BCH2138H: Advanced Electron Microscopy

Coordinator	Dr. John Rubinstein
Term	Fall 2022
Day & Time	Tuesday and Thursday, 10-11am for lectures 1-6 (Oct 4, 6, 11, 13, 18, 20) Leslie Dan Pharmacy Building, 144 College Street, PB255 Tue Oct 25, 10am-12 Lecture 7, PMCRT, Room 15-710 Tue Nov 1, 10am-12 Presentations 1, PMCRT, Room 15-710 Tue Nov 8, 10am-12 Presentations 2, PMCRT, Room 15-710
Location	Lectures 1-6: Leslie Dan Pharmacy Building, 144 College Street, Room PB255 Lecture 7 and presentations: PMCRT, 101 College St, Room 15-710
Recommended Prerequisites	None
Module Goals	To give a working understanding of the use of electron cryomicroscopy in modern structural biology
Evaluation Method	Participation: 20%; Assignment: 30%; Presentation evaluation: 50%

Schedule

Date	Instructor	Lecture
October 4 October 6	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.
October 11 October 13	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.
October 18 October 20	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.
October 25	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 November 1 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 8 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.