Laurea Magistrale in Biotecnologie molecolari e bioinformatica

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1 Laurea Magistrale in Biotecnologie molecolari e bioinformatica Approfondisce le conoscenze dei meccanismi molecolari dei sistemi viventi e le loro applicazioni con i metodi di indagine avanzati della biologia cellulare e molecolare, della biochimica e della bioinformatica.

2 Biochemistry & Biotechnology Conoscere i metodi di studio avanzati delle relazioni tra struttura e funzione delle proteine e, in particolare, degli enzimi e di grande importanza per la ricerca di base e la ricerca applicata per: - Complementare le conoscenze derivate da approcci genetici e di biologia cellulare e molecolare su (micro)organismi e cellule isolate - Fornire informazioni dettagliate su cui si basano gli approcci bioinformatici per la predizione della funzione di geni e la comprensione di sistemi complessi - Verificare le predizioni della bioinformatica - Fornire informazioni dettagliate sugli enzimi che formano le vie metaboliche in microrganismi, piante e animali - Ingegnerizzare proteine ed enzimi per migliorarne le proprieta a scopo applicativo e per guidare interventi di ingegneria metabolica - Contribuire a comprendere le basi di malattie e Sviluppare nuovi farmaci Le competenze in campo biochimico sono molto richieste dalle industrie farmaceutiche classiche e dalle industrie biotecnologiche

3 I corsi di biochimica nella LM in Biotecnologie molecolari e bioinformatica Year 1, Semester 2 (all students) Biochemistry applied to the rational design of biologically active molecules (in English) Anno 2, Semestre 2 (in alternativa a Systems biology (curriculum bioinformatico) o a scelta) Proteomica strutturale

4 Biochemistry applied to the rational design of biologically active molecules (in English) Aim: To provide knowledge on the theory and practice needed to characterize proteins and enzymes in the context of basic and applied research and, in particular, to develop biologically active molecules (drugs). This course is nicely complemented by some specific parts of: Metodi chimici avanzati applicati alle biotecnologie, which deals also with: - Fundamental concepts that also explain how proteins are built and function - The theory behind some experimental and computational methods to study them - Chemical approaches to drug development Metodi matematici e fisici applicati alle biotecnologie, which also teaches: - The theory and applications of spectroscopic methods used to study biological (macro)molecules - Some fundamental mathematical concepts and methods we need to use to analyse the data obtained with some physical and chemical approaches in order to obtain structure-function information on our proteins

5 Biochemistry applied to the rational design of biologically active molecules The content of Part 1, 2 CFU :Structural biology: - Introduction to the identification and validation of drug molecular targets by bioinformatic, genomic, transcriptomic, and proteomic techniques. - Review of information on the three-dimensional architectures of proteins - Structure-sequence correlation: homology modelling. - Molecular recognition, localization and nature of ligand binding sites. - Structure-function relationships for enzymes - Strategies for the identification of catalytic residue and of interaction sites with ligands and effectors (docking techniques). - Structural basis of enzyme inhibition. Examples.

6 The structural approaches will be further developed in Proteomica strutturale, which will focus on the 3D structure determination and analysis of proteins by using biocrystallographic and bioinformatic techniques. The Proteomica strutturale course will discuss. - Experimental techniques for protein crystal growth - X-ray diffraction on protein crystals and on solution samples (SAXS) and data analysis - Protein model validation techniques - Structural proteomic projects - Theory and practice of dynamic light scattering and molecular dynamics techniques 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.

7 Biochemistry applied to the rational design of biologically active molecules The content of Part 2, 3 CFU Enzymology The Enzymology lectures will cover: - The general principles of chemical and enzyme catalysis, which are needed to understand how enzymes work, their substrate specificity, their catalytic power and the diversity of reactions they catalyze - How to design robust in vitro assays of enzymatic activity, which are at the basis of kinetic methods used to characterize the enzyme mechanism of action and to test potential effectors (activators or inhibitors) - The kinetic approaches (Steady-state and pre-steady-state) used to dissect the enzyme s mechanism, which is the fundamental information for rational drug design - The types of inhibitors we can develop, keeping in mind that most drugs are specific and powerful enzyme inhibitors, and the methods we need to use to determine their mechanism of action and their potency. Throughout the classes, specific examples taken from the literature will be discussed. Furthermore, students will be walked through data analysis.

8 Biochemistry applied to the rational design of biologically active molecules requires: good previous knowledge of the topics covered by basic courses in Biochemistry and Methods in Biochemistry (e.g.: Biochimica applicata alle biotecnologie for LT in BIA) of any Laurea triennale including these subjects. An understanding of the theory and methods discussed in Metodi chimici avanzati applicati alle biotecnologie and Metodi matematici e fisici applicati alle biotecnologie (first year, first semester), which in turn require one to be familiar with the basic concepts and methods taught in classes of general and organic chemistry, including principles of thermodynamics applied to chemical reactions, offered by any Laurea triennale including these subjects.