BCM 6200 - Macromolecular Structure

• Course timetable - 2018

Useful Web links
Protein crystallography

• Crystal Symmetry
• X-ray Diffraction - I
• X-ray Diffraction - II
• Protein crystallization
• X-ray Sources
• SAXS new 28/09/2015
• Space_group
• Escher Web Sketch (official M.C. Escher symmetry sketches )
• Bragg's Law and Diffraction
• Fourier transform
• Crystal Structure Diffraction
  • The interactive Course of crystallography
  • --> Crystallographic applets obtained from http://escher.epfl.ch/eCrystallography/ <--
• Notes on Electron Density, Phase Problem & Intensity Measurement
• Review of Diffraction Basics

Protein crystallization
• How to grow protein crystals
• Pictorial Library of Crystallization Drop Phenomena
• Atomic Force Microscopy(and see links therein)

  
  

  • Crystals at Birth
  • Growth of 3D Protein Molecules- Basics
  • Nucleation and Growth of Macromolecules

Cryo-crystallography

• How does Radiation Damage in Protein Crystals depend on X-ray Dose
• Heat transfer from protein crystals

X-ray Sources
• Synchrotron crystallography overview
• Strategies for macromolecular synchrotron crystallograph

Getting started
• 1 2 3 shoot
• Cryo-Notes from Bernard Rupp

Phasing
• The Patterson by Patterson
• Isomorphous Replacement
• Anomalous Scattering and Molecular Replacement

Modelling
• Phase Improvement, Model Building & Refinement

Docking
• Molecular Docking new 24/11/2018

CryoEM
• Introduction revised 10/23/2020
• Theory & Image Analysis revised 10/27/2020
• CryoElectron Tomography Movie
• Modeling & Refinement new 10/30/2020
• Advances in cryo-EM new 11/02/2020

Links

• Ewald Sphere and Diffraction
• Protein Crystallographic Data Movies

NMR

1. Nuclear Magnetic Resonance Spectroscopy
2. NMR Relaxation
3. NMR Indirect Spin-Spin Coupling
4. NMR Parameters new 02/11/2015
5. Magnetization Transfer
6. NMR Pulse Sequences I
7. NMR Pulse Sequences II
8. NMR Spectroscopy Studies of Nucleic Acids
9. NMR Sequential Assignment Strategies
10. NMR Structure Calculations
11. NMR Chemical Exchange new 16/11/2015
12. Structure-based Drug Design

Modelling to be replaced in 2018 with CryoEM Structure Determination

• Potential Energy Functions new 21/11/2015
• Energy Minimization & Molecular Dynamics new 21/11/2015
• Free Energy & Applications new 21/11/2015

Seminar topics The seminars will be held on Friday December 3rd, 2015 in D-560 at 11H30-15H00 . A Powerpoint or acetate presentation would be appreciated. Your presentation should last no more than 15 minutes leaving time for 5 minutes of questions. Please focus your presentation on the technique used in the article that you have chosen - whenever possible be ready to justify the use of this technique, why it was used and its advantages in the context of its application. Please consult the evaluation profile for which presentation has been assigned to you from the list of seminar topics.
Term paper - 2012 new 13/12/2012

This year instead of an oral presentation, each student will choose from a list of topics and submit a term paper summarizing the technical concepts in their chosen reference. The due date is January 11th, 2013 and it must be submitted electronically.

A recommended format of the term paper should include a title page, an abstract, an introduction to place the importance of the technique in relation to its field, a description of the method, a summary of the results obtained by the method, and importantly your analysis of the method of why it was used and its advantages in the context of its application, and any pertinent references to support your contentions. The acceptable length of the term paper is 10 pages maximum including any figures and tables but excluding the cover page and references. The term paper should use a 12 pt font and have a 2 cm margin all around.

Please append the PDF file of your chosen article to your term paper. Please contact me if you cannot access a PDF copy of your chosen article.
Additional information

1. Crystallography 101
2. Crystallographic facts
3. Protein Crystallography on the Web

Reference Books :

1. Principles of Protein Crystallography by J. Drenth, Springer-Verlag Inc., New York
2. Practical Protein Crystallography by D. McRee, Academic Press Inc., San Diego