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Cellular Interactome Dynamics during Paclitaxel Treatment
Interactome changes in cells treated with mitotic inhibitors using quantitative cross-linking and mass spectrometry
Cell Reports. Volume 29, Issue 8, P2371-2383.E5, Nov 19, 2019, doi:10.1016/j.celrep.2019.10.063
In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes
Molecular interactions between two different classes of β-lactamase enzymes and outer membrane protein A (OmpA) were studied by in vivo chemical cross-linking of a multi-drug-resistant strain of Acinetobacter baumannii AB5075
J. Am. Soc. Mass Spectrom. 2019. doi: 10.1021/jasms.9b00021
Systems structural biology measurements by in vivo cross-linking with mass spectrometry
Protocol for large scale PIR experiments
Nature Protocols volume 14, pages2318–2343(2019), doi:10.1038/s41596-019-0181-3
Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies
Here we determine the theoretical number of possible inter- and intraprotein cross-links in available PDB structures of proteins bound in complexes to predict a maximum expected fraction of interprotein cross-links in large scale in vivo cross-linking studies
J Proteome Res. 2019 Jul 3. doi: 10.1021/acs.jproteome.9b00189
Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry
A collaborative work from the Tian, Marcinek, Shadel and Bruce Laboratories sheds new light on protein structures and interactions in mitochondria
PNAS 2017 ; published ahead of print January 27, 2017, doi:10.1073/pnas.1617220114
Mitochondria meet the majority of living cells’ demand for ATP and, as important regulators of redox homeostasis, metabolite levels, and calcium buffering, are a critical link between cell energetics and signaling. Disruption of these processes can induce adaptive or pathological signaling responses to stress and under severe stress promote cell death. Mitochondria have a complex proteome with conformations and interactions that are not well understood. Mitochondrial dysfunction is a direct cause of rare inherited diseases and is implicated in common metabolic diseases and age-related pathology. This study illuminates protein interactions and conformational features of nearly one-third of the mitochondrial proteome. Network information on this scale will enable groundbreaking insights into mitochondrial function, dysfunction, and potential therapeutic targets for mitochondrial-based pathology.
A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry
Targeted PRM analysis of cross-linked peptide pairs in a cross-laboratory study with Cold Spring Harbor Laboratory 2016 Proteomics Course
December 20, 2016. PLoS ONE 11(12): e0167547.doi:10.1371/journal.pone.016754
In Vivo Conformational Dynamics of Hsp90 and Its Interactors
Cross-linked peptides quantified with cellular Hsp90 inhibitor treatment
June 23 2016, Volume 23, Issue 6


Superbug attacks protective lung proteins during infection
Protein interactions reveal purpose of a virulent bacteria’s GUNKs, or genes of unknown function

Deciphering how cancer cells resist chemotherapy
Changes in the molecular machinery inside cancer cells might ward off anti-cancer drugs

Cell Press Interview Apr. 28th, 2015
Where the Wild Ideas Are—A Chat with James E. Bruce:Biology in 3D