Advanced Electron Microscopy
BCH 2138H
This course will give a working understanding of the use of electron cryomicroscopy in modern structural biology
| September 5 & 10 | John Rubinstein | Introduction and theoretical background. Abbe’s equation, electron wavelength, elastic and inelastic interactions, interaction cross sections, bright field and dark field optics, depth of field, amplitude contrast and phase contrast.
Instrumental considerations. High vacuum systems, spatial and temporal coherence, thermionic and field emission electron sources, magnetic lenses, stained and vitrified specimens, electron sensors, Shannon-Nyquist sampling theorem, depth of field, contrast transfer functions. |
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| September 12 & 17 | John Rubinstein | Concepts in classical image analysis, Part 1. Fourier slice theorem and 3D reconstruction, image alignment and averaging in 2D, cross correlation coefficients, cross correlation functions, cross correlation functions with Fourier transforms, representation of images in high-dimensional spaces, image classification.
Concepts in classical image analysis, Part 2. Euler angles, representing rotations as matrices, Euler angle determination by random conical tilting, Euler angle determination with the common lines theorem, Euler angle determination by projection matching. |
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| September 19 & 24 | John Rubinstein | Modern inference methods in 3D structure estimation and classification. Structure determination as an optimization problem, stochastic gradient descent for nonconvex optimization in structure estimation and classification, branch and bound methods for high-resolution map refinement
Application of cryoEM to protein structure determination. State-of-the-art research examples including use of the methods to investigate protein high-resolution structure, protein dynamics, and protein-drug interactions. |
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| Tuesday, October 1 | John Rubinstein | Practical considerations in structure determination and validation: Beam-induced motion correction, Fourier shell correlation, non-uniform map refinement, three-dimensional variability analysis, construction of atomic models, model-to-map Fourier shell correlation, model validation statistics. | |
| Tuesday, October 15
Student Presentations #1 (2 hr) |
John Rubinstein | Each student will select a classic paper about cryoEM methods and present it to the other graduate students in the class. | |
| Tuesday November 22
Student Presentations #2 (2 hr) |
John Rubinstein | Each student will select a classic paper about cryoEM methods and present it to the other graduate students in the class. | |
Course Next Offered
Fall 2024
Course Time and Location
Tuesday and Thursday, 10-11am for lectures 1-6 (Sept. 5, 10, 12, 17, 19 and 24)
Tuesday Lectures: Wallberg 119
Thursday Lectures: Bahen 2145
Tue Oct 1, 10am-12pm Lecture 7, PMCRT, Room 15-710
Tue Oct 15, 10am-12pm Presentation 1, PMCRT, Room 15-710
Tue Oct 22, 10 am-12pm Presentation 2, PMCRT, Room 15-710
Lectures 1, 3, 5: Wallberg 119, 184 College St, Toronto
Lectures 2, 4, 6, Bahen 2145, 40 St George St, Toronto
Lecture 7 and presentations: PMCRT, 101 College St, Room 15-710
Enrollment Limit
Yes — 12
6 spaces for Biochemistry / 6 spaces for Medical Biophysics
Method of Student Evaluation
Participation: 20%; Assignment: 30%; Presentation evaluation: 50%
Coordinator
John L. Rubinstein
Rm. 20-9705
Peter Gilgan Centre for Research and Learning
The Hospital for Sick Children
686 Bay Street, Toronto
416-813-7255
john.rubinstein@utoronto.ca