Joseph H. Davis

A conserved archaeal ribosome-associated factor linking bacterial hibernation and eukaryotic energy sensing

This study identifies AHA, a conserved archaeal ribosome-associated factor involved in hibernation and energy sensing, linking prokaryotic translational silencing to eukaryotic energy sensing.

A proteome-wide biochemical screen defines binding determinants of the core autophagy protein LC3B

The paper screens a proteome-wide peptide library to identify LC3B binding determinants, revealing exceptions to the canonical LIR motif and highlighting sequence features that influence binding affinity and specificity.

Heterogeneous reconstruction algorithms for cryoEM achieve limited particle classification accuracy on real benchmark datasets

This study evaluates heterogeneous reconstruction algorithms in cryoEM using benchmark datasets with ground-truth labels, finding limited accuracy in particle classification despite resolving structural heterogeneity.

Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryoEM reconstruction methods

The paper develops an experimentally grounded benchmark dataset for heterogeneous cryoEM reconstruction using engineered Cas9 complexes with defined DNA extensions.

Capturing ribosomal structures in cellular extracts with cryoPRISM: A purification-free cryoEM approach reveals novel structural states

The paper introduces cryoPRISM, a purification-free cryoEM method for analyzing ribosomal structures in cell lysates, revealing over twenty distinct ribosomal states in E. coli.

NCOA4 initiates ferritinophagy by avidly binding GATE16 using two short linear interaction motifs

This paper identifies two short linear motifs in NCOA4 that bind GATE16 with high avidity, enabling ferritinophagy and revealing a mechanism for iron-dependent regulation of this process.

Ribosome-associated quality control of aberrant protein production during amino acid limitation

The paper investigates how amino acid limitation affects translation by analyzing ribosome stalling and the role of RQC pathways and RNF14 in response to arginine depletion.

Bulk and selective autophagy cooperate to remodel a fungal proteome in response to changing nutrient availability

The paper develops a method to globally monitor protein degradation in yeast and finds that bulk and selective autophagy cooperatively drive proteome remodeling in response to nutrient changes.

An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins

The paper presents structures of native FtsH-HflK/C complexes in E. coli, revealing an asymmetric nautilus-like assembly that facilitates membrane protein degradation.

Rapid structural analysis of bacterial ribosomes in situ

The paper develops a rapid in situ cryo-ET workflow for bacterial ribosome structure analysis, achieving sub-nm resolution in E. coli within 10 days.

A proteolytic AAA+ machine poised to unfold a protein substrate

The paper presents a cryo-EM structure of a ClpXP-substrate complex, revealing an intermediate state in protein unfolding by the AAA+ proteolytic machine.

Automated model-free analysis of cryo-EM volume ensembles with SIREn

This paper introduces SIREn, a tool for automated analysis of cryo-EM volume ensembles to identify structural states and quantify their occupancies.

Integrated proteasomal and lysosomal activity shape mTOR-regulated proteome remodeling

This study quantifies proteome dynamics during mTOR inhibition, revealing distinct kinetics between proteasomal and lysosomal degradation and coordinated synthesis-degradation of translation factors.

Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN

This paper introduces tomoDRGN, a deep learning tool for analyzing cryo-ET sub-tomograms, revealing structural heterogeneity in macromolecules like ribosomes.

CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks

CryoDRGN uses deep neural networks to reconstruct heterogeneous protein complexes and their motion from cryo-EM data, revealing previously unseen structural states.

Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit

This study investigates Era's role in 30S ribosomal subunit assembly using mass spectrometry, cryo-EM, and in-cell footprinting, showing that most rRNA domains can fold without Era and that Era binding affects the decoding center.