Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles

Area of Science:

• Structural biology
• Biophysics
• Cryo-electron microscopy

Background:

• Electron cryomicroscopy (cryo-EM) enables near-atomic resolution structural determination of membrane proteins and complexes within lipid vesicles.
• Particle selection from cryo-EM micrographs of vesicles is challenging due to strong lipid bilayer signals, necessitating laborious manual workflows.
• Automated particle selection is crucial for efficient high-resolution cryo-EM analysis of membrane protein structures.

Purpose of the Study:

• To develop an automated method for identifying and selecting particles from vesicles in cryo-EM micrographs.
• To improve the efficiency and accuracy of particle selection workflows in cryo-EM studies of membrane proteins.
• To facilitate high-resolution structural analysis of protein complexes within native biological vesicles.

Main Methods:

• Development of Vesicle Picker, an open-source program utilizing the Segment Anything model for vesicle identification.
• Implementation of automated particle selection at vesicle perimeters or uniformly across vesicle projections.
• Integration of Vesicle Picker with cryoSPARC for seamless micrograph processing and single particle analysis.

Main Results:

• Vesicle Picker achieves high recall and precision in identifying vesicles within cryo-EM micrographs.
• The program successfully automates particle selection, reducing the need for manual intervention.
• Demonstrated utility in determining a high-resolution map of vacuolar-type ATPase from synaptic vesicle micrographs.
• Enabled identification of an additional protein complex in the synaptic vesicle membrane.

Conclusions:

• Vesicle Picker significantly enhances the efficiency of cryo-EM structural studies involving membrane proteins and complexes in vesicles.
• The automated approach simplifies particle selection, making high-resolution cryo-EM more accessible.
• This tool aids in the discovery of novel protein interactions and structural insights within native biological systems.