Advanced Techniques in Structural Biology (2007)

Schedule

A 4-credit course; 35 classes of 1.25 h each.

Lectures: Monday, 10:30-11:45am, Wednesdays 10:30-11:45am. Location: Skirball 3^rd floor seminar room

Lab exercises: Fridays, 10:30-11:45am. Location: 4^th floor seminar room.

There will be homework and a final exam.

REFERENCES

X-ray protein crystallography



Feb 5: Protein structure and dynamics (Tim Cardozo)
(class notes)

Feb 7: Mathematics tools (Xiangpeng Kong)
(class notes)

Feb 9: Lab exercise: O and CNS
(class notes)

Feb 12: X-ray and protein crystals (Xiangpeng Kong)
(class notes)
(homework)

Feb 14: Symmetry and space groups of protein crystals (Xiangpeng Kong)
(class notes)

Feb 16: Lab exercise: data collection of lysozyme crystals
(class notes)

Feb 19: (holiday)


Feb 21: X-ray diffractions, Bragg’s law, phase problem (Xiangpeng Kong)
(class notes)

Feb 23: X-ray diffractions, Bragg’s law, phase problem (Xiangpeng Kong)
(class notes)

Feb 26: Phasing by MR, MIR and MAD (Stevan Hubbard)
(class notes)

Feb 28: Phasing by MR, MIR and MAD (Stevan Hubbard)
(class notes)

Mar 2: Lab exercise: determining lysozyme structure by molecular replacement method
(class notes)

Mar 5: Electron density calculation and interpretation, model building (Rui-Ming Xu)
(class notes)

Mar 7: Model refinement and structure presentation (Rui-Ming Xu)

Mar 9: Lab exercise: structure determination by MIR/MAD (molecule to be selected)

Electron microscopy

Mar 12: Electron microscopy: math basics (David Stokes)
(class notes)

Mar 14: Electron microscopy: optics and 2D crystals (Da Neng Wang)
(class notes)
(homework)

Mar 16: Lab exercise: using electron microscope

Mar 19: Electron microscopy: 2D crystals continued (Da Neng Wang)
(class notes)

Mar 21: Electron microscopy: helical crystals (David Stokes)
(class notes)

Mar 23: Lab exercise: tomography data collection

Mar 26: Electron microscopy: SPA (Da Neng Wang)
(class notes)

Mar 28: Electron microscopy: tomography and fitting (David Stokes)
(class notes)

Mar 30: Lab exercise: 3D reconstruction of the tomography data set

(ONE WEEK BREAK)

Light microscope (two longer sessions)

Apr 11: Principles of confocal and two-photon microscopy (Wenbiao Gan)
(class notes)

Apr 13: Lab exercise: using confocal and two-photon microscopes (Wenbiao Gan)
(class notes)

NMR

Apr 16: NMR: Basics: Spin, Isotopes, Couplings, FTNMR (Alexej Jerschow)
(class notes 1)
(class notes 2)

Apr 18: NMR: Multidimensional NMR, Correlation Spectroscopy (Alexej Jerschow)

Apr 20: NMR: Protein and Peptide Structure Determination using NMR (Alexej Jerschow)

(ONE WEEK BREAK)

MRI and ultrasound

Apr 30: MRI: Basic principles and techniques (Dan Turnbull)
(class notes)

May 2: MRI and Ultrasound data acquisition (Dan Turnbull)
(class notes)

May 4: Lab exercise: In vivo MRI and Ultrasound of mice (Dan Turnbull)

Mass Spectrometry

May 7: Mass spectrometry: MALDI and Q-TOF (Thomas Neubert)
(class notes)

May 9: Mass spectrometry: MALDI and Q-TOF (Thomas Neubert)
(class notes)

May 11: Lab exercise: peptide mass mapping and MS/MS peptide fragmentation
(class notes)

May 18: Final exam