Tools for 3D Interactome Visualization

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2018 Dec 7

PMID 30520642

Citations 16

Authors

Andrew Keller

Juan D Chavez

Jimmy K Eng

Zorian Thornton

James E Bruce

Affiliations

Soon will be listed here.

Abstract

In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable the detection of both intra- and intermolecular protein interactions in organelles, cells, tissues, and organs. Quantitative XL-MS enables the detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. We have developed new informatics capabilities, the first to enable 3D visualization of multiple quantitative interactome data sets, acquired over time or with varied perturbation levels, to reveal relevant dynamic interactome changes. These new tools are integrated within release 3.0 of our online cross-linked peptide database and analysis tool suite XLinkDB. With the recent rapid expansion in XL-MS for protein structural studies and the extension to quantitative XL-MS measurements, 3D interactome visualization tools are of critical need.

Citing Articles

Intra-organ cell specific mitochondrial quantitative interactomics.

Bakhtina A, Campbell M, Sibley B, Sanchez-Contreras M, Sweetwyne M, Bruce J bioRxiv. 2024; .

PMID: 38915719 PMC: 11195139. DOI: 10.1101/2024.06.10.598354.

Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS.

Keller A, Tang X, Bruce J J Proteome Res. 2023; 22(9):2900-2908.

PMID: 37552582 PMC: 10866149. DOI: 10.1021/acs.jproteome.3c00191.

Studying Protein-Ligand Interactions by Protein Denaturation and Quantitative Cross-Linking Mass Spectrometry.

Mathay M, Keller A, Bruce J Anal Chem. 2023; 95(25):9432-9436.

PMID: 37307416 PMC: 10848897. DOI: 10.1021/acs.analchem.2c04501.

Skeletal muscle mitochondrial interactome remodeling is linked to functional decline in aged female mice.

Bakhtina A, Pharaoh G, Campbell M, Keller A, Stuppard R, Marcinek D Nat Aging. 2023; 3(3):313-326.

PMID: 37118428 PMC: 10154043. DOI: 10.1038/s43587-023-00366-5.

Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.

Keller A, Bakhtina A, Chavez J, Bruce J J Proteome Res. 2022; 21(6):1475-1484.

PMID: 35594376 PMC: 9278563. DOI: 10.1021/acs.jproteome.2c00109.

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