New advances in cross-linking mass spectrometry toward structural systems biology

Yu, Clinton; Huang, Lan

doi:10.1016/j.cbpa.2023.102357

Cited by 16 publications

(7 citation statements)

References 68 publications

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“…Additionally, the integration of isotope-labeling-based quantitative XL-MS strategies will allow accurate determination of conditionspecific PPIs for revealing cancer-specific interactomes and their association with disease progression. 76 Moreover, coupling cross-linking with co-Fractionation can facilitate the elucidation of functional protein modules. 77 Overall, the analytical workflow established here offers a promising avenue for comprehending PPIs in disease contexts to advance our understanding of human pathologies and uncover new molecular targets for improved therapeutic strategies.…”

Section: ■ Conclusionmentioning

confidence: 99%

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

Jiao,

Yu,

Wheat

et al. 2024

J. Proteome Res.

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Protein–protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.

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Section: ■ Conclusionmentioning

confidence: 99%

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

Jiao,

Yu,

Wheat

et al. 2024

J. Proteome Res.

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“…Application of cross-linkers combined with mass spectrometry has been developed as a new technology, called cross-linking mass spectrometry (XL-MS), which can provide a wealth of structural information on proteins and protein complexes. 32–34 Cross-linkers are used to covalently connect two amino acid residues of proteins in close proximity. After digestion, the resulting peptides were analysed by MS. Generally, cross-linked peptides bury in large amounts of non-cross-linked peptides.…”

Section: Introductionmentioning

confidence: 99%

“…Consideration of the steric hindrance of biotin that may affect the linking efficiency, smaller functionalities, such as alkyne-tagged cross-linkers, have been broadly developed. 32,43,44 Accordingly, azide biotin reagents have been developed allowing for appending biotin through click chemistry after the protein labelling. Additionally, diverse cleavable moieties have been inserted between azide and biotin, producing cleavable reagents for the purpose of releasing peptides.…”

Section: Introductionmentioning

confidence: 99%

Chemical reagents for the enrichment of modified peptides in MS-based identification

Huangfu,

Yu,

Sun

et al. 2024

Chem. Commun.

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“…Over the last couple of years, the field has seen significant technological and conceptual progress and by now the structural probing of recombinantly expressed protein complexes is firmly established. Recent applications of XL-MS on the systems level and in living cells have spurred great interest and hint at the exciting prospect that XL-MS will soon be able to facilitate the structural interrogation of interaction partners of any protein of interest within living cells or even organisms 3,4 .…”

Section: Introductionmentioning

confidence: 99%

Kinetic principles of chemical cross-link formation for protein-protein interactions

Kammer,

Pellarin,

Stengel

2024

Preprint

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Proteins play a central role in most biological processes within the cell and deciphering how they interact is key to understand their function. Cross-linking coupled to mass spectrometry is an essential tool for elucidating protein-protein interactions. Despite its importance, we still know surprisingly little about the principles that underlie the process of chemical cross-link formation itself and how it is influenced by different physico-chemical factors. To understand the molecular details of cross-link formation, we have set-up a comprehensive kinetic model and carried out simulations of protein cross-linking on large protein complexes. We dissect the contribution on the cross-link yield of parameters such as amino acid reactivity, cross-linker concentration, and hydrolysis rate. Our model can compute cross-link formation based solely on the structure of a protein complex, thereby enabling realistic predictions for a diverse set of systems. We quantitatively show how cross-links and mono-links are in direct competition and how the hydrolysis rate and abundance of cross-linker and proteins directly influence their relative formation. We show how cross-links and mono-links exist in a all-against-all competition due to their simultaneous formation, resulting in a non-intuitive network of inter-dependence. We show that this interdependence is locally confined and mainly limited to direct neighbors or residues in direct vicinity. These results enable us to identify the optimal cross-linker concentration at which the maximal number of cross-links are formed. Taken together, our study establishes a comprehensive kinetic model to quantitatively describe cross-link formation for protein-protein interactions.

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New advances in cross-linking mass spectrometry toward structural systems biology

Cited by 16 publications

References 68 publications

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

Chemical reagents for the enrichment of modified peptides in MS-based identification

Kinetic principles of chemical cross-link formation for protein-protein interactions

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