Systems structural biology measurements by in vivo cross-linking with mass spectrometry

Chavez, Juan D.; Mohr, Jared P.; Mathay, Martin; Zhong, Xuefei; Keller, Andrew; Bruce, James E.

doi:10.1038/s41596-019-0181-3

Cited by 60 publications

(63 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The PIR cross-linker Biotin Aspartate Proline - N-hydroxyphthalamide (BDP-NHP) (Chavez et al, 2019) was synthesized by solid phase peptide synthesis using a Liberty Lite peptide synthesizer (CEM). FMOC N-terminal protected amino acids were coupled in the following order biotin Lys, Lys, Pro, Asp, succinic anhydride on Gly-SASRIN resin.…”

Section: Methodsmentioning

confidence: 99%

Cellular Interactome Dynamics during Paclitaxel Treatment

et al. 2019

Self Cite

View full text Add to dashboard Cite

Graphical Abstract Highlights d Quantitative cross-linking/mass spectrometry analysis of mitotic inhibitor-treated cells d Cross-links reflect paclitaxel stabilization of microtubules d Drug-specific changes to intermediate and microfilament structures d Paclitaxel treatment alters mitochondrial respiration and ATP synthase structure In Brief Chavez et al. reveal interactome changes in cells treated with mitotic inhibitors using quantitative cross-linking and mass spectrometry. Cross-links reflect interaction/conformational changes specific for drug type and concentration, which are not evident by protein expression levels. Microtubule stabilization, cytoskeletal alteration, and changes to mitochondrial function are visualized in cross-link levels. ratio Drug conc. Quantitative cross-linking Mitotic Inhibitor Protein interaction/structural changes vs SUMMARYCell-cycle inhibitors, including paclitaxel, are among the most widely used and effective cancer therapies. However, several challenges limit the success of paclitaxel, including drug resistance and toxic side effects. Paclitaxel is thought to act primarily by stabilizing microtubules, locking cells in a mitotic state. However, the resulting cytotoxicity and tumor shrinkage rates observed cannot be fully explained by this mechanism alone. Here we apply quantitative chemical cross-linking with mass spectrometry analysis to paclitaxel-treated cells. Our results provide large-scale measurements of relative protein levels and, perhaps more importantly, changes to protein conformations and interactions that occur upon paclitaxel treatment. Drug concentrationdependent changes are revealed in known drug targets including tubulins, as well as many other proteins and protein complexes involved in apoptotic signaling and cellular homeostasis. As such, this study provides insight into systems-level changes to protein structures and interactions that occur with paclitaxel treatment.

show abstract

Section: Methodsmentioning

confidence: 99%

Cellular Interactome Dynamics during Paclitaxel Treatment

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

“…To deal with the enormous complexity of samples in proteome-wide network studies, a number of methodological challenges have to be overcome [6][7][8][9]. Currently, the maximum number of cross-links identified in system-wide studies is approximately 10,000 and it remains to be seen how far this limit can be pushed.…”

mentioning

confidence: 99%

Cross-linking/mass spectrometry at the crossroads

Piersimoni

Sinz

2020

Anal Bioanal Chem

View full text Add to dashboard Cite

Cross-linking/mass spectrometry (XL-MS) has come a long way. Originally, XL-MS was used to study relatively small, purified proteins. Meanwhile, it is employed to investigate protein-protein interactions on a proteome-wide level, giving snapshots of cellular processes. Currently, XL-MS is at the intersection of a multitude of workflows and the impact this technique has in addressing specific biological questions is steadily growing. This article is intended to give a bird's-eye view of the current status of XL-MS, the benefits of using MS-cleavable cross-linkers, and the challenges posed in the future development of this powerful technology. We also illustrate how XL-MS can deliver valuable structural insights into protein complexes when used in combination with other structural techniques, such as electron microscopy.

show abstract

“… Start with an NHS-reactive linker; however, the combination of several linkers targeting different amino acids might increase the coverage, if needed. Useful and detailed protocols using DSBU, CDI, 82 DSSO, 24 or the enrichable PIR 200 linker for proteome-wide approaches can be found in the literature. …”

Section: Workflow and Experiments Designmentioning

confidence: 99%

“…Useful and detailed protocols using DSBU, CDI, 82 DSSO, 24 or the enrichable PIR 200 linker for proteome-wide approaches can be found in the literature.…”

Section: Workflow and Experiments Designmentioning

confidence: 99%

Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

Matzinger

Mechtler

2020

J. Proteome Res.

View full text Add to dashboard Cite

Cross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein−protein interactions or to uncover protein structures in living cells, tissues, or organelles. The unique ability to investigate the interplay of proteins within their native environment delivers valuable complementary information to other advanced structural biology techniques. This Review gives a comprehensive overview of the current possible applications as well as the remaining limitations of the technique, focusing on cross-linking in highly complex biological systems like cells, organelles, or tissues. Thanks to the commercial availability of most reagents and advances in user-friendly data analysis, validation, and visualization tools, studies using XL-MS can, in theory, now also be utilized by nonexpert laboratories.

show abstract

Systems structural biology measurements by in vivo cross-linking with mass spectrometry

Cited by 60 publications

References 62 publications

Cellular Interactome Dynamics during Paclitaxel Treatment

Cellular Interactome Dynamics during Paclitaxel Treatment

Cross-linking/mass spectrometry at the crossroads

Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

Contact Info

Product

Resources

About