PCprophet: a framework for protein complex prediction and differential analysis using proteomic data

Fossati, Andrea; Li, Chen; Uliana, Federico; Wendt, Fabian; Frommelt, Fabian; Sykacek, Peter; Heusel, Moritz; Hallal, Mahmoud; Bludau, Isabell; Capraz, Tümay; Xue, Peng; Song, Jiangning; Wollscheid, Bernd; Purcell, Anthony W.; Gstaiger, Matthias; Aebersold, Ruedi

doi:10.1038/s41592-021-01107-5

Cited by 46 publications

(61 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The discrepancy between protein complex coverage and co-elution in our dataset—and, indeed, in all SEC-MS studies to date (Fossati et al, 2021; Heusel et al, 2019, 2020; Kirkwood et al, 2013; Larance et al, 2013, 2016)—is likely due to a number of factors. For one, not all CORUM-annotated complexes will be present in all cell types.…”

Section: Resultsmentioning

confidence: 65%

“…Using PCprophet's differential analysis workflow, we identified 699 proteins and 49 protein complexes as being significantly altered between our two conditions (Fig 3E, Tables S7-S8). As a percentage of the total positive IDs in the analysis, both the altered proteins (13.4 %) and complexes (15.3 %) were lower than that observed by Fossati et al using the same PCprophet analysis workflow for comparing HeLa-CCL2 cells at interphase vs. mitosis (approximately 30 % and 26 %, respectively) (Fossati et al, 2021). This was not necessarily surprising, given that HSP90 is not a typical molecular chaperone responsible for general folding of the majority of the proteome (as opposed to HSC70, for example), but rather has a small subset of clients.…”

Section: Identification Of Differential Protein Complexes Based On Se...mentioning

confidence: 54%

“…When assessing coeluting subunits from the SEC fraction profiles, CCprofiler identified 247 CORUM protein complexes, defined as at least 50 % of the CORUM annotated subunits classified as co-eluting at 5 % FDR (Fig 3B). An alternative SEC-MS protein complex predictor, PCprophet (Fossati et al, 2021), identified 408 CORUM complexes with the same threshold of at least 50 % of subunits co-eluting (Fig 3B).…”

Section: Resultsmentioning

confidence: 99%

“…Another useful future comparison would be SEC-MS with other HSP90 inhibitors-especially those that bind HSP90 outside of its N-terminal ATPase pocket, such as C-terminal domain binders of the novobiocin family (Donnelly and Blagg, 2008) or covalent inhibitors targeting cysteine residues (Li et al, 2021;Zhu et al, 2021). C-terminal HSP90 binders represent an area of renewed interest (Armstrong et al, 2016;Bhatia et al, 2018;Goode et al, 2017;Park et al, 2020;Terracciano et al, 2018) due to their general propensity to inhibit chaperone activity without inducing the cytoprotective heat shock response-one of the major explanations proposed for the limited tumor-killing effect of Nterminal HSP90 inhibitors (Bickel and Gohlke, 2019).…”

Section: Discussionmentioning

confidence: 99%

See 3 more Smart Citations

Native size exclusion chromatography-based mass spectrometry (SEC-MS) identifies novel components of the Heat Shock Protein 90-dependent proteome

Samant

Batista

Larance

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

The molecular chaperone heat shock protein 90 (HSP90) works in concert with co-chaperones to stabilize its client proteins, which include multiple drivers of oncogenesis and malignant progression. Pharmacologic inhibitors of HSP90 have been observed to exert a wide range of effects on the proteome, including depletion of client proteins, induction of heat shock proteins, dissociation of co-chaperones from HSP90, disruption of client protein signaling networks, and recruitment of the protein ubiquitylation and degradation machinery---suggesting widespread remodeling of cellular protein complexes. However, proteomics studies to date have focused on inhibitor-induced changes in total protein levels, often overlooking protein complex alterations. Here, we use size-exclusion chromatography in combination with mass spectrometry (SEC-MS) to characterize the changes in native protein complexes following treatment with the HSP90 inhibitor tanespimycin (17-AAG) in the HT29 colon adenocarcinoma cell line. After confirming the signature cellular response to HSP90 inhibition (e.g., induction of heat shock proteins, decreased total levels of client proteins), we were surprised to find only modest perturbations to the global distribution of protein elution profiles in inhibitor-treated cells. Similarly, co-chaperones that co-eluted with HSP90 displayed no clear difference between control and treated conditions. However, two distinct analysis strategies identified multiple inhibitor-induced changes, including several known components of the HSP90 proteome, as well as numerous proteins and protein complexes with no previous links to HSP90. We present this dataset as a resource for the HSP90, proteostasis, and cancer communities (https://www.bioinformatics.babraham.ac.uk/shiny/HSP90/SEC-MS/), laying the groundwork for future mechanistic and therapeutic studies related to HSP90 pharmacology. Data are available via ProteomeXchange with identifier PXD033459.

show abstract

Section: Resultsmentioning

confidence: 65%

Section: Identification Of Differential Protein Complexes Based On Se...mentioning

confidence: 54%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Native size exclusion chromatography-based mass spectrometry (SEC-MS) identifies novel components of the Heat Shock Protein 90-dependent proteome

Samant

Batista

Larance

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Migration profiles of the same entity (protein, phosphosites) showing multiple peaks (i.e. potentially being present in multiple assemblies) were deconvoluted based on the detection of local maxima, and the resulting single peaks from different proteins/phosphosites were grouped by unsupervised hierarchical clustering into co-migrating modules (see Material and Methods and the reference 25 ). Critically, the YAP1 profile across the analyzed fractions indicates the existence of electrophoretically well-resolved peaks of varying abundance and MW (Figure S5d and S3, S4 for the visualization of raw and smoothed profiles).…”

Section: Resultsmentioning

confidence: 99%

Systematic dissection of phosphorylation-dependent YAP1 complex formation elucidates a key role for PTPN14 in Hippo signal integration

Uliana

Ciuffa

Mishra

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Cellular signaling relies on the temporal and spatial control of the formation of transient protein complexes by post-translational modifications, most notably by phosphorylation. While several computational methods have been developed to predict the functional relevance of phosphorylation sites, assessing experimentally the interdependency between protein phosphorylation and protein-protein interactions (PPIs) remains a major challenge. Here, we describe an experimental strategy to establish interdependencies between specific phosphorylation events and complex formation. This strategy is based on three main steps: (i) systematically charting the phosphorylation landscape of a target protein ; (ii) assigning distinct proteoforms of the target protein to different protein complexes by electrophoretic separation of native complexes (BNPAGE) and protein/phopho correlation profiling; and (iii) genetically deleting known regulators of the target protein to identify which ones are required for given proteoforms and complexes. We applied this strategy to study phosphorylation-dependent modulation of complexes containing the transcriptional co-regulator YAP1. YAP1 is highly phosphorylated and among the most extensively connected proteins in the human interactome. It functions as the main signal integrator and effector protein of the Hippo pathway which controls organ size and tissue homeostasis. Using our workflow, we could identify several distinct YAP1 proteoforms specifically associated with physically distinct complexes and infer how their formation is affected by known Hippo pathway members. Importantly, our findings suggest that the tyrosine phosphatase PTPN14 controls the co-transcriptional activity of YAP1 by regulating its interaction with the LATS1/2 kinases. In summary, we present a powerful strategy to establish interdependencies between specific phosphorylation events and complex formation, thus contributing to the functionalization of phosphorylation events and by this means provide new insights into Hippo signaling.

show abstract

The complex machinery of human cobalamin metabolism

McCorvie

Ferreira

Yue

et al. 2023

J of Inher Metab Disea

View full text Add to dashboard Cite

Vitamin B 12 (cobalamin, Cbl) is required as a cofactor by two human enzymes, 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) and methylmalonyl-CoA mutase (MMUT). Within the body, a vast array of transporters, enzymes and chaperones are required for the generation and delivery of these cofactor forms. How they perform these functions is dictated by the structure and interactions of the proteins involved, the molecular bases of which are only now being elucidated. In this review, we highlight recent insights into human Cbl metabolism and address open questions in the field by employing a protein structure and interactome based perspective. We discuss how three very similar proteins-haptocorrin, intrinsic factor and transcobalamin-exploit slight structural differences and unique ligand receptor interactions to effect selective Cbl absorption and internalisation. We describe recent advances in the understanding of how endocytosed Cbl is transported across the lysosomal membrane and the implications of the recently solved ABCD4 structure. We detail how MMACHC and MMADHC cooperate to modify and target cytosolic Cbl to the client enzymes MTR and MMUT using ingenious modifications to an ancient nitroreductase fold, and how MTR and MMUT link with their accessory enzymes to sustainably harness the supernucleophilic potential of Cbl. Finally, we provide an outlook on how future studies may combine structural and interactome based approaches and incorporate knowledge of post-translational modifications to bring further insights.

show abstract

PCprophet: a framework for protein complex prediction and differential analysis using proteomic data

Cited by 46 publications

References 54 publications

Native size exclusion chromatography-based mass spectrometry (SEC-MS) identifies novel components of the Heat Shock Protein 90-dependent proteome

Native size exclusion chromatography-based mass spectrometry (SEC-MS) identifies novel components of the Heat Shock Protein 90-dependent proteome

Systematic dissection of phosphorylation-dependent YAP1 complex formation elucidates a key role for PTPN14 in Hippo signal integration

The complex machinery of human cobalamin metabolism

Contact Info

Product

Resources

About