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Facoltā di Scienze Agrarie e Alimentari Universitā degli Studi di Milano
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Protein biotechnology and bioinformatics
Code: G6109-
Teacher:  Marcello Maria Duranti
CFU subdivision: Lectures: 5
Practices in classroom: 1
Basic aims:  To provide the molecular basis of the structure/function
relationships of proteins and to understand the details of the
experimental approaches for their modification (protein
Acquired skills:  Structural and functional dynamics of proteins. Modern approach
to study the proteins. Strategies to set up a protein engineering
Course contents:  1. Structural/functional maturation of proteins: from biosynthesis
to folding. 2. Protein targeting and intra-/extra-celluar localisation.
3. Protein turnover. 4. Proteome analyses. 5. Protein
bioinformatics. 6. Protein engineering. 7. Protein bioinformatic
Program:  Introduction to protein structure and function and their targeted modification (protein engineering) 1. Structural/functional maturation of proteins: from biosynthesis to folding 1.1 Fundamentals of protein biosynthesis and structure 1.2 In vitro folding 1.2.1 Bioenergetics 1.2.2 Kinetics 1.2.3 Mechanisms 1.2.4 Toward a unifying theory 1.2.5 How to study 3D protein structure 1.3 In vivo folding 1.3.1 Assisted folding 1.3.2 Molecular chaperones 1.3.3. Quality control 1.3.4 How to study folding in vivo 1.4 Post-biosynthetic modifications of proteins 1.4.1 Covalent modifications (disulphide bond formation, glycosylation, lipid and nucleotide interactions) 1.4.2 Non covalent modifications: cofactor binding 1.4.3 Effects of cofactor binding on 3D protein structure 2. Application of biotechnologies to enzymology 2.1 Oligomeric enzymes, supramolecular complexes, redox centres 2.2 Stability of the structural folding and enzyme active site plasticity 2.3 How to monitor conformational changes 2.4 Advanced kinetics 2.5 How to study enzyme mechanisms 2.6 Design of novel catalytic activities from a common scaffold 3 Protein sorting; intra- and extra-cellular location of proteins 3.1 Cell crowd 3.2 Molecular aspects of targeting and the biotechnology approach 3.3 Seed storage proteins: location, properties, role 4 Protein turnover 4.1 Protein degradation 4.1.1 In vitro 4.1.2 In vivo: Random (digestive enzymes) Storage protein degradation Targeted degradation (ubiquitin, degradosome) 5. How to study proteomes 5.1 2D electrophoretic techniques and proteomics 5.2 Protein arrays 5.3 Interactomics 5.3.1 Biological meaning of protein interactions 5.3.2 How to study protein interactions In vitro tecniques (spectroscopy, antibodies, SPR, etc.) In vivo techniques (double hybrid yeast, etc.) 6. Bioinformatics 6.1 Data mining 6.2 Protein databases 6.3 How to get the best from a protein database (searching for motifs, domains and families) 7. Elements of protein engineering 8. Bioinformatic laboratory
Prerequisites:  Biochemistry and molecular biology
Preparatory instructions:  Biochemistry and molecular biology
Learning materials:  Marcello Duranti (2015) Introduzione allo studio delle proteine.
Zanichelli Editore Bologna (Italy)
Other info:  Written exam
Program of Protein biotechnology and bioinformatics (pdf version)
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