Learning objectives
After attending the course, participants should be able to do the following:<br />
Understand the structural organization of biological macromolecules and their complexes.<br />
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 unit content
Physico-chemical properties of amino acids, the peptide bond, phi and psi angle of rotation, the Ramachandran diagram.<br />
Secondary structures: Alpha helixes, 3.10 and Greek pi, beta sheets, loop regions.<br />
Topological diagrams, calcium-binding helix-turn-helix motifs, beta hairpins, Greek a motif, beta-alpha-beta motif.<br />
Alpha helix structures: inter-helix contacts and superstructural organization of alpha-helix proteins, four helix bundle, globin folding.<br />
Alpha-beta structures: TIM barrel structure, Rossmann folding.<br />
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.<br />
Proteins with enzyme activity: serin protease, enzyme-substrate complex, Km, Kcat, Vmax, the transition state, mechanism of action of chimotrypsin, specificity, convergent evolution.<br />
DNA structure.<br />
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.<br />
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.<br />
Membrane proteins: bacteriorodopsin, porines, potassium channel, hydropathy graphs.<br />
Protein folding: conformational flexibility, thermodynamic and kinetic factors that affect folding, isomerization of proline residues, structure and function of GroEL/GroES chaperonines.<br />
Quaternary structures.<br />
Notes on the determination of protein structure by means of X rays.
Bibliography
Petsko, G.A., Ringe D., PROTEIN STRUCTURE AND FUNCTION: (New Science Press Ltd, 2002). <br />
Branden C., Tooze J. INTRODUZIONE ALLA STRUTTURA DELLE PROTEINE (Zanichelli, II Ed., 2001)<br />
Nelson D.L., Cox M.M. I PRINCIPI DI BIOCHIMICA DI LEHNINGER (Zanichelli, III ed., 2002)
