Structural Biochemistry A
Code
11193
Academic unit
Faculdade de Ciências e Tecnologia
Department
Departamento de Química
Credits
6.0
Teacher in charge
Pedro Manuel Henriques Marques Matias, Ricardo Saraiva Loureiro Oliveira Louro
Weekly hours
4
Total hours
60
Teaching language
Inglês
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
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.
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
- Theoretical classes - direct contact with the teaching staff in a classroom for presentation and discussion of the theoretical and theoretical-practical concepts included in the syllabus.
- Practical classes - direct contact with the teaching staff in classroom or laboratory for application of the concepts presented in the theoretical classes. The students will be divided into groups and each group will choose a project dealing with the structural characterization of a protein by X-ray crystallography and/or NMR. The work progress will follow as closely as possible the contents of the theoretical classes so as to allow the students a better assimilation of the concepts presented.
- Independent study - time used by the students to prepare project reports and study for the final examination.
Evaluation method
Evaluation will consist of a written examination (45% of the final grade) and an oral presentation and discussion of the project(s) executed by the student (55% of the final grade).