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Structure and Function of Proteins

Code 12486
Year 1
Semester S2
ECTS Credits 6
Workload TP(60H)
Scientific area Biotecnologia
Entry requirements Not applicable.
Mode of delivery Face to face.
Work placements Not applicable.
Learning outcomes The main objective of this course is to study the structural and conformational characteristics of proteins and their biological function. It is also intended to relate conformational changes with certain diseases through examples of proteins that perform diverse biological functions.

At the end of this course students should be able to:
-Identify and describe the fundamental principles that define the structure and conformation of proteins and the mechanisms that control in vitro and in vivo protein folding;
-Describe the relation between the onset of neurodegenerative diseases with protein conformational changes;
-Explain the role of the ubiquitin and proteasome system in protein turnover;
-Apply different methods in the detection, identification and analysis of proteins (circular dichroism, mass spectrometry, nuclear magnetic resonance, surface plasmon resonance);
-Demonstrate capacity for critical analysis and presentation of scientific papers.
Syllabus 1- Visualization and computational design of organic molecules. Analysis of molecular interactions between protein receptors and ligands by computational methods (Docking).
2-Physical methods for structure determination of proteins: X-rays diffraction crystallography and nuclear magnetic ressonance. Circular Dichroism (CD). Determination of protein-ligand interactions by Surface Plasmon Resonance.
3-The structure and function of membrane proteins. Expression, purification and crystallization methods.
4-Protein turnover: ubiquitin and proteasome system.
5-Protein Folding. Conformational stability. In vitro and in vivo folding mechanisms. Misfolding and disease: molecular mechanisms of formation of protein aggregates in neurodegenerative diseases.
6-Experimental work:
-Crystallization of lysozyme.
-CD-Denaturation of proteins.
-Determination of structure of a protein by NMR.
-Structural Analysis of Protein-ligands Interactions by SPR.
--Two-dimensional electrophoresis and MALDI-TOF MS
Main Bibliography 1. Required reading
Xiong, J (2012) Essential Bioinformatics, Cambridge University Press (ISBN: 9780511806087)
-Petsko, G. & Ringe, D. (2008) "Protein Structure and Function", Primers in Biology, Oxford University Press (ISBN: 9780199556847)
-Whitford, D. (2005) "Proteins: Structure and Function", Wiley (ISBN: 978-0-471-49894-0)
- Young, D. (2009) Computational drug design: a guide for computational and medicinal chemists, John Wiley & Sons, Ltd. (ISBN: 978-0-470-12685-1)
-Selected scientific papers.

2. Recommended reading
-Muñoz, V (2008) Protein Folding, Misfolding and Aggregation, RSC Biomolecular Siciences (ISBN 978-1-84755-828-2)
- Patrick, G.L. (2010) An Introduction to Medicinal Chemistry, 4th Ed., Oxford University Press. ISBN: 9780198749691
Teaching Methodologies and Assessment Criteria Teaching process will be focused on the student, where its active participation in the learning process will allow greater development of thinking skills and self-evaluation. The pedagogical methodology is based on teaching educational objectives and problem based learning. The tutor guides students in searching relevant information to reach the expected results at the end of the learning process. The laboratorial lectures involve experimental work in which students apply their knowledge in the execution of experimental techniques as well as in data analysis and results interpretation.
Assessment - Final Mark (FM): Mod1 (15%) + Mod2 and 3 (30% + 40%) + Seminar (15%).
Mod1: Bioinformatics work. Mod 2 and 3: Two partial written tests. Seminar: Oral presentation of an experimental protocol. The Final Exam (FE) corresponds to 70% of the FM (Mod 2 and 3). Minimum Frequency Note: 9.5 pts in Mod 1 and 9.5 in the Seminar. A minimum of 9.5 pts are needed to pass in Mod2 and 3.
Language Portuguese. Tutorial support is available in English.
Last updated on: 2020-05-17

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