Enabling cryo-EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures.
AI-guided
computational analysis
cryo-EM
homogenates
protein structure prediction
structural proteomics
Journal
Proteomics
ISSN: 1615-9861
Titre abrégé: Proteomics
Pays: Germany
ID NLM: 101092707
Informations de publication
Date de publication:
09 2023
09 2023
Historique:
revised:
23
03
2023
received:
14
09
2022
accepted:
24
03
2023
medline:
6
9
2023
pubmed:
5
4
2023
entrez:
4
4
2023
Statut:
ppublish
Résumé
In the cellular context, proteins participate in communities to perform their function. The detection and identification of these communities as well as in-community interactions has long been the subject of investigation, mainly through proteomics analysis with mass spectrometry. With the advent of cryogenic electron microscopy and the "resolution revolution," their visualization has recently been made possible, even in complex, native samples. The advances in both fields have resulted in the generation of large amounts of data, whose analysis requires advanced computation, often employing machine learning approaches to reach the desired outcome. In this work, we first performed a robust proteomics analysis of mass spectrometry (MS) data derived from a yeast native cell extract and used this information to identify protein communities and inter-protein interactions. Cryo-EM analysis of the cell extract provided a reconstruction of a biomolecule at medium resolution (∼8 Å (FSC = 0.143)). Utilizing MS-derived proteomics data and systematic fitting of AlphaFold-predicted atomic models, this density was assigned to the 2.6 MDa complex of yeast fatty acid synthase. Our proposed workflow identifies protein complexes in native cell extracts from Saccharomyces cerevisiae by combining proteomics, cryo-EM, and AI-guided protein structure prediction.
Identifiants
pubmed: 37016452
doi: 10.1002/pmic.202200096
doi:
Substances chimiques
Cell Extracts
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2200096Informations de copyright
© 2023 The Authors. Proteomics published by Wiley-VCH GmbH.
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