Learning outcomes of the course unit
After attending the course, participants should be able to do the following:
Understand the structural organization of biological macromolecules and their complexes.
Analyze a 3D protein structure, highlight features such as bound ligands and active site residues, create, save and export customized views of the 3D model.
Course contents summary
Physico-chemical properties of amino acids, the peptide bond, phi and psi angle of rotation, the Ramachandran diagram.
Secondary structures: Alpha helixes, 3.10 and Greek pi, beta sheets, loop regions.
Topological diagrams, calcium-binding helix-turn-helix motifs, beta hairpins, Greek a motif, beta-alpha-beta motif.
Alpha helix structures: inter-helix contacts and superstructural organization of alpha-helix proteins, four helix bundle, globin folding.
Alpha-beta structures: TIM barrel structure, Rossmann folding.
Beta structure: "barrels" formed by antiparallel beta strands; Greek key motif; "jelly roll" (vitamin A-binding proteins; neuraminidase; gamma-crystallin; immunoglobulin and immunoglobulin-like proteins.
Proteins with enzyme activity: serin protease, enzyme-substrate complex, Km, Kcat, Vmax, the transition state, mechanism of action of chimotrypsin, specificity, convergent evolution.
DNA recognition by prokaryotic transcription factors: the helix-turn-helix motif, specific and non-specific interactions, Cro, lambda repressor, Lac operon repressor, CAP, tryptophan repressor, allosteric effectors that alter the affinity of protein for DNA.
DNA recognition by eukaryotic transcription factors: TBP, specific sequence interactions, hydrophobics and plasticity of DNA, homeodomain proteins, POU regions. Zinc finger motifs, GCN4 leucin zipper.
Membrane proteins: bacteriorodopsin, porines, potassium channel, hydropathy graphs.
Protein folding: conformational flexibility, thermodynamic and kinetic factors that affect folding, isomerization of proline residues, structure and function of GroEL/GroES chaperonines.
Notes on the determination of protein structure by means of X rays.
Petsko, G.A., Ringe D., PROTEIN STRUCTURE AND FUNCTION: (New Science Press Ltd, 2002).
Branden C., Tooze J. INTRODUZIONE ALLA STRUTTURA DELLE PROTEINE (Zanichelli, II Ed., 2001)
Nelson D.L., Cox M.M. I PRINCIPI DI BIOCHIMICA DI LEHNINGER (Zanichelli, III ed., 2002)
Assessment methods and criteria
Written and oral exam