Structure and Modeling of Biomacromolecules

Recommended Prerequisites

Not applicable.

Teaching Methods

Lectures and tutorials. The lectures are taught by the teacher in an interactive way, presenting the basic concepts of the curriculum. The tutorials have two major components: i) self-learning based computational classes to become familiar with the operation of databases accessible online and software tools related to points 4 and 8 of the program, ii) oral presentation of thematic works based on review of the literature performed by the students.

Learning Outcomes

1.1 Knowledge and understanding of the most relevant concepts in the chemistry of biological systems, in particular those related to the structure, dynamics and energetics of biological macromolecules and their interaction with other macromolecules, small molecules and natural ligands in order to understand the basis for the rational design of compounds with therapeutic potential.
1.2. Contribute for the global understanding of the inter-relationship among different courses of the curriculum
1.3. Stimulate the ability to summarize information.
2.1. Apply knowledge to solve problems in new situations
3.1. To interpret data, substantiate and argue orally and in writing options taken
4.1. To understand and use multiple heterogeneous sources of information
4.2. Knowing how to search and use bibliography
4.2. Know adequately to convey their knowledge, even for the non-specialist public
5.1. Ability to learn autonomously.

Work Placement(s)

No

Syllabus

1. Biological macromolecules
1.1 Chemical composition and physical-chemical properties of nucleic acids and proteins
2. Structure of single-stranded and double-stranded nucleic acids
3. Protein Structure
3.1 Levels of protein structure organization
3.2 Analysis and comparison of protein structures
4. Structure-function relationships in proteins
4.1 Structural motifs and protein function
4.2 Major classes of biological receptors and enzymes
5. Protein Stability and Folding
6. Experimental determination of the structure of biomacromolecules
6.1 Circular Dichroism
6.2 X-ray Crystallography
6.3 Nuclear Magnetic Resonance (NMR)
7. Protein-Ligand (P-L) Interactions
7.1 Equilibrium and kinetics of P-L association
7.2 Methods to study P-L interactions: ITC, Fluorescence, NMR
8. Computer modeling of protein structure and P-L interactions
8.1 Visualization and analysis of the structure of biomacromolecules
8.2 Protein structure prediction and modeling
8.3 Modeling of protein-ligand interactions.

Head Lecturer(s)

Rui Manuel Pontes Meireles Ferreira de Brito

Assessment Methods

Evaluation
Synthesis work: 25.0%
Frequency: 75.0%

Bibliography

1. Thomas E Creighton , “Proteins: Structures and Molecular Properties”, W.H. Freeman and Comp., ISBN: 0-7167-7030-X
2. Alan Fersht, “Structure and Mechanism in Protein Science”, W.H. Freeman and Company, ISBN: 0-7167-3268-8
3. Arthur M. Lesk, “Introduction to Protein Architecture”, Oxford University Press, ISBN: 0-19-850474-8
4. William P. Jencks, “Catalysis in Chemistry and Enzymology”, Dover Publications, ISBN: 0486654605
5. Orengo, Jones and Thornton, “Bioinformatics. Genes, Proteins and Computers”, BIOS Scientific Publishers, ISBN: 1-85996-054-5