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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

Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue

XL-MS enables systems structural biology studies at the tissue level
Cell Systems, published online November, 29 2017, doi:10.1016/j.cels.2017.10.017

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

Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers

Development of quantitative XL-MS methods using isotope labeled PIR cross-linkers
Publication Date (Web): November 14, 2016

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

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

Updated data storage site and visualization tool for cross-linking results
April 29 2016

Journal of Virology Spotlight

February 2016, Volume 90, Issue 4

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology

The latest from the Bruce and Cilia lab collaboration

Superbug attacks protective lung proteins during infection

Protein interactions reveal purpose of a virulent bacteria’s GUNKs, or genes of unknown function

Host-Microbe Protein Interactions during Bacterial Infection

Devin K. Schweppe is lead author on a paper in Chemistry and Biology along with members of the Bruce, Singh and Manoil Labs

Deciphering how cancer cells resist chemotherapy

Changes in the molecular machinery inside cancer cells might ward off anti-cancer drugs

Quantitative interactome analysis reveals a chemoresistant edgotype

Juan D. Chavez is lead author on a paper in Nature Communications along with members of the Bruce Lab

Persistent lung bacteria may evolve like Darwin’s finches

Different strains can emerge in different areas of one organ, researchers learn

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs

Xia Wu and James E. Bruce are co-authors on a paper with the Singh Lab

Cell Press Interview Apr. 28th, 2015

Where the Wild Ideas Are—A Chat with James E. Bruce:Biology in 3D

Dynamic proteome response of Pseudomonas aeruginosa to tobramycin antibiotic treatment

Xia Wu is lead author on paper in Molecular & Cellular Proteomics along with members of the Bruce, Manoil, and Singh labs.

Ph.D. Dissertation Defense - Chunxiang "Jake" Zheng

Thursday July 30th. 2:00pm in the Chemistry Building

Jim Bruce Upcoming Presentations

2015 Wisconsin Human Proteomics Symposium
Focus: Posttranslational modifications in human disease
Friday Aug. 2nd 2015