Francis J. O’Reilly

Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy

The paper uses PhIX-MS and cryo-EM to map transient interactions at proteasomes, revealing structural details of proteins like TXNL1 and PSMD5.

Interface swapping orchestrates carbon transfer in the archaeal acetyl-CoA decarbonylase/synthase

The paper investigates the structure and dynamics of the archaeal ACDS complex, revealing a mechanism for efficient carbon transfer through transient interactions rather than stable complexes.

Substrate recognition by human separase

This study determines cryoEM structures of human separase in apo and substrate-bound forms, revealing substrate recognition mechanisms and cleavage regulation.

Phosphorylation-dependent tuning of mRNA deadenylation rates

The paper shows phosphorylation modulates deadenylation rates via multivalent interactions in RNA adaptors, enabling graded regulation of mRNA decay.

An NADH-controlled gatekeeper of ATP synthase

The paper identifies AIFM1/AK2 interaction as a gatekeeper of mitochondrial ATP synthase, showing it is NADH-dependent and linked to metabolic state, with implications for mitochondrial diseases.

Molecular insights into dynamic protein structures by high-contrast crosslinking mass spectrometry

This paper improves crosslinking mass spectrometry by using diazirine-based photo-crosslinking to better study dynamic protein regions and their conformational changes.

Protein Complexes in cells by AI-assisted structural proteomics

The paper uses AI to predict protein complex structures in Bacillus subtilis using crosslinking and cofractionation mass spectrometry data.

Specific recognition and ubiquitination of slow-moving ribosomes by human CCR4-NOT

This study identifies how human CCR4-NOT complex recognizes and ubiquitinates stalled ribosomes during mRNA decay in response to sub-optimal codons.

Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers

The paper evaluates MS-cleavable crosslinkers, finding that improved peptide backbone fragmentation, not mass resolution, is the main advantage of DSSO.

Mpe1 senses the polyadenylation signal in pre-mRNA to control cleavage and polyadenylation

The paper shows Mpe1 interacts with the polyadenylation signal in pre-mRNA to activate CPF and control polyadenylation in yeast.

Reliable identification of protein-protein interactions by crosslinking mass spectrometry

The paper demonstrates a reliable false-discovery rate estimation method for protein-protein interactions identified by crosslinking mass spectrometry using Escherichia coli cell lysate.

Cryo-EM reveals the complex architecture of dynactin's shoulder and pointed end

The paper uses cryo-EM to determine the structure of dynactin's shoulder and pointed end, revealing their architecture and subunit interactions.

A Structure-Based Mechanism for DNA Entry into the Cohesin Ring

This study uses cryo-EM and biochemical experiments to reveal the mechanism of DNA entry into the cohesin ring, showing how ATP binding and hydrolysis regulate the process.

In-cell architecture of an actively transcribing-translating expressome

The paper determines the in-cell architecture of a transcribing and translating expressome in Mycoplasma pneumoniae using integrative structural methods.

A folded conformation of MukBEF and Cohesin

This study investigates the structural architecture of two SMC-kleisin complexes, revealing a folded conformation mediated by a dynamic coiled-coil discontinuity.