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

Summary Hsp90 belongs to a family of some of the most highly expressed heat shock proteins that function as molecular chaperones to protect the proteome not only from the heat shock, but from other misfolding events. As many client proteins of Hsp90 are involved in oncogenesis, this chaperone has been in focus of intense research efforts. Yet, we lack structural information for how Hsp90 interacts with co-chaperones and client proteins. Here, we develop a mass spectrometry based approach that allows quantitative measurements of in vitro and in vivo effects of small molecule inhibitors on Hsp90 conformation, and interaction with co-chaperones and client proteins. From this analysis we were able to derive structural models for how Hsp90 engages its interaction partners in vivo and how different drugs affect these structures. Additionally, the methodology described here offers a new approach to probe the effects of virtually any inhibitor treatment on the proteome level.

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“…S2 (Schweppe et al, 2016; Zheng et al, 2013). The cross-linked proteins spanned a wide range of cellular abundance (Kulak et al, 2014) (Fig.…”

Section: Resultsmentioning

confidence: 99%

In Vivo Conformational Dynamics of Hsp90 and Its Interactors

Chavez

Schweppe

Eng

et al. 2016

Cell Chemical Biology

133

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“…Together these data illustrate that previously identified cross-linked peptide pairs from large scale in vivo cross-linking efforts can be reliably detected and quantified using the PRM methods described herein. This makes large repositories of cross-linked peptide pairs, such as XlinkDB [25, 26], increasingly important as now any of the cross-linked peptide pairs existing therein can serve as readily available targets for researchers to probe cross-linked peptide pairs representing a particular conformation of a protein or interactions between proteins with varying biological stimuli. This is analogous to the SRMAtlas [27] for tracking protein expression levels in standard quantitative proteomics experiments, only now providing molecular structure and interaction information.…”

Section: Resultsmentioning

confidence: 99%

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry

et al. 2016

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Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.

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“…Moreover, ProXL allows to store and share cross‐linking data between researchers. XLinkDB also allows to store and share cross‐linking projects. It also gives the option to map cross‐linking data on to structures that are generated by homology modeling with Modeller, or on to complexes that are obtained by docking with PatchDock .…”

Section: Visualization Of Identified Cross‐linked Peptidesmentioning

confidence: 99%

“…Various platforms already exist to share protein structure data: the longest running such repository is the PDB, which contains protein structures that were determined by X‐ray crystallography, NMR or high resolution electron microscopy. And, as mentioned above, XLinkDB and ProXL provide online databases for cross‐linking experiments.…”

Section: Data Management and Dissemination Of Identified Cross‐linkedmentioning

confidence: 99%

Cross‐linked peptide identification: A computational forest of algorithms

Yılmaz

Shiferaw

Rayó

et al. 2018

Mass Spectrometry Reviews

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Chemical cross-linking analyzed by mass spectrometry (XL-MS) has become an important tool in unravelling protein structure, dynamics, and complex formation. Because the analysis of cross-linked proteins with mass spectrometry results in specific computational challenges, many computational tools have been developed to identify cross-linked peptides from mass spectra and subsequently interpret the identified cross-links within their structural context. In this review, we will provide an overview of the different tools that are currently available to tackle the computational part of an XL-MS experiment. First, we give an introduction on the computational challenges encountered when processing data from a cross-linking experiment. We then discuss available tools to identify peptides that are linked by intact or MS-cleavable cross-linkers, and we provide an overview of tools to interpret cross-linked peptides in the context of protein structure. Finally, we give an outlook on data management and dissemination challenges and opportunities for cross-linking experiments.

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

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 54 publications

References 11 publications

In Vivo Conformational Dynamics of Hsp90 and Its Interactors

In Vivo Conformational Dynamics of Hsp90 and Its Interactors

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry

Cross‐linked peptide identification: A computational forest of algorithms

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