Fundamentals of Structural Biochemistry
Maria dos Anjos Lopes de Macedo, Maria João Lobo de Reis Madeira Crispim Romão
Weekly - 3
Total - 46
- “Introduction to Protein Structure” Branden, C.-I. & Tooze, J. Garland Pub. (1999)
- “Crystallography made Crystal Clear- A Guide for users of Macromolecular Models” G. Rhodes, 2nd Ed., Academic Press: San Diego, London (2000)
- “Biomolecular NMR Spectroscopy”, Evans, J.N.S., Oxford University Press (1995)
- Teng, Q. “Structural Biology: Practical NMR applications” Springer Science, USA (2005)
- Wüthrich, K. “NMR of Protein and Nucleic Acids”, Wiley-Interscience Pub., (1986)
- Friebolin, H. “Basic One- and Two-Dimensional NMR Spectroscopy”, VCH publishers, New York-Germany, 2ª ed. (1993)
- Determinação de estruturas tridimensionais de proteinas, Anjos L. Macedo & Brian J. Goodfellow, Quimica, 63, 1996
Lectures, laboratory sessions and problem-solving sessions with power-point presentations as well as several on-line tools and 3D animations. There will be computer sessions with two students per pc. Students will have access to pdfs of the lectures presentations, problems and protocols, as well as typical exam questions.
- 2 Test (average > = 9.5 ) or Written final exam (individual) (50%)
- Practical (two students) (20%); A- Continuous evaluation B- Take-home PC test (individual)
- Seminar (30%). Seminar about one (or more) scientific papers, which will include the critical analysis of the structural model of proteins in correlation to its function.
Chapter 1 - Introduction. Basic Structural principles - secondary, supersecondary and tertiary structure of proteins. Structural domains and motifs. Quaternary protein structure. Biological implications of the quaternary structure and of the type of folding. Main classes of proteins and homologous protein families.
Chapter 2 - Determination of the Three-dimensional Structure of Proteins - 2,1 – Basics of X-ray Crystallography. Protein crystallization. X-ray diffraction and measurement of the experimental data. The structural model and its validation. Biological and enzymatic activity of crystalline proteins. 2.2 - NMR - Basic theory of 1D and 2D NMR. Structural Information: angles, distances, chemical environment. Experimental Methods: Sequences of pulses for acquisition of data and spectral attribution. Bi-dimensional (homo- and heteronuclear) and tri-dimensional methods. Protein structure by NMR. Methodology: proteins 15kDa; isotopic labeling: 2 H, 13 C, 15 N.
2.3 – Complementary Methods (Cryo-EM, SAXS, ITC, DLS) 2.4 - Interpretation of the structural results - Validation Criteria. Databases. Conformacional analysis, quality of the model and accuracy of the three-dimensional structure. Validation. Comparison of crystalline structures and solution structures. Comparison of protein.