1st Edition
Novel Developments in Cryo‐EM of Biological Molecules Resolution in Time and State Space
Cryo-EM, as it is currently practiced in many laboratories, is limited to the visualization of molecules that are in thermal equilibrium at the time before freezing. A further limitation is that the existing software does not fully exploit the information that is contained in the images of large ensembles of molecules in thermal equilibrium. This book is a collection of recent articles by the author, reprinted with introductions, and they mainly describe two novel methods in cryo-EM, one computational and the other experimental that requires the use of a microfluidic device. Both methods have the capacity to shed light on the dynamic behavior of biomolecules. Combined, they greatly expand the range of applications of cryo-EM.
The book describes a successful approach in which, based on cryo-EM data, all states visited by the molecule in thermal equilibrium are mapped by manifold embedding—a method of geometric machine learning—and the energy landscape of the molecule is derived. It also discusses methods and biological results of time-resolved cryo-EM, following a reaction in a non-equilibrium system over a short period of time and resulting in the capture of short-lived states that have been inaccessible by standard methods of cryo-EM.
Part I: Single-Particle Cryo-EM of Molecules in Thermal Equilibrium
1. Generalized Single-Particle Cryo-EM:. A Historical Perspective
2. Advances in the Field of Single-Particle Cryo-Electron Microscopy Over the Last Decade
3. Single‐Particle Reconstruction of Biological Molecules:Story in a Sample (Nobel Lecture)
Part II: Machine Learning Applied to Ensembles of Molecules in Thermal Equilibrium: Resolution in State Space
4. Structural Characterization of mRNA-tRNA Translocation Intermediates
5. Trajectories of the Ribosome as a Brownian Nanomachine
6. Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM
7. New Opportunities Created by Single-Particle Cryo-EM: The Mapping of Conformational Space
8. POLARIS: Path of Least Action Analysis on Energy Landscapes
9. Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding
10. Retrieving Functional Pathways of Biomolecules from Single-Particle Snapshots
11. A Glycan Gate Controls Opening of the SARS-CoV-2 Spike Protein
12. Recovery of Conformational Continuum from Single-Particle Cryo-EM images: Optimization of ManifoldEM Informed by Ground Truth
Part III: Non-Equilibrium Methods: Resolution in Time
13. Structural Dynamics of Ribosome Subunit Association Studied by Mixing-Spraying Time-Resolved Cryo-EM
14. Two Promising Future Developments of Cryo-EM: Capturing Short-Lived States and Mapping a Continuum of States of a Macromolecule
15. Key Intermediates in Ribosome Recycling Visualized by Time-Resolved Cryo-Electron Microscopy
16. A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM
17. Time-Resolved Cryo-Electron Microscopy: Recent Progress
18. Time-Resolved Cryo-Electron Microscopy Using a Microfluidic Chip
19. Late Steps in Bacterial Translation Initiation Visualized Using Time-Resolved Cryo-EM
20. The Structural Basis for Release Factor Activation During Translation Termination Revealed by Time-Resolved Cryogenic Electron Microscopy
21. A Time-Resolved Cryo-EM study of Saccharomyces cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source
Biography
Joachim Frank is a professor of biochemistry and molecular biophysics and of biological sciences at Columbia University, USA. Dr. Frank’s lab has developed techniques of single-particle reconstruction of biological macromolecules, specializing in mathematical and computational approaches. He has applied these techniques of visualization to explore the structure and dynamics of the ribosomes during the process of protein synthesis and to elucidate the structure and function of several ion channels. He is a member of the National Academy of Sciences and of the American Academy of Microbiology. He is also a fellow of the American Academy of Arts and Sciences and of the American Association for the Advancement of Science. In 2014, he was honored with the Franklin Medal for Life Sciences. In 2017, he shared the Wiley Prize in Biomedical Sciences with Richard Henderson and Marin van Heel. He was awarded the 2017 Nobel Prize in Chemistry together with Jacques Dubochet and Richard Henderson for "developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution."
