The course has a practical formulation, with several practical exercises in the lab, to provide the students with advanced techniques and methodologies in the field of biophysics, in particular for the determination, prediction and analysis of the structure and the dynamics of proteic systems.
Basic knowledge of the structure of biological macromolecules. Fundamental principles of quantum mechanics.
Course contents summary
Introduction on the structure of biological macromolecules, in particular of proteins. Fold classification. Comparative modeling and fold recognition methods.
Search engines in biological databases.
Bioinformatics: protein and nucleic acid sequence analysis and sequence alignment tools. Secondary structure prediction and protein physico-chemical profiles.
Experimental techniques for the study of proteins’ structure and dynamics:
Static and time resolved Fluorescence spectroscopy;
Atomic Force Microscopy.
Computational techniques for the study of proteins’ structure and dynamics:
analysis of protein structure by means of molecular graphics softwares;
molecular mechanics and force fields, energy minimization, molecular dynamics simulations;
molecular interaction simulations: docking and drug design.
C.R. Cantor and P.R. Schimmel, "Biophysical chemistry - part II: techniques for the study of biological structure and function", W.H. Freeman and Company, San Francisco.
A.M. Lesk, "Introduzione alla Bioinformatica", McGraw-Hill Ed.
G. Valle, M. Helmer Citterich, M. Attimonelli, G. Pesole, "Introduzione alla Bioinformatica", Zanichelli Ed.
D.E. Krane, M.L. Raymer, "Fondamenti di Bioinformatica", Pearson Education Ed.
Notes on the lessons and review articles will be given by the lecturer.
Oral lessons and practice in the laboratory.
Assessment methods and criteria
Discussions on the reports of the practical exercises performed in the lab and oral examination.
A report on each practical exercise performed in the lab will be required.