Protein secondary structure elements. Torsion angles and Ramachandran plot. Motifs and structural domains. Main fold types in protein structures.
Membrane proteins. Protein Data Bank. Protein Folding and Methods for studying. Folding processes in vivo and molecular chaperones. Protein aggregation. DNA Structures and protein-DNA interactions. RNA structures. Techniques for structure determination: NMR spectroscopy, X-ray diffraction, electron microscopy.Dynamic characterization of biomolecules.
- Carl Branden &John Tooze: Introduction to Protein Structure
- Jack Kyte Structure in Protein Chemistry.
- Banci, Cantini “Structural features of proteins” in NMR of Biomolecules: Towards Mechanistic Systems Biology -Wiley
Book chapters and review articles on specific subjects will be also provided to the students.
Learning Objectives
The course aims at providing the students with a detailed knowledge of various aspects of structural biology, focusing on the fold and organization of biological macromolecules, particularly of proteins and nucleic acids. The relationship between structure and function for some selected classes of proteins will be discussed. The molecular basis for the protein folding process will be presented. The basic concepts of the spectroscopic and biophysical methods used for structural characterization, as well as of the major techniques (NMR spectroscopy, X-ray diffraction, and cryo-EM) for 3D structural determination will be presented.
Prerequisites
Courses required: none
Courses recommended: none
Teaching Methods
Total number of hours for Lectures (hours): 48
Total number of hours for Laboratory-field practice : 10
Type of Assessment
The examination involves passing an oral exam on the topics covered in the course.
To take the exam, registration at the UniFi website, which enables electronic record of the exam, it is required. The list closes two days before the date of the examination.
It is guaranteed a minimum number of exam rounds and the teacher is available to enter further exam rounds upon student request.
The exam schedule for the academic year 2018/2019 is available at:
https://sol.unifi.it/docprenot/docprenot
Examination commission: L. Banci, M. Lelli, F. Cantini, V. Calderone
Course program
The primary sequence: the aminoacids and the peptide bond. Elements of secondary structure: helices, strands and sheets, turns. Torsion angles and Ramachandran plot. Structural motifs: helix-loop-helix, beta hairpin, Greek key, etc. Tertiary structure. Motifs and domains. The most common types of folds, classifies as alpha folds, beta folds, alpha/beta and alfa+beta. Quaternary structure. The structural classification of proteins. The Protein Data Bank (pdb). Properties of cellular membranes and membrane proteins structural features. Non covalent interactions and the folding processes in proteins. Structural stability of proteins. Approaches for characterizing the folding processes. The folding “funnel”. The unstructured states. The transition states in the folding process. The molten globule state. In vivo folding processes. The function of molecular chaperons. Protein aggregation and fibril formation. Protein flexibility and dynamical properties of biomolecules. Approaches for the characterization of the overall and internal dynamics of macromolecules. The DNA structures and the interactions protein-DNA, in eukaryotic and in prokaryotic organisms. Structural features of RNA. Experimental methods for 3D structure determination. Basic knowledge of NMR spectroscopy, X-ray crystallography, and cryo-EM for the structural characterization and the determination of 3D structure of biomolecules. Integrated structural biology approaches for cellular structural biology.