Learning outcomes of the course unit
KNOWLEDGE AND UNDERSTANDING
The main goal of the course is to provide students with the tools necessary for a detailed and critique analysis of the structure of proteins and their macromolecular complexes. The first part of the course is dedicated to the understanding of the physical-chemical properties of the amino acids and their interaction within a protein. During the second part of the course, students are challenged with practical exercises on the structural analysis of protein models by means of open source software.
APPLYING KNOWLEDGE AND UNDERSTANDING
The educational objective of the course is to achieve the necessary knowledge for a critical analysis of the structure of proteins and nucleic acids. By the end of the course students will have acquired the skills necessary to deal with the analysis and experimental study of biological macromolecules. They will learn how to retrive protein and nucleic acid coordinates from the PDB database, recognize the fold and use sofware for a detailed analysis of their structure.
The course is aimed at increasing the ability to critically analyze the structure of proteins, nucleic acids and their interactions.
The course includes significant activity of classroom discussion aimed at developing the ability of students to transfer skills acquired in support of their arguments. In the final exam, students must take an oral presentation on the structure and function of an assigned protein.
The many advancements of scientific research, particularly in the field of molecular biology require a continuous updating of skills. For this reason, the course aims to provide the necessary tools to achieve a wider knowledge and to align skills to the advancement in molecular biology research.
Course contents summary
The amino acids
Methods for the determination of protein structure
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.
Protein folding: conformational flexibility, thermodynamic and kinetic factors that affect folding, isomerization of proline residues, structure and function of GroEL/GroES chaperonines.
Proteins with enzyme activity: serin protease, enzyme-substrate complex, Km, Kcat, Vmax, the transition state, mechanism of action of chimotrypsin, specificity, convergent evolution.
Post-traslational modifications: phosphorylation, acetylation, n-linked glycosylation, methylation, ubiquitylation, palmitoylation.
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, Cys-loop ion channels.
F1F0 ATPase structure.
Fibrous proteins: alpha cheratines, collagen, fibroin.
Methods for the determination of protein structure.
Branden C., Tooze J. INTRODUZIONE ALLA STRUTTURA DELLE PROTEINE (Zanichelli, II Ed., 2001)
Petsko, G.A., Ringe D., STRUTTURA E FUNZIONE DELLE PROTEINE (Zanichelli, 2006).
Nelson D.L., Cox M.M. I PRINCIPI DI BIOCHIMICA DI LEHNINGER (Zanichelli, III ed., 2002)
David Whitford, PROTEINS STRUCTURE AND FUNCTION (Wiley)
The course consists of lectures that covers the main topics of the program and practical exercises. Exercises are carried out in a compueter room with the use of open source software for the visualization of the tridimensional structure of macromolecules. Beside textbooks, students have access to lectures' slides, scientific articles, and other teaching resources made available trough the web site.
Assessment methods and criteria
The assessment of learning outcomes is based on a written test and an oral report in which students are asked to describe the structure and function of an assigned protein. The oral report can be sustained after passing the written test. The written test to be held in a maximum time of two hours, consists of six questions designed to assess the degree of learning and critical analysis of the topics covered.