Structural Biochemistry
Code
7637
Academic unit
Faculdade de Ciências e Tecnologia
Department
Departamento de Química
Credits
6.0
Teacher in charge
Maria dos Anjos Lopes de Macedo, Maria João Lobo de Reis Madeira Crispim Romão
Weekly hours
4
Total hours
83
Teaching language
Português
Objectives
This discipline intends to teach the students the basic principles that determine the protein structure and structure-function relationships, as well as the fundamentals of the most used techniques for the determination of 3D structures of proteins. At the end of the semester, the students should have acquired the necessary knowledge in: (1) principles that determine the macromolecular structure,(2) main protein classes and biological implications, (3) biological implications of the quaternary structure. (4) Moreover, they will have acquired basic knowledge on the 3 main techniques for structure determination: X-ray Crystallography, Nuclear Magnetic Resonance and Cryo-electron Microscopy. (5) Finally they must have the necessary abilities to interpret the structural results and to use validation tools. (6) They should master on-line computational tools as well as programs of visualization and molecular representation.
Subject matter
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; Sequential attribution, characteristic patterns; elements of secondary structure, information on chemical shifts. Proteins >15kDa; isotopic labeling: 2 H, 13 C, 15 N.
2.3 – Crio-electron Microscopy : Image reconstruction and Electron Crystallography. 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.
Chapter 3 – Structure and Function of Proteins - Complexes of proteins with nucleic acids- Proteins that recognize DNA and specific motives. Metalloproteins. Drug design.
Chapter 4 - Complementary methods in Structural Analysis
Bibliography
- “Structural Bioinformatics” Philip E. Bourne (Editor), Helge Weissig (Editor) (2003)
- “Introduction to Protein Structure” Branden, C.-I. & Tooze, J. Garland Pub. (1999)
- “Introduction to Protein Architecture: The Structural Biology of Proteins” Arthur M. Lesk, Oxford U.P. (2001)
- “Practical Protein Crystallography “ D. E. McRee, Academic Press: San Diego (1999).
- “Biomolecular NMR Spectroscopy”, Evans, J.N.S., Oxford University Press (1995)
Teaching method
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. All the information about the discipline is accessible through a dedicated web page (http://www.dq.fct.unl.pt/cadeiras/be/). In this site are all the pdfs of the lectures presentations, problems, as well as type of exams.
Evaluation method
- 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, which will include the critical analysis of the structural model of proteins (or DNAs) in correlation to its function.
Courses
