Structural biology and enzymology

A.Y. 2015/2016
Overall hours
Learning objectives
Expected learning outcomes
Course syllabus and organization

Single session

Lesson period
Second semester
Course syllabus
- Introduction to the identification of drug molecular targets by bioinformatic, genomic, transcriptomic, and proteomic techniques. Criteria for the validation of pharmacological targets.
- Review of information on the covalent structure of proteins, their three-dimensional architectures and the factors that stabilize their native conformation. Protein modules and classification of globular proteins. Subunit-subunit interactions. Structure-sequence correlation: homology modelling. Protein stability and flexibility.
- Molecular recognition, localization and nature of ligand binding sites. Structure-function relationships for enzymes: active site geometry, proximity factor and destabilization of the fundamental state, stabilization of the transition state and water exclusion. Strategies for the identification of catalytic residue and of interaction sites with ligands and effectors (docking techniques). Structural basis of enzyme inhibition. Examples.
- Chemical and enzyme catalysis: general principles
- Design of in vitro assays of enzymatic activity for the testing of putative effectors (activators/inhibitors) and for the determination of the reaction mechanism of enzymes as drug targets. Continuous and discontinuous methods. Coupled reactions. Design of methods for the high-throughput screening of effectors.
- Design of in vitro protein-ligand binding assays.
- Kinetic approaches (Steady-state and pre-steady-state) to dissect enzyme mechanisms. Relevance of the structure of substrate analogs, reaction reaction intermediates and of the transition state for the rational design of high affinity inhibitors. - Enzyme inhibition mechanisms. Kinetic methods to determine the effect of inhibitors on the reaction steady-state kinetic paramenters and their potency. Reversible active site inhibitors, substrate, intermediate and transition state analogs. Covalent inhibitors. Suicide substrates (Mechanism based inhibitors). Isotope effects as a powerful tool to determine transition state structures.
BIO/10 - BIOCHEMISTRY - University credits: 6
Lessons: 48 hours
Thursday, 10:30-12:30
Dept. of Biosciences, C tower, 5th floor
Monday, 1 pm -2 pm
Protein Biochemistry Unit, DSBB, Via Celoria 26, 5C