Enabling cryo‐EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures

• Published in: Proteomics (Weinheim) Vol. 23; no. 17; pp. e2200096 - n/a
• Main Authors: Tüting, Christian, Schmidt, Lisa, Skalidis, Ioannis, Sinz, Andrea, Kastritis, Panagiotis L.
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 01.09.2023
• Subjects: AI‐guided; Biomolecules; Cellular structure; Community involvement; Community participation; computational analysis; cryo‐EM; Density; Electron microscopy; Fatty acids; Fatty-acid synthase; homogenates; Information processing; Machine learning; Mass spectrometry; Mass spectroscopy; Protein interaction; Protein structure; protein structure prediction; Proteins; Proteomics; Scientific imaging; structural proteomics; Workflow; Yeast; structural proteomics; computational analysis; homogenates; cryo-EM; protein structure prediction; AI-guided
• ISSN: 1615-9853; 1615-9861; 1615-9861
• DOI: 10.1002/pmic.202200096

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.