Johannes C. Walter

GolgiFold: A Structural Predictome of Human Golgi Protein Complexes

The paper develops GolgiFold, a structure-based PPI map of human Golgi proteins, identifying over 1,800 interactions and confirming new protein contacts through experimental validation.

A cell-free system for mitotically-stimulated TMEJ

The paper develops a cell-free system using Xenopus egg extracts to study TMEJ, showing that Pol theta and Cyclin B-CDK1 are essential for efficient DNA joining.

A CDK1 phospho-switch reprograms TRAIP to unload replisomes in mitosis

The paper identifies a phospho-switch mechanism that reprograms TRAIP to ubiquitylate replisomes in mitosis, enabling disassembly of unreplicated DNA.

In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer

The paper uses AlphaFold-Multimer to predict nanobody binders to MRGPRX2, demonstrating in silico antibody discovery for a GPCR target.

Structure and function of IWS1 in transcription elongation

This study identifies IWS1 as a modular scaffold that organizes the transcription elongation complex through its disordered region, revealing its role in recruitment and stimulation of elongation.

Proteome-wide in silico screening for human protein-protein interactions

The paper develops a computational pipeline to predict human protein-protein interactions, identifying 16,000 high-confidence interactions, many previously unknown or structurally unresolved.

USP37 prevents premature disassembly of stressed replisomes by TRAIP

This study shows that USP37 prevents premature TRAIP-mediated disassembly of stalled replisomes, maintaining genome stability under replication stress.

EndoMAPV1, a Structural Protein Complex Landscape of Human Endosomes

The paper creates a structural interactome of human endosomes using cross-linking, mass spectrometry, and AlphaFold, identifying structural models for endosomal protein complexes.

The NHEJ machinery is translocated off DNA ends toenable resection

The paper shows that Ku is translocated off DNA ends in an ATP-dependent manner requiring MRN and CtIP, distinct from resection, to enable HR.

The aPBP-type cell wall synthase PBP1b plays a specialized role in fortifying the Escherichia coli division site against osmotic rupture

This study identifies PBP1b's specialized role in E. coli division site fortification against osmotic rupture, showing it functions independently of LpoB and requires an extended N-terminus for recruitment by FtsA.

Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions

The paper introduces SPOC, a classifier to improve AlphaFold-Multimer predictions of protein-protein interactions, and curates a database of predicted interactions for human genome maintenance proteins.

STK19 positions TFIIH for cell-free transcription-coupled DNA repair

The paper investigates the role of STK19 in transcription-coupled DNA repair by showing it positions TFIIH for repair in a cell-free system.

In silico screening identifies SHPRH as a novel nucleosome acidic patch interactor

The paper uses AlphaFold-Multimer to screen human proteins for nucleosome acidic patch binding, identifies SHPRH as a novel binder, and determines its structure.

The HMCES DNA-protein cross-link functions as a constitutive DNA repair intermediate

This study shows that HMCES-DPC forms as a constitutive intermediate in replication-coupled DNA repair, suppressing DSBs and influencing TLS.

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation

This study identifies ELOF1 as a factor that directs CRL4CSA to ubiquitylate RNAPII at K1268, facilitating TCR and protecting CSB-deficient cells from transcription-replication collisions.

Single-Strand DNA Breaks Cause Replisome Disassembly

This study shows that single-strand breaks cause replisome disassembly by generating different fork collapse structures depending on the strand, with CMG being passively removed during leading strand collapse and actively unloaded during lagging strand collapse.

The sequential and cooperative action of CSB, CSA and UVSSA targets the TFIIH complex to DNA damage-stalled RNA polymerase II

This study defines the sequential and cooperative assembly mechanism of the TCR complex and reveals how TFIIH is recruited to DNA damage-stalled RNAPIIo.

A mechanism to minimize errors during non-homologous end joining

This study reveals how NHEJ minimizes errors by confining end processing to a Lig4-dependent short-range synaptic complex, ensuring accurate DNA ligation.

Mechanism of replication-coupled DNA-protein crosslink proteolysis by SPRTN and the proteasome

This study shows that both SPRTN and the proteasome degrade DNA-protein crosslinks during DNA replication, using distinct mechanisms involving ubiquitylation and polymerase extension.