Structural Biochemistry A
Objectives
This curricular unit will provide the students with theoretical and practical skills to:
- plan, execute and analyze protein crystallization assays;
- carry out a crystallographic characterization of the crystals obtained;
- collect and process diffraction data from a protein crystal;
- plan and execute the 3D structure determination of a protein;
- build, refine and critically analyze the 3D structural model of a protein;
- perform the structural analysis of the model obtained, compare it with models obtained by other methods and find similar structures in databases;
- carry out a basic interpretation of 1D and 2D NMR spectra of proteins;
- collect and process 1D and 2D NMR spectra of proteins;
- determine by NMR the structure of a protein with MW < 15 kDa
General characterization
Code
11193
Credits
6.0
Responsible teacher
Pedro Manuel Henriques Marques Matias, Ricardo Saraiva Loureiro Oliveira Louro
Hours
Weekly - 4
Total - Available soon
Teaching language
Português
Prerequisites
Available soon
Bibliography
“Crystallography made Crystal Clear - A Guide for users of Macromolecular Models” G. Rhodes, 2nd Ed., Academic Press: San Diego, London (2000)
“Introduction to Protein Structure” Branden, C.-I. & Tooze, J. Garland Pub. (1999)
“Structural Biology; Practical NMR applications” Q. Teng, Springer Science +Business Media, Inc, NY (2005)
Wlodawer, A., Minor, W., Dauter, Z., and Jaskolski, M. (2008) "Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures", FEBS J 275, 1-21. doi:10.1111/j.1742-4658.2007.06178.x
Teaching method
Available soon
Evaluation method
Available soon
Subject matter
- Crystal symmetry; crystallization methods; characterization of crystals;
- sources of X-rays, diffraction by single crystals, instruments and methods for diffraction data collection;
- The structure factor, electron density maps, the "phase problem" and methods for its solution;
- Methods for building and refining a crystallographic structural model; convergence criteria;
- Electron Crystallography and Electron Microscopy for 3D structure analysis;
- Validation methods for crystallographic protein 3D structures; structural comparison; crystallographic databases. Comparison with other methods of 3D structural analysis. On-line computational tools;
- Basic theory of 1D and 2D NMR. Structural information: angles, distances, chemical environment.
- Pulse sequences for data acquisition and spectral assignment. 2D and 3D methods.
- Protein structure determination methods by NMR: Proteins with MW15kDa.