• About SFB 1309
  • Research Areas
    • Area A – Modifications on Nucleic Acids
      • A01 – Kaiser (Kellner)
      • A02 – Sattler
      • A04 – Carell
      • A05 – Walter
      • A07 – Jung
      • A08 – Giehr
    • Area B – Modifications on Proteins
      • B02 – Küster
      • B03 – Imhof
      • B04 – Ladurner
      • B05 – Michalakis
      • B06 – R. Schneider
      • B08 – Kielkowski
      • B09 – S. Schneider
    • Area C – Mechanisms and Tools
      • C01 – Huber, Groll
      • C02 – Lang
      • C03 – Zipse
      • C04 – Ochsenfeld
      • C05 – Daumann
      • C06 – Bracher
      • C07 – Huc
      • C08 – Traube
      • C09 - Schütz, Fingerhut
    • Finished Projects
  • Investigators
    • Principal Investigators
    • Associate Investigators
    • All Investigators - alphabetical
  • Publications
  • Events
  • Apply
  • IRTG
    • About IRTG
    • IRTG Contact
    • Student Representatives
    • Events
  • ICEM
    • ICEM Concept
    • Research groups
      • Prof. Thomas Carell
      • Dr. Pascal Giehr
      • Prof. Ivan Huc
      • Dr. Pavel Kielkowski
      • Dr. Sabine Schneider
      • Dr. Franziska Traube
  • Contact
SFB 1309 – Chemical Biology of Epigenetic Modifications
  • About SFB 1309
  • Research Areas
    • Area A – Modifications on Nucleic Acids
      • A01 – Kaiser (Kellner)
      • A02 – Sattler
      • A04 – Carell
      • A05 – Walter
      • A07 – Jung
      • A08 – Giehr
    • Area B – Modifications on Proteins
      • B02 – Küster
      • B03 – Imhof
      • B04 – Ladurner
      • B05 – Michalakis
      • B06 – R. Schneider
      • B08 – Kielkowski
      • B09 – S. Schneider
    • Area C – Mechanisms and Tools
      • C01 – Huber, Groll
      • C02 – Lang
      • C03 – Zipse
      • C04 – Ochsenfeld
      • C05 – Daumann
      • C06 – Bracher
      • C07 – Huc
      • C08 – Traube
      • C09 - Schütz, Fingerhut
    • Finished Projects
  • Investigators
    • Principal Investigators
    • Associate Investigators
    • All Investigators - alphabetical
  • Publications
  • Events
  • Apply
  • IRTG
    • About IRTG
    • IRTG Contact
    • Student Representatives
    • Events
  • ICEM
    • ICEM Concept
    • Research groups
      • Prof. Thomas Carell
      • Dr. Pascal Giehr
      • Prof. Ivan Huc
      • Dr. Pavel Kielkowski
      • Dr. Sabine Schneider
      • Dr. Franziska Traube
  • Contact
Publications SFB 1309
SFB 1309

Publications

2025

2025

Influence of Rare-Earth-Elements on Prebiotic Reaction Networks Resembling the
Biologically Relevant Krebs Cycle

Angew. Chem. Int. Ed. 2025, e16853
2025-11-26
  C05 
Lena Daumann (Board member)

From Pharmacophore to Warhead: NAD+-Targeting Triazoles as Mechanism-Based Sirtuin Inhibitors

Angew. Chem. Int. Ed. 2025, e16782
2025-08-19
  B03 
Axel Imhof

Hijacking a bacterial ABC transporter for genetic code expansion

Nature (2025) 
2025-10-15
C01  C02 
Michael Groll, Kathrin Lang

Lead Structure-Based Hybridization Strategy Reveals Major Potency Enhancement of SirReal-Type Sirt2 Inhibitors

Int. J. Mol. Sci. 2025, 26, 9855
2025-10-10
  C06 
Franz Bracher

Aldehyde or Hydrate? Investigation into the Oxidation of 5-Formylcytosine Derivatives Using a Computational and Experimental Approach

ChemBioChem 2025, 26, e70085
2025-09-23
C03  C05 
Lena Daumann (Board member), Hendrik Zipse

Balsalazide-Derived Heterotriaryls as Sirtuin 5 Inhibitors: A Case Study of a Reversible Covalent Inhibition Strategy 

Molecules 2025, 30, 3821 
2025-09-20
  C06 
Franz Bracher

Molecular Mechanism of ATP Hydrolysis Catalyzed by p97: A QM/MM Study

J. Chem. Theory Comput. 2025, XXXX, XXX, XXX-XXX
2025-09-05
Christian Ochsenfeld

Tailored SirReal-type inhibitors enhance SIRT2 inhibition through ligand stabilization and disruption of NAD+ co-factor binding

RSC Med. Chem., 2025, Open Access
2025-08-19
C01  C06 
Franz Bracher, Michael Groll, Eva Huber (Board member)

Proteomic analyses identify targets, pathways, and cellular consequences of oncogenic KRAS signaling

Sci. Signal. 18, eadt6552 (2025)
2025-07-29
Bernhard Küster

The Isopropylstilbene Precursor Cinnamic Acid Inhibits Anthraquinone Pigment Production by Targeting AntI

J. Am. Chem. Soc. 2025, 147, 20246−20250
2025-06-23
  C01 
Michael Groll

Structure-based design of an aromatic helical foldamer–protein interface

Chem. Sci., 2025, 16, 12385
2025-06-02
Ivan Huc

The human proteome with direct physical access to DNA

Cell 188, 1–17, 2025
2025-05-22
B02
Bernhard Küster

Interfacing B-DNA and DNA Mimic Foldamers

Angew. Chem. Int. Ed. 2025, e202505273
2025-05-09
A04  C07 
Thomas Carell (Spokesperson), Ivan Huc

Serendipitous and Systematic Chemoproteomic Discovery of MBLAC2, HINT1, and NME1‑4 Inhibitors from Histone Deacetylase-Targeting Pharmacophores

ACS Chem. Biol. 2025
2025-05-08
B02  C06 
Franz Bracher, Bernhard Küster

Lead-Structure-Based Rigidization Approach to Optimize SirReal-Type Sirt2 Inhibitors

Molecules 2025, 30, 1728
2025-04-11
C06
Franz Bracher

Computational Prediction of One-Electron Oxidation Potentials for Cytosine and Uracil Epigenetic Derivatives

J. Phys. Chem. A
2025-04-08
C03
Hendrik Zipse

Display selection of peptide ligands for helical aromatic foldamers

Org. Biomol. Chem., 2025, 23, 4641
2025-04-03
Ivan Huc

Self-assembled PROTACs enable glycoproteins degradation in the living cells

Chem. Sci., 2025, 16, 8060
2025-04-02
B08
Pavel Kielkowski

Quantification of objective concentrations of DNA impurities in mRNA vaccines

Vaccine 55 (2025) 127022
2025-03-22
A01
Stefanie Kaiser (Kellner)

Novel Tet3 enzymes for next-generation epigenetic sequencing

RSC Chem. Biol. 2025
2025-03-10
A04
Thomas Carell (Spokesperson), Sabine Schneider (Board member)

NAIL-MS reveals tRNA and rRNA hypomodification as a consequence of 5-fluorouracil treatment

Nucleic Acids Research, Volume 53, Issue 4, 2025
2025-02-25
A01
Stefanie Kaiser (Kellner)

Chemical nucleases are a robust alternative for RNase H cleavage of human ribosomal RNA

PLoS ONE 20(2):e0318697, 2025
2025-02-24
A01
Stefanie Kaiser (Kellner)

Chemical reactivity of RNA and its modifications with hydrazine

Comm. Chem. (2025)8:48
2025-02-14
A01
Stefanie Kaiser (Kellner)

Molecular basis for azetidine-2-carboxylic acid biosynthesis

Nat. Comm. (2025)16:1348
2025-02-04
C01
Michael Groll

Human TRMT1 and TRMT1L paralogs ensure the proper modification state, stability, and function of tRNAs

Cell Reports 44, 115092, 2025
2025-01-28
A01
Stefanie Kaiser (Kellner)

AMPylation regulates PLD3 processing

bioRxiv
2025-01-09
B08
Pavel Kielkowski
2024

2024

DNA Mimic Foldamer Recognition of a Chromosomal Protein

Angew. Chem. Int. Ed. 2025, 64, e202422958
2024-12-23
C07
Ivan Huc

Aryl Radicals Generated from Aryl Pinacol Boronates Modify Peptides and Proteins

Eur. J. Org. Chem. 2025, 28, e202401246
2024-11-26
B08  B09  C09 
Pavel Kielkowski, Sabine Schneider (Board member), Anne Schütz

Robust Bisulfite-Free Single-Molecule Real-Time Sequencing of Methyldeoxycytidine Based on a Novel hpTet3 Enzyme

Angew. Chem. Int. Ed. 2024, 63, e202418500
2024-11-25
A04  A08 
Thomas Carell (Spokesperson), Peter Pascal Giehr

A Phosphotriester-Masked Dideoxy-cGAMP Derivative as a Cell-Permeable STING Agonist

Angew. Chem. Int. Ed. 2024, e202416353
2024-11-12
A04
Thomas Carell (Spokesperson)

Aromatic Amino Acid Hydroxylases as Off-Targets of Histone Deacetylase Inhibitors

 ACS Chem. Neurosci. 2024, 15, 4143−4155
2024-11-11
C06
Franz Bracher

Aryl Radicals Generated from Aryl Pinacol Boronates Modify Peptides and Proteins

Eur. J. Org. Chem. 2025, 28, e202401246
2024-11-09
B08  B09 
Pavel Kielkowski, Sabine Schneider (Board member), Anne Schütz

Direct RNA sequencing of the Escherichia coli epitranscriptome uncovers alterations under heat stress

bioRxiv
2024-11-07
A01
Stefanie Kaiser (Kellner), Kirsten Jung, Peter Pascal Giehr

Interrogating the potential of helical aromatic foldamers for protein recognition

Org. Biomol. Chem., 2024, 22, 9342
2024-10-29
C07
Ivan Huc

Depletion of m6A-RNA in Escherichia coli reduces the infectious potential of T5 bacteriophage

Microbiology Spectrum, 2024, 12, 12
2024-10-18
A04
Thomas Carell (Spokesperson), Kirsten Jung

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

Beilstein J. Org. Chem.,  20, 2323–2341, 2024
2024-09-12
B08
Pavel Kielkowski

Isofunctional but Structurally Different Methyltransferases for Dithiolopyrrolone Diversification

Angew. Chem. Int. Ed. 2024, 63, e202410799
2024-08-24
C01
Michael Groll, Eva Huber (Board member)

Deciphering the SAM- and metal-dependent mechanism of O-methyltransferases in cystargolide and belactosin biosynthesis: A structure–activity relationship study

J. Biol. Chem., 300(9) 107646, 2024
2024-08-07
C01
Michael Groll

Gradual evolution of a homo-L-peptide world on homo-D-configured RNA and DNA

Chem. Sci., 2024, 15, 14171–14176
2024-08-02
A04
Thomas Carell (Spokesperson)

Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins

EMBO Rep, 2024, 25: 3202-3220
2024-08-02
B06
Robert Schneider

Structural basis of tRNA recognition by the m3C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase

Nature Structural & Molecular Biology, 2024, 31, 1614–1624
2024-06-25
B06
Robert Schneider

The type of DNA damage response after decitabine treatment depends on the level of DNMT activity

 Life Science Alliance, vol.7, no9, e202302437, 2024
2024-06-21
B05
Stylianos Michalakis, Franziska Traube

Decrypting the functional design of unmodified translation elongation factor P

Cell Reports, 2024, 43, 114063
2024-05-28
B03
Axel Imhof, Kirsten Jung, Pavel Kielkowski

Efficient Tandem Copper-Catalyzed Click Synthesis of Multisugar-Modified Oligonucleotides

Angew. Chem. Int. Ed. 2024, e202405161
2024-04-12
A04  B09 
Thomas Carell (Spokesperson), Sabine Schneider (Board member)

T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme

bioRxiv 2024.2004.2004.588121
2024-04-04
A01
Stefanie Kaiser (Kellner)

Potent hydroxamate-derived compounds arrest endodyogeny of Toxoplasma gondii tachyzoites

Experimental Parasitology, 259, 108727, 2024
2024-04-01
C06
Franz Bracher

Systematic QM/MM Study for Predicting ³¹P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment

J. Chem. Theory Comput. 2024, 20, 2433−2444
2024-03-18
C04  C09 
Christian Ochsenfeld, Anne Schütz

Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments

Adv. Sci. 2024, 11, 2400184
2024-03-16
C01
Michael Groll

Assessing Lanthanide-Dependent Methanol Dehydrogenase Activity: The Assay Matters

ChemBioChem 2024, 25, e202300811
2024-03-01
C05
Lena Daumann (Board member), Sabine Schneider (Board member)

RNA-Templated Peptide Bond Formation Promotes L-Homochiralty

Angewandte Chemie, Volume 63, Issue 19, e202319235, 2024
2024-02-26
A04
Thomas Carell (Spokesperson)

Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein

Biomacromolecules, 2024
2024-02-11
B09
Sabine Schneider (Board member)

Exploring Chemical Space Using Ab Initio Hyperreactor Dynamics

ACS Cent. Sci., 10, 2, 302–314, 2024
2024-01-31
C04
Christian Ochsenfeld

Enhancing the Features of DNA Mimic Foldamers for Structural Investigations

 Chem. Eur. J. 2024, 30, e202303650
2024-01-30
C07
Ivan Huc

Cu-Catalyzed Azide−Alkyne−Thiol Reaction Forms Ubiquitous Background in Chemical Proteomic Studies

J. Am. Chem. Soc, 2024
2024-01-12
B08
Pavel Kielkowski
2023

2023

Characterization of the cystargolide biosynthetic gene cluster and functional analysis of the methyltransferase CysG

J. Biol. Chem. (2024) 300(1) 105507
2023-11-27
C01
Michael Groll

3′‑tRF‑CysGCA overexpression in HEK‑293 cells alters the global expression profile and modulates cellular processes and pathways

Integr Genomics, 23, 341, 2023
2023-11-21
A04
Thomas Carell (Spokesperson)

Synthesis and Structure Elucidation of Glutamyl-Queuosine

J. Am. Chem. Soc, 2023
2023-11-15
A04
Thomas Carell (Spokesperson), Axel Imhof

Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications

ACS Chem. Biol., 18, 12, 2441–2449, 2023
2023-11-14
A04
Thomas Carell (Spokesperson), Stefanie Kaiser (Kellner), Andrea Rentmeister

Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry

Acc. Chem. Res.,56, 22, 3121–3131,  2023
2023-11-09
A01
Stefanie Kaiser (Kellner)

Disordered protein regions partner up the cBAF remodeler for a chromatin dance

Molecular Cell, 83, November 2, 2023
2023-11-02
B04
Andreas Ladurner (Board member)

The histone chaperone ANP32B regulates chromatin incorporation of the atypical human histone variant macroH2A

Cell Reports 42, 113300, 2023
2023-10-18
B04
Andreas Ladurner (Board member)

The role of RNA in the maintenance of chromatin domains as revealed by antibody mediated proximity labelling coupled to mass spectrometry

bioRxiv, 2023
2023-10-18
B03
Axel Imhof

The fruit fly acetyltransferase chameau promotes starvation resilience at the expense of longevity

EMBO Reports, e57023, 2023
2023-09-19
B03
Axel Imhof

Display Selection of a Hybrid Foldamer–Peptide Macrocycle

Angew. Chem. Int. Ed., 62, e202308408, 2023
2023-09-14
C07
Ivan Huc

DNA mimic foldamers affect chromatin composition and disturb cell cycle progression

Nucleic Acids Research, gkad681, 2023
2023-08-31
B03
Axel Imhof, Ivan Huc

Pharmacological perturbation of the phase-separating protein SMNDC1

Nature Communications | (2023)14:4504
2023-08-16
A02
Michael Sattler

Pioneers conquer core histones at the chromatin frontier

Nat.Struct.Mol Biol,1050–1053, 2023
2023-08-10
B04
Andreas Ladurner (Board member)

Conformation and structural dynamics of the Xist lncRNA A‐repeats

bioRxiv 2023
2023-07-31
A02
Michael Sattler

Chemoproteomic target deconvolution reveals Histone Deacetylases as targets of (R)-lipoic acid

Nat Commun., 14, 3548, 2023
2023-06-15
B02
Bernhard Küster

Depletion of pyruvate kinase (PK) activity causes glycolytic intermediate imbalances and reveals a PK-TXNIP regulatory axis

Mol. Metabolism, 2023, 74, 101748
2023-06-07
A04
Thomas Carell (Spokesperson), Robert Schneider

Optimization and Automation of Helical Aromatic Oligoamide Foldamer Solid-Phase Synthesis

Chem. Eur. J., e202300898, 2023
2023-04-06
C07
Ivan Huc

Decrypting drug actions and protein modifications by dose- and time-resolved proteomics

J. Zecha et al., Science, 2023
2023-03-16
B02
Bernhard Küster

Epigenetic CpG duplex marks probed by an evolved DNA reader via a well-tempered conformational plasticity

Nucleic Acids Research, gkad134, 2023
2023-03-15
A03
Rasmus Linser

Loading of Amino Acids onto RNA in a Putative RNA-Peptide World

Angew. Chem., Volume 62, Issue 21, e202302360, 2023
2023-03-07
A04
Thomas Carell (Spokesperson)

Temporal resolution of NAIL-MS of tRNA, rRNA and Poly-A RNA is overcome by actinomycin D†

RSC Chem. Biol., 4, 354, 2023
2023-02-24
A01
Stefanie Kaiser (Kellner)

UHMK1 is a novel splicing regulatory kinase

J. Biol. Chem., 299(4) 103041, 2023
2023-02-18
B02
Bernhard Küster

Chapter Nine - Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes

Methods Enzymol 2023, 678, 263-297
2023-01-01
A02
Michael Sattler
2022

2022

Quantitative RNA imaging in single live cells reveals age-dependent asymmetric inheritance

Cell Reports 41, 111656, 2022
2022-11-15
B06
Robert Schneider

Efficient Method for the Computation of Frozen-Core Nuclear Gradients within the Random Phase Approximation

J. Chem. Theory Comput., 18, 12, 7359–7372, 2022
2022-11-04
C04
Christian Ochsenfeld

Fully Automated Generation of Prebiotically Relevant Reaction Networks from Optimized Nanoreactor Simulations

J. Chem. Theory Comput., 18, 11, 6700–6712, 2022
2022-10-21
C04
Christian Ochsenfeld

Altered expression response upon repeated gene repression in single yeast cells

PLoS Comput Biol.18(10): e1010640, 2022
2022-10-18
B06
Robert Schneider

Chemical Proteomics Reveals Protein Tyrosination Extends Beyond the Alpha-Tubulins in Human Cells

ChemBioChem, 23, e202200414 (1 of 6), 2022
2022-10-11
B08
Pavel Kielkowski

Aza-SAHA Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout

J. Am. Chem. Soc. 2022, 144, 41, 18861–18875, 2022
2022-10-06
B02
Bernhard Küster

Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units

J. Chem. Theory Comput., 18, 10, 6010–6020, 2022
2022-09-22
C04
Christian Ochsenfeld

Comprehensive comparison between azacytidine and decitabine treatment in an acute myeloid leukemia cell line

Clin Epigenet, 14, 113, 2022
2022-09-11
A01
Stefanie Kaiser (Kellner), Franziska Traube

Isoxazole Nucleosides as Building Blocks for a Plausible Proto-RNA

Angew. Chem. Int. Ed., 61, e202211945, 2022
2022-09-05
A04
Thomas Carell (Spokesperson)

From free-energy profiles to activation free energies

J. Chem. Phys. 157, 084113, 2022
2022-08-24
C04
Christian Ochsenfeld

Epipolythiodioxopiperazine-Based Natural Products: Building Blocks, Biosynthesis and Biological Activities

ChemBioChem 2022, e202200341
2022-08-23
C01
Eva Huber (Board member)

Differential Peptide Multi-Macrocyclizations at the Surface of a Helical Foldamer Template

Angew. Chem. Int. Ed. 2022, 61, e202211138
2022-08-22
C07
Ivan Huc

XPC–PARP complexes engage the chromatin remodeler ALC1 to catalyze global genome DNA damage repair

Nat Commun 13, 4762, 2022
2022-08-13
B04
Andreas Ladurner (Board member)

Tensor-Hypercontracted MP2 First Derivatives: Runtime and Memory Efficient Computation of Hyperfine Coupling Constants

J. Chem. Theory Comput. 18, 9, 5233–5245, 2022
2022-08-09
C04
Christian Ochsenfeld

Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead

Nat. Chem., 2022
2022-07-29
C01
Michael Groll

Novel Poxin Stable cGAMP-Derivatives Are Remarkable STING Agonists

Angew. Chem. Int. Ed. 2022, 61, e202207175 (1 of 5), 2022
2022-07-25
A04
Thomas Carell (Spokesperson)

A Specialized Polythioamide-Binding Protein Confers Antibiotic Self-Resistance in Anaerobic Bacteria

Angew. Chem. Int. Ed. 2022, e202206168
2022-07-19
C01
Michael Groll

Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli

ChemBioChem 2022, 23, e202200270
2022-07-13
A01
Stefanie Kaiser (Kellner), Kirsten Jung

Statistically optimal analysis of the extended-system adaptive biasing force (eABF) method

J. Chem. Phys. 157, 024110, 2022
2022-07-13
C04
Christian Ochsenfeld

Suppression of SARS-CoV-2 Replication with Stabilized and Click- Chemistry Modified siRNAs

Angew. Chem. Int. Ed., 61, e202204556, 2022
2022-07-08
A04
Thomas Carell (Spokesperson), Stylianos Michalakis, Sabine Schneider (Board member), Franziska Traube

Development of hetero-triaryls as a new chemotype for subtype-selective and potent Sirt5 inhibition

European Journal of Medicinal Chemistry, 2022, Volume 240, 114594
2022-07-08
C06
Franz Bracher, Bernhard Küster, Christian Ochsenfeld

Transforming Chemical Proteomics Enrichment into a High-Throughput Method Using an SP2E Workflow

JACS Au, 2022, 2, 7, 1712–1723
2022-06-30
B01
Anja Hoffmann-Röder, Pavel Kielkowski

A prebiotically plausible scenario of an RNA–peptide world

Nature, 2022, 605, 279–284
2022-05-11
A04
Thomas Carell (Spokesperson)

Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target

Nat Chem Biol, 2022
2022-04-28
B02
Bernhard Küster

Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX

Structure, 2022, 30, 1–13, July 7
2022-04-25
C01
Michael Groll, Eva Huber (Board member)

Histone post-translational modifications — cause and consequence of genome function

Nat Rev Genet 23, 563–580, 2022
2022-03-25
B06
Robert Schneider

Exponential averaging versus umbrella sampling for computing the QM/MM free energy barrier of the initial step of the desuccinylation reaction catalyzed by sirtuin 5†

Phys. Chem. Chem. Phys.24, 7723, 2022
2022-03-16
C04
Christian Ochsenfeld

How to obtain reaction free energies from free-energy profiles

J. Chem. Phys. 156, 114105, 2022
2022-03-15
C04
Christian Ochsenfeld

Epigenetic Anti-Cancer Treatment With a Stabilized Carbocyclic Decitabine Analogue

Chem. Eur. J. 2022, 28, e202200640
2022-03-14
A04  C03  C08 
Thomas Carell (Spokesperson), Hendrik Zipse, Franziska Traube

Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition

J. Chem. Theory Comput., 18, 4, 2530–2542, 2022
2022-02-28
C04
Christian Ochsenfeld

Structural effects of m6 A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1

Nucleic Acids Res 2022, 50 (4), 2350-2362
2022-02-15
A02
Michael Sattler

Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1

Nucleic Acids Research, 2022, Volume 50, Issue 4, Pages 2350–2362
2022-02-15
A02
Michael Sattler

Clickable report tags for identification of modified peptides by mass spectrometry

J Mass Spectrom. 2022; 57:e4812
2022-02-13
B08
Pavel Kielkowski, Sabine Schneider (Board member)

1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives

ACS Phys. Chem Au, 2, 237−246, 2022
2022-02-11
A04
Thomas Carell (Spokesperson)

The pH-Dependence of the Hydration of 5-Formylcytosine - an Experimental and Theoretical Study

Chem. Bio. Chem., 2022,  e202100651
2022-01-27
C03
Hendrik Zipse

Structure and mechanism of the RNA dependent RNase Cas13a from Rhodobacter capsulatus

Commun Biol., 2022, 5, 71
2022-01-20
B09
Sabine Schneider (Board member)

Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR

PNAS, 2022, Vol. 119 No. 4, e2114690119
2022-01-20
A03
Rasmus Linser

Evolved DNA Duplex Readers for Strand-Asymmetrically Modified 2 5‑Hydroxymethylcytosine/5-Methylcytosine CpG Dyads

JACS, 2022
2022-01-14
A03
Rasmus Linser

Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling

Nat Commun., 2022, 13, 165
2022-01-10
B02
Bernhard Küster
2021

2021

AMPylation profiling during neuronal differentiation reveals extensive variation on lysosomal proteins

iScience, 2021, 24,103521
2021-12-17
B08
Pavel Kielkowski

Benchmarking the Accuracy of the Direct Random Phase Approximation and σ‑Functionals for NMR Shieldings

J. Chem. Theory Comput., 2022, 18, 1, 192–205
2021-12-13
C04
Christian Ochsenfeld

Efficient low-scaling computation of NMR shieldings at the second-order Møller–Plesset perturbation theory level with Cholesky-decomposed densities and an attenuated Coulomb metric

J. Chem. Phys., 2021, 155, 224107
2021-12-10
C04
Christian Ochsenfeld

Evolution of a histone variant involved in compartmental regulation of NAD metabolism

Nat Struct Mol Biol 28, 1009–1019, 2021
2021-12-09
B04
Andreas Ladurner (Board member)

Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine

Nat Commun., 2021 12, 7123
2021-12-08
A04
Thomas Carell (Spokesperson)

A modular toolbox to generate complex polymeric ubiquitin architectures using orthogonal sortase enzymes

Nat Commun., 2021, 12, 6515
2021-11-11
C02
Kathrin Lang, Michael Sattler

Evaluation of Disposable Trap Column nanoLC−FAIMS−MS/MS for the Proteomic Analysis of FFPE Tissue

J-Proteomw Res., 20, 5402 − 5411, 2023
2021-11-04
B02
Bernhard Küster

The histone chaperone FACT facilitates heterochromatin spreading by regulating histone turnover and H3K9 methylation states

Cell Reports, 37, 109944, 2021
2021-11-02
B04
Andreas Ladurner (Board member)

TET-Like Oxidation in 5-Methylcytosine and Derivatives: A Computational and Experimental Study

ChemBioChem, 2021, 22, 1– 9
2021-09-09
C05
Lena Daumann (Board member), Hendrik Zipse

Intragenomic Decarboxylation of 5-Carboxy-2′-deoxycytidine

Angew. Chem. Int. Ed., 2021, 60, 23207 –23211
2021-08-25
A04
Thomas Carell (Spokesperson)

Crosstalk between Drp1 phosphorylation sites during mitochondrial remodeling and their impact on metabolic adaptation

Cell Reports, 2021, 36, 109565
2021-08-24
B04
Andreas Ladurner (Board member)

Chemical synthesis of linear ADP-ribose oligomers up to pentamer and their binding to the oncogenic helicase ALC1

Chemical Science, 2021, Issue 37
2021-08-18
B04
Andreas Ladurner (Board member)

Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses

Angew. Chem. Int. Ed., 2021, Volume 60, Issue 44, Pages 23885–23893
2021-08-02
A01
Stefanie Kaiser (Kellner)

Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry

Methods in Enzymology, 2021, Volume 658, Pages 111–135
2021-07-27
A01
Stefanie Kaiser (Kellner)

Deformylation of 5-Formylcytidine in Different Cell Types

Angew. Chem. Int. Ed., 2021, 60, 16869 –16873
2021-07-10
A04
Thomas Carell (Spokesperson)

Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons

Nat Commun., 2021, 12, 4100
2021-07-02
A04
Thomas Carell (Spokesperson), Stylianos Michalakis

Biomimetic Iron Complex Achieves TET Enzyme Reactivity

Angew. Chem. Int. Ed. 2021, Volume 60, Issue 39, Pages 21457–21463
2021-06-28
A04
Thomas Carell (Spokesperson), Lena Daumann (Board member)

Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism

EMBO Rep (2021)e52774
2021-06-23
B06
Robert Schneider

Comparative Nucleosomal Reactivity of 5-Formyl-Uridine and 5-Formyl-Cytidine

Chem. Eur. J. 2021, 27, 12747 – 12752
2021-06-21
A04
Thomas Carell (Spokesperson)

Structural and Mechanistic Insights into C−S Bond Formation in Gliotoxin

Angew. Chem. Int. Ed. 2021, 60, 14188 – 14194
2021-06-14
C01
Michael Groll, Eva Huber (Board member)

Accelerating seminumerical Fock-exchange calculations using mixed single- and double-precision arithmethic

J. Chem. Phys., 2021, 154, 214116
2021-06-07
C04
Christian Ochsenfeld

5-Hydroxymethyl-, 5-Formyl- and 5-Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks

Chem. Eur. J. 2021, 27, 8100 – 8104
2021-03-26
A04
Thomas Carell (Spokesperson)

Wie das Histon-Chaperon FACT aktives und stilles Chromatin bewahrt

BIOspektrum, 2021, 03.21
2021-03-01
B04
Andreas Ladurner (Board member)

Metabolic Analysis of Vitreous/Lens and Retina in Wild Type and Retinal Degeneration Mice

Int. J. Mol. Sci., 2021, 22, 2345.
2021-02-26
B03
Axel Imhof, Stylianos Michalakis

Instrumental analysis of RNA modifications

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 2021, VOL. 56, NO. 2, 178–204
2021-02-22
A01
Stefanie Kaiser (Kellner)

Highly Efficient Resolution-of-Identity Density Functional Theory Calculations on Central and Graphics Processing Units

J. Chem. Theory Comput., 2021, 17, 1512−1521
2021-02-22
C04
Christian Ochsenfeld

Robust Microflow LC-MS/MS for Proteome Analysis: 38 000 Runs and Counting

Anal. Chem. 2021, 93, 8, 3686–3690
2021-02-17
B02
Bernhard Küster

Succinylation of H3K122 destabilizes nucleosomes and enhances transcription

EMBO Rep., 2021, e51009
2021-01-29
B06
Robert Schneider

Formation of Cisplatin Adducts with the Epigenetically Relevant Nucleobase 5-Methylcytosine

Eur. J. Inorg. Chem., 2021, Issue 1, Pages 30–36
2021-01-08
A03
Petra Rovó, Lena Daumann (Board member)

A Short Approach to N-Aryl-1,2,3,4-tetrahydroisoquinolines from N-(2-Bromobenzyl)anilines via a Reductive Amination/Palladium- Catalyzed Ethoxyvinylation/Reductive N-Alkylation Sequence

Synthesis, 2021
2021-01-07
C06
Franz Bracher

MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility

Life Science Alliance, 2021, Isa 202000672
2021-01-06
B03
Axel Imhof
2020

2020

The Enzymatic Decarboxylation Mechanism of 5-Carboxy Uracil: A Comprehensive Quantum Chemical Study

J. Chem. Theory Comput. 2021, 17, 1, 96 – 104
2020-12-24
C04
Christian Ochsenfeld

S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling

Science Advances, 2020, Vol 6, Issue 51
2020-12-16
B03
Axel Imhof

Machine learning a model for RNA structure prediction

NAR Genomics and Bioinformatics, 2020, Volume 2, Issue 4, lqaa090
2020-11-16
A02
Michael Sattler

The Oncogenic Helicase ALC1 Regulates PARP Inhibitor Potency by Trapping PARP2 at DNA Breaks

Molecular Cell, 2020, 80, 1–14
2020-10-29
B04
Andreas Ladurner (Board member)

Efficient Reduced-Scaling Second-Order Møller−Plesset Perturbation Theory with Cholesky-Decomposed Densities and an Attenuated Coulomb Metric

Journal of Chemical Theory and Computation, 2020, 16, 11, 6856–6868
2020-10-19
C04
Christian Ochsenfeld

The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics

Angew. Chem. Int. Ed., 2020, Volume 59, Issue 51, Pages 22916–22921
2020-09-23
A03
Rasmus Linser

A set of rhamnosylation-specific antibodies enables detection of novel protein glycosylations in bacteria

Org. Biomol. Chem., 2020, 18, 6823–6828
2020-08-24
B01
Anja Hoffmann-Röder

Welcome @ SFB1309!

2020-08-14
B08
Pavel Kielkowski, Olivia Merkel, Sabine Schneider (Board member), Stephan A. Sieber

Active turnover of genomic methylcytosine in pluripotent cells

Nat Chem Biol., 2020, 16, 1411–1419
2020-08-10
A04
Thomas Carell (Spokesperson)

Identification of the subtype-selective Sirt5 inhibitor balsalazide through systematic SAR analysis and rationalization via theoretical investigations

European Journal of Medicinal Chemistry, 2020, 206, 112676
2020-08-01
C06
Franz Bracher, Christian Ochsenfeld

Proteome activity landscapes of tumor cell lines determine drug responses

Nat Commun., 11, 3636, 2020
2020-07-20
B02
Bernhard Küster

Restraining and unleashing chromatin remodelers – structural information guides chromatin plasticity

Current Opinion in Structural Biology, 2020, Volume 65 Pages 130-138
2020-07-18
B04
Andreas Ladurner (Board member)

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

Nucleic Acids Research, 2020, Volume 48, Issue 15, Pages 8796–8807
2020-07-11
A04
Thomas Carell (Spokesperson), Petra Rovó

Protein Motional Details Revealed by Complementary Structural Biology Techniques

Structure, 2020, 28, p 1024–2034
2020-06-23
A03
Rasmus Linser, Petra Rovó

Rational Design of Covalent Cobaloxime−Covalent Organic Framework Hybrids for Enhanced Photocatalytic Hydrogen Evolution

J. Am. Chem. Soc., 2020, 142, 12146–12156
2020-06-20
A03
Petra Rovó, Christian Ochsenfeld

Important components for accurate hyperfine coupling constants: electron correlation, dynamic contributions, and solvation effects

Molecular Physics, 2020, Article: e1772515
2020-06-03
C04
Christian Ochsenfeld

Folding and Unfolding of the Short Light-Triggered β‑Hairpin Peptide AzoChignolin Occurs within 100 ns

J. Phys. Chem. B, 2020, 124, 25, 5113–5121
2020-06-01
B01
Anja Hoffmann-Röder

Structural basis of HapEP88L-linked antifungal triazole resistance in Aspergillus fumigatus

Life Science Alliance, 2020, vol 3, no 7, e202000729
2020-05-28
C01
Michael Groll, Eva Huber (Board member)

Synthesis and metabolic fate of 4-methylthiouridine in bacterial tRNA

ChemBioChem, 2020, 21, 1–5
2020-05-12
A01
Stefanie Kaiser (Kellner)

Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory

Molecular Cell, 2020,  78, 1–11
2020-05-08
B06
Robert Schneider

Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes

Journal of Molecular Biology, 2020, Pages 2890–2912
2020-04-17
A02
Michael Sattler

You are what you eat – How nutrition and metabolism shape the genome through epigenetics

MOLECULAR METABOLISM, 2020, Volume 38, 100987
2020-04-15
B06
Robert Schneider

Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

Angew. Chem. Int. Ed., 2020, 59, 12669–12673
2020-04-02
C04
Christian Ochsenfeld

The rRNA m6A methyltransferase METTL5 is involved in pluripotency and developmental programs

 

Genes & Dev., 2020, 34, 715–729
2020-03-26
A01
Stefanie Kaiser (Kellner), Robert Schneider

Bromodomain AAA+ ATPases get into shape

Nucleus, 2020, 11:1, 32–34
2020-03-19
B04
Andreas Ladurner (Board member)

Structures in Tetrahydrofolate Methylation in Desulfitobacterial Glycine Betaine Metabolism at Atomic Resolution

ChemBioChem 2020, 21, 776 – 779
2020-03-16
C01
Michael Groll

Synthesis of Galactosyl-Queuosine and Distribution of Hypermodified Q-Nucleosides in Mouse Tissues

Angew. Chem. Int. Ed., 2020, 59, 1 – 6
2020-03-11
A04
Thomas Carell (Spokesperson), Stefanie Kaiser (Kellner), Stylianos Michalakis

Synthesis and Incorporation of k2U into RNA

Helv. Chim. Acta, 2020, 103 (3) e2000016
2020-02-18
A04
Thomas Carell (Spokesperson)

Highly Efficient, Linear-Scaling Seminumerical Exact-Exchange Method for Graphic Processing Units

J. Chem. Theory Comput., 2020, 16, 3, 1456–1468
2020-02-13
C04
Christian Ochsenfeld

The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions

Molecular Cell, 2020, Volume 77, Issue 3, P 501–513.e7
2020-02-06
B04
Andreas Ladurner (Board member)

Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription

Molecular Cell, 2020, Vol. 77, Iss. 6, P1322–1339
2020-01-31
B02
Bernhard Küster

Analysis of an Active Deformylation Mechanism of 5‐Formyl‐deoxycytidine (fdC) in Stem Cells

Angew. Chem. Int. Ed., 2020, 59 (14), 5591–5594
2020-01-30
A04
Thomas Carell (Spokesperson)

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

Nat Commun., 2020, 11, 157
2020-01-09
B02
Bernhard Küster
2019

2019

METTL6 is a tRNA m3C methyltransferase that regulates pluripotency and tumor cell growth

Science Advances, 2020, Vol. 6, no. 35, eaaz4551
2019-08-26
A01
Stefanie Kaiser (Kellner), Robert Schneider

Non‑uniform sampling in quantitative assessment of heterogeneous solid‑state NMR line shapes

Journal of Biomolecular NMR, 2020, 74, pages 71–82
2019-12-13
A03
Rasmus Linser

NAIL-MS reveals the repair of 2-methylthiocytidine by AlkB in E. coli

Nat. Commun., 2019, 10, Article number: 5600
2019-12-06
A01
Stefanie Kaiser (Kellner), Kirsten Jung

TLR8 Is a Sensor of RNase T2 Degradation Products

Cell, 2019, 179, 1264–1275
2019-11-27
A04
Thomas Carell (Spokesperson)

Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5

J. Chem. Theory Comput. 2019, 15, 12, 6660 – 6667
2019-11-25
C04
Christian Ochsenfeld

ProteomicsDB: a multi-omics and multi-organism resource for life science research

Nucleic Acids Research, 2020, Vol. 48, Database issue D1153–D1163
2019-10-30
B02
Bernhard Küster

Fast Microsecond Dynamics of the Protein–Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy

J. Am. Chem. Soc., 2019, 141, 49, 19276–19288
2019-10-24
A03
Rasmus Linser, Petra Rovó, Hendrik Zipse

A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

Chem Bio Chem., 2019, 21 (1-2), 103–107
2019-10-08
A04
Thomas Carell (Spokesperson)

Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides

Science, 2019, 366 (6461), pp. 76–82
2019-10-04
A04
Thomas Carell (Spokesperson)

Proto‐Urea‐RNA (Wöhler RNA) Containing Unusually Stable Urea Nucleosides

Angewandte Chemie International Edition, 2019, 58 (51), 18691–18696
2019-10-01
A04
Thomas Carell (Spokesperson), Petra Rovó

Low-Scaling Self-Consistent Minimization of a Density Matrix Based Random Phase Approximation Method in the Atomic Orbital Space

J. Chem. Theory Comput., 2019, 15, 8, 4468−4477
2019-08-01
C04
Christian Ochsenfeld

Challenges and perspectives for structural biology of lncRNAs—the example of the Xist lncRNA A-repeats

Journal of Molecular Cell Biology, 2019, Vol.11, Issue 10, Pages 845 – 859
2019-07-23
A02
Michael Sattler

5-Methylcytosine is Oxidized to the Natural Metabolites of TET Enzymes by a Biomimetic Iron(IV)-Oxo Complex

Chem. Eur. J., 2019, 25, 12091–12097
2019-06-18
C05
Lena Daumann (Board member)

Influencing Epigenetic Information with a Hydrolytically Stable Carbocyclic 5‐Aza‐2′‐deoxycytidine

Angew. Chem. Int. Ed., 2019, 58 (37), 12984 
2019-06-17
A04
Thomas Carell (Spokesperson)

Exact distance measurements for structure and dynamics in solid proteins by fast-magic anglespinning NMR†

Chem. Commun., 2019, 55, 7899
2019-06-05
A03
Rasmus Linser

Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques

J. Am. Chem. Soc., 2019, 141, 2, 858–869
2019-01-08
A03
Rasmus Linser, Petra Rovó

Calculating free energies from the vibrational density of states function: Validation and critical assessment

J. Chem. Phys., 2019, 150, 194111
2019-05-20
C04
Christian Ochsenfeld

The interactome of a family of potential methyltransferases in HeLa cells

Sci Rep., 2019, 9, 6584
2019-04-29
B06
Robert Schneider

Identifying Free Energy Hot-Spots in Molecular Transformations

J. Phys. Chem. A 2019, 123, 10, 2163–2170
2019-03-01
C04
Christian Ochsenfeld

Label‐Free Quantification of 5‐Azacytidines Directly in the Genome

Helv. Chim. Acta, 2019, 102 (3), e1800229
2019-02-13
A04
Thomas Carell (Spokesperson)

Assessment of a Large Enzyme–Drug Complex by Proton-Detected Solid-State NMR Spectroscopy without Deuteration

Angew.Chemie Int. Ed., 2019, 58, p 5758–5762
2019-01-28
A03
Rasmus Linser

Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis

Genes, 2019, 10(1), 26
2019-01-05
A01
Stefanie Kaiser (Kellner), Stylianos Michalakis

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Speaker: Prof. Dr. Thomas Carell

Ludwig-Maximilians-Universität München
Institut für Chemische Epigenetik (ICEM)
Department of Chemistry

Office:
Würmtalstrasse 201
81377 Munich
Germany

Mailing address:
Butenandtstr. 5 - 13
81377 Munich
Germany

Phone: +49 (0)89 2180-77750
Fax: +49 (0)89 2180-77756
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Management: Dr. Nada Raddaoui
Institute for Chemical Epigenetics Munich (ICEM)

Office:
Würmtalstrasse 201, Building L, Room 03.004
81377 Munich
Germany

Mailing address:
Butenandtstr. 5 - 13
81377 Munich
Germany

Phone: +49 (0)89 2180-77755
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Secretary: Birgit Carell
Institute for Chemical Epigenetics Munich (ICEM)

Office:
Würmtalstrasse 201, Building L, Room 00.007
81377 Munich
Germany

Mailing address:
Butenandtstr. 5 - 13
81377 Munich
Germany

Phone: +49 (0)89 2180-77751
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IRTG Contact


Prof. Dr. Lena Daumann

LMU Munich
Department of Chemistry
Butenandtstr. 5 - 13
House D, Room 3.075
81377 Munich, Germany

Phone: +49 89 2180 77486

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Dr. Sabine Schneider

LMU Munich
Institute for Chemical Epigenetics
Butenandtstr. 5 - 13
House L
81377 Munich, Germany

Phone: +49 89 2180 77716

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Dr. Martin Sumser (Coordinator)

LMU Munich
Institute for Chemical Epigenetics
Butenandtstr. 5 - 13
House L
81377 Munich, Germany

Phone: +49 89 2180 77765

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