Towards Whole-Organelle Structure Analysis with Solve-MS and Cryo-Electron Imaging

With recent advances in machine learning and cryo-electron imaging, it has become possible to predict the 3-dimensional structures of protein complexes on a cellular scale with near-atomic resolution.

However, for a complete understanding, we must be able to capture biological processes in the context of their cellular environment.

It was recently demonstrated that membrane protein complexes can be analyzed directly from native lipid vesicles using mass spectrometry (Solve-MS).

We propose that Solve-MS facilitates the analysis of entire protein networks from native environments, conserving the effects of transient interaction partners (e.g. chaperones), conformational constraints (e.g. crowding), and non-protein components (e.g. ions).

We will develop lipid vesicles as microenvironment vehicles to preserve native protein interactions of functional cellular units for nMS and cryo-electron imaging analysis. We will then apply the approach to uncover structural features for chromatin remodeling inside nucleolar condensates.

The approach will be extended to nMS analysis of vesicle-embedded, native chromatin injected directly into the mass spectrometer.

By integrating AlphaFold predictions and low-resolution in situ structure data from cryo-electron tomography, we will generate detailed models of functional cellular units in a native-like micro-environment. The project thus combines method development, biological discovery, and future research opportunities.