Dorothee Kern

Graphene Device for High-Temperature Crystallography Visualizes How Enzymatic Reactivity is Rooted in Ensemble Probability

The paper develops a graphene device for high-temperature crystallography to study enzymatic reactivity across temperature ranges, revealing how transition state ensembles relate to catalytic rates.

Learning millisecond protein dynamics from what is missing in NMR spectra

Trained on missing NMR amide assignments in the Biological Magnetic Resonance Data Bank, Dyna-1 (ESM-3 layer 22 embeddings) predicts micro-to-millisecond conformational exchange seen in relaxation data.

Comparing the evolvability of an ancestrally reconstructed and modern adenylate kinase

This study compares the evolvability of an ancestrally reconstructed and modern adenylate kinase, finding that the ancestral enzyme tolerates more mutations and generates more viable variants.

Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling

This study investigates how pathogenic mutations in SHP2's SH2 domains alter conformational dynamics, leading to hyperactivation by stabilizing a zipped β-sheet state.

Does Sequence Clustering Confound AlphaFold2?

This paper refutes claims that AF-Cluster fails to use local evolutionary couplings in its MSA clusters and shows they play an important role in predictions.

The dramatic impact of the PER-DBT interaction on circadian timekeeping and temperature compensation

The paper identifies a conserved PER-DBT interaction critical for circadian timing and temperature compensation through structural and functional analyses in Drosophila and human cells.

Dual-Action Kinase Inhibitors Influence p38α MAP Kinase Dephosphorylation

The paper identifies dual-action kinase inhibitors that block the active site and enhance p38α dephosphorylation by stabilizing an accessible activation loop conformation.

The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale

This paper characterizes the conformational landscape of KaiB, revealing its slow interconversion between states and how evolution tunes this process to match circadian rhythms.

Protein language models learn evolutionary statistics of interacting sequence motifs

The paper investigates how ESM-2, a protein language model, predicts protein contacts by analyzing coevolving residue statistics and local sequence context.