists
Science 2019

A. Sabantsev, R.F. Levendosky, X. Zhuang, G.D. Bowman and S. Deindl
Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling
Nature Communications 2019

L.C. Lehmann, G. Hewitt, S. Aibara, A. Leitner, E. Marklund, S.L. Maslen, V. Maturi, Y. Chen, D. van der Spoel, J.M. Skehel, A. Moustakas, S. J. Boulton, and S. Deindl
Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1
Molecular Cell 2017

W.L. Hwang*, S. Deindl*, B.T. Harada, and X. Zhuang
Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA
*equal contribution
Nature 2014

S. Deindl, W.L. Hwang, S.K. Hota, T.R. Blosser, P. Prasad, B. Bartholomew, and X. Zhuang
ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps
Cell 2013

S. Deindl, T.A. Kadlecek, T. Brdicka, X. Cao, A. Weiss and J. Kuriyan
Structural basis for the inhibition of tyrosine kinase activity of ZAP-70
Cell 2007

O.S. Rosenberg, S. Deindl, R.J. Sung, A.C. Nairn, J. Kuriyan
Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme
Cell 2005

Complete list of publications

F. Liu, C. Wen, S. Deindl and Z. Zhang
Stability and reliability of carbon-coated solid-state nanopores for single molecule analysis
Nanotechnology 2026

F. Liu, Q. Hu, A. Sabantsev, G. Di Muccio, S. Zeng, M. Chinappi, S. Deindl and Z. Zhang
A Nanopore-Gated Subattoliter Silicon Nanocavity for Single-Molecule Trapping and Analysis without Applying an External Force
ACS Nano 2026

H. R. Bridges, L. Bacic, S. Deindl and G. Gaullier
Cryo-EM structure of ALC1 in an open conformation bound to a PARylated nucleosome
Acta Crystallographica Section D, Structural Biology 2026

A. N. Kapanidis, L. Muras, K. Sreenivasa, J. P. Hazra, J. van Noort, C. Joo and S. Deindl
From sequence to function: Bridging single-molecule kinetics and molecular diversity
Science 2026

M. Panfilov*, G. Mao*, J. Guo, J. Aguirre Rivera, A. Sabantsev and S. Deindl
Multiplexed single-molecule characterization at the library scale
*equal contribution
Nature Protocols 2026

H. Osterholz, A. Stevens, M. L. Abramsson, D. Lama, K. Brackmann, A. Rising, A. Elofsson, E. G. Marklund, S. Deindl, A. Leppert and M. Landreh
Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains
JACS Au 2025

A. Sabantsev and S. Deindl
The voyage is as important as the harbor
eLife 2024

E. Marklund, G. Mao*, J. Yan*, S. Zikrin, E. Abdurakhmanov, S. Deindl*, J. Elf*
Sequence specificity in DNA binding is mainly governed by association
*equal contribution
Science 2022

B. Luescher, I. Ahel, M. Altmeyer, A. Ashworth, P. Bai, P. Chang, M. Cohen, D. Corda, F. Dantzer, M. D. Daugherty, T. M. Dawson, V. L. Dawson, S. Deindl, A. R. Fehr, K. L. H. Feijs, D. V. Filippov, J-P. Gagné, G. Grimaldi, S. Guettler, N. C. Hoch, M. O. Hottiger, P. Korn, W. L. Kraus, A. Ladurner, L. Lehtiö, A. K. L. Leung, C. J. Lord, A. Mangerich, I. Matic, J. Matthews, G-L. Moldovan, J. Moss, G. Natoli, M. L. Nielsen, M. Niepel, F. Nolte, J. Pascal, B. M. Paschal, K. Pawlowski, G. G. Poirier, S. Smith, G. Timinszky, Z-Q. Wang, J. Yélamos, X. Yu, R. Zaja, M. Ziegler
ADP-ribosyltransferases, an update on function and nomenclature
FEBS Journal 2022

S. Deindl, J. Elf
More Than Just Letters and Chemistry: Genomics Goes Mechanics
Trends in Biochemical Sciences 2021

L. C. Lehmann, L. Bacic, G. Hewitt, K. Brackmann, A. Sabantsev, G. Gaullier, S. Pytharopoulou, G. Degliesposti, H. Okkenhaug, S. Tan, A. Costa, J. M. Skehel, S. J. Boulton, S. Deindl
Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch
Cell Reports 2020

L. Bacic, A. Sabantsev, and S. Deindl
Recent advances in single-molecule fluorescence microscopy render structural biology dynamic
Current Opinion in Structural Biology 2020

G. Bowman and S. Deindl
Remodeling the genome with DNA twists
Science 2019

C. Romilly, S. Deindl and E.G.H. Wagner
The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5′ structure element
PNAS 2019

A. Sabantsev, R.F. Levendosky, X. Zhuang, G.D. Bowman and S. Deindl
Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling
Nature Communications 2019

Q. Liao, M. Lüking , D.M. Krüger , S. Deindl , J. Elf , P.M. Kasson and S.C.L. Kamerlin
Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition
J. Phys. Chem. B 2019

E. Marklund*, E. Amselem*, K. Kipper, X. Zheng, M. Johansson, S. Deindl and J. Elf
Direct observation of rotation-coupled protein diffusion along DNA on the microsecond timescale
bioRxiv 2018

C. Ballet, M. S. P. Correia, L. P. Conway, T. L. Locher, L.C. Lehmann, N. Garg, M. Vujasinovic, S. Deindl, J.-M. Löhr, and D. Globisch
New enzymatic and mass spectrometric methodology for the selective investigation of gut microbiota-derived metabolites
Chemical Science 2018

K. Kipper, N. Eremina, E. Marklund, S. Tubasum, G. Mao, L. C. Lehmann, J. Elf, and S. Deindl
Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI
PLoS One 2018

R. Levendosky, A. Sabantsev, S. Deindl, G. Bowman
The Chd1 chromatin remodeler shifts hexasomes unidirectionally
eLife 2016

F. Saupe, M. Reichel, E. Huijbers, J. Femel, P. Markgren, E. Andersson, S. Deindl, H. Danielsson, L. Hellman, and A. Olsson
Development of a novel therapeutic vaccine carrier that sustains high antibody titers against several targets simultaneously
FASEB J 2016

B.T. Harada, W.L. Hwang, S. Deindl, N. Chatterjee, B. Bartholomew, X. Zhuang
Stepwise nucleosome translocation by RSC remodeling complexes
eLife 2016

W.L. Hwang*, S. Deindl*, B.T. Harada, and X. Zhuang
Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA
*equal contribution
Nature 2014

Q. Yan, T. Barros, P.R. Visperas, S. Deindl, T.A. Kadlecek, A. Weiss, and J. Kuriyan
Structural basis for activation of ZAP-70 by phosphorylation of the SH2-kinase linker
Molecular and Cellular Biology 2013

S.K. Hota, S.K. Bhardwaj, S. Deindl, Y. Lin, X. Zhuang, and B. Bartholomew
Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains
Nature Structural & Molecular Biology 2013

S. Deindl and X. Zhuang
Monitoring conformational dynamics with single-molecule fluorescence energy transfer: applications in nucleosome remodeling
Methods in Enzymology 2012

L.H. Chao, P. Pellicena, S. Deindl, L.A. Barclay, H. Schulman, and J. Kuriyan
Inter-subunit capture of regulatory segments is a component of cooperative CaMKII activation
Nature Structural & Molecular Biology 2010

N. Jura, N.F. Endres, K. Engel, S. Deindl, X. Zhang, and J. Kuriyan
Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment
Cell 2009

B.B. Au-Yeung, S. Deindl, H. Lih-Yun, E.H. Palacios, S.E. Levin, J. Kuriyan, and A. Weiss
The structure, regulation, and function of ZAP-70
Immunological Reviews 2009

S. Deindl, T.A. Kadlecek, X. Cao, J. Kuriyan, and A. Weiss
Stability of an autoinhibitory interface in the structure of the tyrosine kinase ZAP-70 impacts T cell receptor response
PNAS 2009

S. Deindl, T.A. Kadlecek, T. Brdicka, X. Cao, A. Weiss and J. Kuriyan
Structural basis for the inhibition of tyrosine kinase activity of ZAP-70
Cell 2007

O.S. Rosenberg, S. Deindl, L.R. Comolli, A. Hoelz, K.H. Downing, A.C. Nairn, and J. Kuriyan
Oligomerization states of the association domain and the holoenyzme of Ca2+/CaM kinase II
FEBS J 2006

O.S. Rosenberg, S. Deindl, R.J. Sung, A.C. Nairn, J. Kuriyan
Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme
Cell 2005

M. Schütt, S.S. Krupka, A.G. Milbradt, S. Deindl, E.K. Sinner, D. Oesterhelt, C. Renner, L. Moroder
Photocontrol of cell adhesion processes: model studies with cyclic azobenzene-RGD peptides
Chemistry & Biology 2003