Scopo del corso è di fornire allo studente una approfondita panoramica sulle più importanti e recenti metodologie applicate alla proteomica strutturale, focalizzandosi in particolare sugli obiettivi scientifici che tali tecniche possono aiutare a raggiungere. Tali competenze, di carattere sia teorico che pratico, permetteranno allo studente di sviluppare una migliore capacità di analisi della correlazione struttura-funzione delle proteine ed una migliore comprensione delle strategie sperimentali applicate a tale studio.
The course is focused on the 3D structure determination and analysis of proteins by using biocrystallographic and bioinformatic techniques. Experimental techniques for protein crystal growth will be described in details, with application to soluble and membrane proteins. X-ray diffraction on protein crystals and on solution samples (SAXS) will be treated extensively (X-ray sources, synchrotron light, atomic scattering factors, structure factors, the "phase problem", phasing by molecular replacement and heavy atoms, crystallographic refinement). Protein model validation techniques will be analyzed, together with the main features of the Protein Data Bank. Examples of structural proteomic projects will be provided, with emphasis on high-throughput applications of the biocrystallographic and bioinformatic methods learned during the course. In addition, the theoretical basis and the practical applications of dynamic light scattering and molecular dynamics techniques will be treated. The last part of the course will have a more practical approach. Students will solve by molecular replacement, refine, and analyze the 3D structure of a protein. During this practical experience they will learn how to apply techniques and software for protein sequence alignment, secondary structure prediction, molecular modelling, crystallographic refinement and validation.
Informazioni sul programma
Copies of the slides projected in the classroom as well as other materials will be made available through the course website on the ARIEL platform of the University of Milano (http://ariel.ctu.unimi.it). By no means this material replaces the lectures or a textbook. The material is made available only to registered students of the Degree Course in Molecular Biotechnology and Bioinformatics and should not be distributed to others
Prerequisiti e modalità di esame
Written examination with questions with open answers
Traditional: lectures supported by projected material, and visit to the biocrystallography lab. Attendance: highly recommended
Materiale didattico e bibliografia
Principles of protein X-ray crystallography (2nd edition). J. Drenth (Springer) Crystallization of nucleic acids and proteins: a practical approach. Edited by A. Ducruix and R. Giegé (Oxford University press) Crystallography made crystal clear. A guide for users of macromolecular models. By Gale Rhodes (Elsevier)