ID:
511855
Durata (ore):
24
CFU:
3
SSD:
BIOLOGIA MOLECOLARE
Anno:
2025
Dati Generali
Periodo di attività
Secondo Semestre (02/03/2026 - 12/06/2026)
Syllabus
Obiettivi Formativi
At the end of the course, the students are expected to:
1- have understood the physicochemical basis of native protein structures and learned the sequence-structure principle and its limitations,
2- be able to extract primary structure of proteins from sequence databases such as UniProt, analyze them using simple bioinformatic tools, and calculate their general physicochemical properties,
3- have obtained a perspective on the remarkable diversity of protein structures and their classifications, and be able to use the information available in protein structure databases such as PDB,
4- be able to choose the right experimental techniques for characterization and high-resolution determination of protein structures and dynamics depending on general properties of proteins, and apply these knowledge/skills as a guide for selection of their thesis projects,
5- be able to apply the available computational tools to predict protein structures and critically analyze and judge the predicted structures,
6- have learned about the structure-function principle and its limitations,
7- have learned how mutations and post-translational modifications could lead to the unfolding or misfolding of protein structures,
8- have understood how the altered structure and/or dynamics of proteins could cause the loss of a physiological function or the gain of a pathological function,
9- have learned about the role of structure in a large variety of diseases, especially cancers, neurodegenerative, infectious and metabolic diseases, in line with the general objective of the integrated course “Roots of Disease III”.
10- learn the structure-based approaches for drug design and discovery.
1- have understood the physicochemical basis of native protein structures and learned the sequence-structure principle and its limitations,
2- be able to extract primary structure of proteins from sequence databases such as UniProt, analyze them using simple bioinformatic tools, and calculate their general physicochemical properties,
3- have obtained a perspective on the remarkable diversity of protein structures and their classifications, and be able to use the information available in protein structure databases such as PDB,
4- be able to choose the right experimental techniques for characterization and high-resolution determination of protein structures and dynamics depending on general properties of proteins, and apply these knowledge/skills as a guide for selection of their thesis projects,
5- be able to apply the available computational tools to predict protein structures and critically analyze and judge the predicted structures,
6- have learned about the structure-function principle and its limitations,
7- have learned how mutations and post-translational modifications could lead to the unfolding or misfolding of protein structures,
8- have understood how the altered structure and/or dynamics of proteins could cause the loss of a physiological function or the gain of a pathological function,
9- have learned about the role of structure in a large variety of diseases, especially cancers, neurodegenerative, infectious and metabolic diseases, in line with the general objective of the integrated course “Roots of Disease III”.
10- learn the structure-based approaches for drug design and discovery.
Prerequisiti
To grasp the topics covered in this module, a basic understanding of general chemistry/biochemistry notions taught in high school and undergraduate university programs is required, especially in relation to chemical structure of amino acids and nucleotides, the nature of covalent and non-covalent chemical bonds and interactions, such as Van der Waals interactions, electrostatic interactions and hydrogen bonds, and basic thermodynamic concepts. A basic understanding of general physics laws, especially in relation to electrical fields, magnetic fields, general wave theory, electromagnetic radiation, and the interaction of electromagnetic field with matter (processes such as absorbance, scattering and emission), is required to grasp the structural biology methods (X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, Cryo-Electron microscopy and so on) introduced during the course.
Metodi didattici
Teaching will be based on lectures using slide presentations and traditional chalk-and-board method, which will be integrated with active project works in groups of 3-5 students and presentation of the results through flash talks (5 min). The project works will be voluntary but strongly recommended and rewarded with additional scores in the final exam.
Verifica Apprendimento
Written exam (2 hours) with multiple-choice (15 scores out of 30) and open (15 scores out of 30) questions. Project works, if evaluated positively, will be awarded by 1, 2 or 3 additional scores or, if exceeds the score of 30, with “honor”.
Testi
“Textbook of Structural Biology”, Liljas, Anders et al., Second edition, World Scientific Publishing Co., 2017.
“Foundations of Structural Biology”, Banaszak, Leonard J., Academic Press, 2000.
“Introduction to Proteins, Structure, Function, and Motions”, Kessel, Amit & Ben-Tal, Nir, CRC press.
“Protein Physics: A Course of Lectures”, Finkelstein, Alexey V., Academic Press, 2012.
Book chapters and review articles suitable for each session will be introduced in due course.
“Foundations of Structural Biology”, Banaszak, Leonard J., Academic Press, 2000.
“Introduction to Proteins, Structure, Function, and Motions”, Kessel, Amit & Ben-Tal, Nir, CRC press.
“Protein Physics: A Course of Lectures”, Finkelstein, Alexey V., Academic Press, 2012.
Book chapters and review articles suitable for each session will be introduced in due course.
Contenuti
Sessions 1 and 2, Introduction of Structural Biology:
Overview of chemical structure of proteins: amino acids, peptide bonds, disulfide bonds, posttranslational modification of proteins, cyclic peptides, unnatural amino acids; Introduction of publicly available sequence databases and sequence analysis tools; Overview of non-covalent interactions (hydrogen bonds, electrostatic interactions, van der Waals interactions, hydrophobic interactions) influencing protein structures, role of water; Overview of secondary structure of proteins, alpha-helices, beta-sheets, beta-turns, beta-bulges and so on; Tertiary structure of proteins; Quaternary structure of proteins; Protein-protein interaction networks; Protein folding, Anfinsen’s postulate; Protein unfolding/misfolding; Thermodynamic stability of proteins.
Sessions 3 and 4, Classification of Protein Structures:
Introduction of taxonomic concepts used in structural biology, such as domain, family, superfamily, fold and class, and useful concepts such as topology and architecture; Overview of classification systems; Overview of databases and online tools used in classification of protein structures; Review of major classes and folds of protein structures with some examples; Definition of project works for students.
Sessions 5 and 6, Techniques: Protein Structure and Dynamics:
Introduction of low resolution techniques (UV/Vis, fluorescence, circular dichroism and Infrared and Raman spectroscopy); Introduction of X-ray crystallography and cryo-EM; Introduction of nuclear magnetic resonance (NMR) technique, solution and solid-state NMR; Introduction of Electron paramagnetic resonance (EPR) technique, CW and pulsed EPR; Computational structural biology; Protein structure prediction; Definition of project works for students.
Session 7, Unstructural Biology, Intrinsically Disordered Proteins, Protein Misfolding and Aggregation in Neurodegenerative Diseases:
Introduction of IDPs and their physicochemical, structural, dynamical and functional characteristics.; Introduction of biological phase separation and its physicochemical basis; Role of post-translational modifications in regulation of IDPs and biological phase separation; Role of protein aggregation and phase separation of IDPs and other proteins in disease; Structural studies of a few key IDPs with neurodegeneration-related aggregation (e.g., amyloid-β, tau, α-synuclein); Project presentation by students.
Session 8, Structural Insights into Metabolic and Genetic Diseases:
Structural basis of diseases like cystic fibrosis, Tay-Sachs, and phenylketonuria; Gene therapy and CRISPR-Cas9: structural approaches to correcting genetic defects; Project presentation by students.
Session 9, Structural Biology of Bacterial and Viral Infections:
Structural analysis of bacterial proteins and their role in pathogenesis (e.g., bacterial toxins, adhesins); Virus structure and entry mechanisms (e.g., HIV, influenza, coronaviruses); Structural analysis of viral proteins (e.g., spike protein, proteases); Antibiotic resistance and structural changes in bacterial proteins; Project presentation by students.
Session 10, Structural Biology of Cancer:
Structure-function relationship of tumor suppressors and oncogenes; Mutations in cancer and how they affect protein structure and function; Structural mechanisms of drug resistance in cancer therapies; Project presentation by students.
Session 11, Structural Approaches in Drug Design and Development:
Structure-based drug design and high-throughput screening; Case studies of drugs developed using structural biology; Structural-based cancer drug design; Computational approaches: molecular docking, virtual screening; Challenges in translating structure to therapy; Project presentation by students.
Session 12, Emerging Technologies and Future Directions in Structural Biology and Disease Research:
Single-molecule approaches and atomic force microscopy; The future of AI and machine learning in structural biology; Emerging therapeutic technologies: gene editing, nanobodies, and peptide-based therapies; Project presentation by students.
Overview of chemical structure of proteins: amino acids, peptide bonds, disulfide bonds, posttranslational modification of proteins, cyclic peptides, unnatural amino acids; Introduction of publicly available sequence databases and sequence analysis tools; Overview of non-covalent interactions (hydrogen bonds, electrostatic interactions, van der Waals interactions, hydrophobic interactions) influencing protein structures, role of water; Overview of secondary structure of proteins, alpha-helices, beta-sheets, beta-turns, beta-bulges and so on; Tertiary structure of proteins; Quaternary structure of proteins; Protein-protein interaction networks; Protein folding, Anfinsen’s postulate; Protein unfolding/misfolding; Thermodynamic stability of proteins.
Sessions 3 and 4, Classification of Protein Structures:
Introduction of taxonomic concepts used in structural biology, such as domain, family, superfamily, fold and class, and useful concepts such as topology and architecture; Overview of classification systems; Overview of databases and online tools used in classification of protein structures; Review of major classes and folds of protein structures with some examples; Definition of project works for students.
Sessions 5 and 6, Techniques: Protein Structure and Dynamics:
Introduction of low resolution techniques (UV/Vis, fluorescence, circular dichroism and Infrared and Raman spectroscopy); Introduction of X-ray crystallography and cryo-EM; Introduction of nuclear magnetic resonance (NMR) technique, solution and solid-state NMR; Introduction of Electron paramagnetic resonance (EPR) technique, CW and pulsed EPR; Computational structural biology; Protein structure prediction; Definition of project works for students.
Session 7, Unstructural Biology, Intrinsically Disordered Proteins, Protein Misfolding and Aggregation in Neurodegenerative Diseases:
Introduction of IDPs and their physicochemical, structural, dynamical and functional characteristics.; Introduction of biological phase separation and its physicochemical basis; Role of post-translational modifications in regulation of IDPs and biological phase separation; Role of protein aggregation and phase separation of IDPs and other proteins in disease; Structural studies of a few key IDPs with neurodegeneration-related aggregation (e.g., amyloid-β, tau, α-synuclein); Project presentation by students.
Session 8, Structural Insights into Metabolic and Genetic Diseases:
Structural basis of diseases like cystic fibrosis, Tay-Sachs, and phenylketonuria; Gene therapy and CRISPR-Cas9: structural approaches to correcting genetic defects; Project presentation by students.
Session 9, Structural Biology of Bacterial and Viral Infections:
Structural analysis of bacterial proteins and their role in pathogenesis (e.g., bacterial toxins, adhesins); Virus structure and entry mechanisms (e.g., HIV, influenza, coronaviruses); Structural analysis of viral proteins (e.g., spike protein, proteases); Antibiotic resistance and structural changes in bacterial proteins; Project presentation by students.
Session 10, Structural Biology of Cancer:
Structure-function relationship of tumor suppressors and oncogenes; Mutations in cancer and how they affect protein structure and function; Structural mechanisms of drug resistance in cancer therapies; Project presentation by students.
Session 11, Structural Approaches in Drug Design and Development:
Structure-based drug design and high-throughput screening; Case studies of drugs developed using structural biology; Structural-based cancer drug design; Computational approaches: molecular docking, virtual screening; Challenges in translating structure to therapy; Project presentation by students.
Session 12, Emerging Technologies and Future Directions in Structural Biology and Disease Research:
Single-molecule approaches and atomic force microscopy; The future of AI and machine learning in structural biology; Emerging therapeutic technologies: gene editing, nanobodies, and peptide-based therapies; Project presentation by students.
Lingua Insegnamento
INGLESE
Corsi
Corsi
MEDICAL AND PHARMACEUTICAL BIOTECHNOLOGIES
Laurea Magistrale
2 anni
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