Faculdade de Ciências e Tecnologia
Departamento de Química
Teacher in charge
Maria João Lobo de Reis Madeira Crispim Romão
The knowledge and understanding of the relations between structure and function in biological systems requires information, at an atomic level, of the proteins 3D structure . The aim of this discipline is to provide the necessary background and know-how in the determination of protein structures using X-ray Crystallography as well as their analysis and validation.
At the end of the course, the student should be able to (1) prepare and characterize protein crystals, (2) measure and process X-ray diffraction data, (3) use programs for the calculation of electron-density maps, the tracing of the polypeptide chain and refinement. (4) Moreover, the student will have acquired the necessary abilities to analyze, validate and understand the 3D protein structures and (5) will be able to use computational tools on-line as well as diverse programs of visualization and molecular representation.
Introduction to the structural analysis by X-ray diffraction. Methods for protein crystallization. The physics of diffraction and Braggs law. Reciprocal space and the Ewald sphere. Diffraction data collection. The structure factor equation, its Fourier Transform and solution methods for the “phase problem”. Patterson function and the Molecular Replacement Method (MR). Multiple and Single Isomorphous Replacement (SIR and MIR). Anomalous dispersion methods (MAD and SAD). Methods for modifying and improvement of the electron density.Building and refinement of the structural model. Refinement protocols and convergence criteria. Validation tools of protein structures. Structural comparisons and crystallographic data bases. Comparison of the methods used for 3D structure determination (X-Ray, NMR and Cryo-EM)
“Crystallography made Crystal Clear- A Guide for users of Macromolecular Models” G. Rhodes, 2nd Ed., Academic Press: San Diego, London (2000) “Practical Protein Crystallography “ D. E. McRee, Academic Press: San Diego (1999)."Crystal Structure Analysis for Chemists and Biologists" J.P. Glusker, M. Lewis e M. Rossi, , VCH: New York (1994).“Principles of Protein Crystallography”, J. Drenth, Springer Verlag, New York, Berlin, Heidelberg, 2nd ed., (1999)Protein Crystallography Course at the Department of Haematology in the University of Cambridge and the Cambridge Institute for Medical Research (CIMR) http://www-structmed.cimr.cam.ac.uk/Course/
Lectures and problem-solving sessions with power-point presentations as well as several on-line tools. Most of the lectures will be computer sessions with two students per PC. The experimental sessions will be at the X-ray Laboratory of the Department. All the information about the discipline is accessible through a dedicated web page. In this site are all the pdfs of the lectures presentations, problems, as well as type of exams.
Written final exam (individual) (40%)
Practical (two students) (30%); A- Continuous evaluation B- Take-home PC test (individual)
Seminar (30%). Seminar about one (or more) scientific papers on Structural Biology.