High Throughput, High Performance Algorithms for High Resolution Subtomogram Averaging

Explore high-throughput, high-performance algorithms for high-resolution subtomogram averaging in this 47-minute conference talk by Mikhail Kudryashev from the Stiftung Max-Delbrück-Centrum für Molekulare Medizin. Delve into the powerful method of subtomogram averaging from cryo-electron tomograms for determining macromolecular structures in their native state. Discover the tools developed for in situ structural biology, including TomoBEAR for near-automated tomographic processing and SUSAN for high-performance computing. Learn about applications to protein lattices, coats, ribosomes, and membrane proteins, with a focus on overcoming throughput and processing time bottlenecks. Examine the structure of an ion channel determined at side-chain resolution using these advanced tools. Gain insights into sample purification, excitation-contraction coupling in skeletal muscle, and the structure of RyR1 in native membranes. Compare reported structures of RyR1 and explore optimization techniques for subtomogram averaging, including CTF estimation and 3D reconstruction modules in SUSAN.

Intro
Structures of membrane proteins
Excitation-contraction coupling in skeletal muscle
Sample purification workflow
Structure of RyR1 in native membranes
Structure of RyR1 at the resolution of secondary structure
Comparison to the other reported structures of RyR1
Subtomogram averaging is successful for a class of molecules
Throughput considerations
More options for particle picking with user assistance
Benchmarking tomoBEAR
Optimizing subtomogram averaging
Substack analysis with SUSAN
CTF estimation module in SUSAN - "normalization"
CTF estimation module in SUSAN - "linearization"
3D reconstruction in SUSAN
Benchmarking SUSAN
Conclusions and outlook