ID:
510292
Durata (ore):
24
CFU:
3
SSD:
BIOLOGIA MOLECOLARE
Anno:
2026
Dati Generali
Periodo di attivitÃ
Secondo Semestre (01/03/2027 - 11/06/2027)
Syllabus
Obiettivi Formativi
At the end of this course, students will obtain a robust knowledge of NMR theory and its biomolecular applications. More specifically, they:
1- will learn the basic NMR concepts and theory,
2- will gain insight on how NMR spectrometers work,
3- will be able to explain basic 1D NMR experiments at classical level,
4- will learn, mostly at the conceptual level, how the state and time evolution of spin systems are described at quantum mechanical level,
5- will learn how standard multidimensional NMR experiments work,
6- will be able to plan NMR assignment strategies for proteins and use NMR spectra for resonance assignment,
7- will be able to design NMR experiments for protein-ligand interaction studies,
8- will learn how protein structures are calculated using NMR data,
9- will get acquainted with NMR relaxation theory and learn how dynamical parameters of proteins are determined using NMR relaxation rates,
10. will learn how small molecule ligands are discovered and developed against protein targets.
1- will learn the basic NMR concepts and theory,
2- will gain insight on how NMR spectrometers work,
3- will be able to explain basic 1D NMR experiments at classical level,
4- will learn, mostly at the conceptual level, how the state and time evolution of spin systems are described at quantum mechanical level,
5- will learn how standard multidimensional NMR experiments work,
6- will be able to plan NMR assignment strategies for proteins and use NMR spectra for resonance assignment,
7- will be able to design NMR experiments for protein-ligand interaction studies,
8- will learn how protein structures are calculated using NMR data,
9- will get acquainted with NMR relaxation theory and learn how dynamical parameters of proteins are determined using NMR relaxation rates,
10. will learn how small molecule ligands are discovered and developed against protein targets.
Prerequisiti
General knowledge of spectroscopy and protein biochemistry.
Metodi didattici
Teaching will be based on lectures using slide presentations and traditional chalk-and-board method, which will be combined with supervised hands-on tasks.
Verifica Apprendimento
Final written exam (2 hours) with open questions.
Testi
1. Lecture handouts
2. Keeler. Understanding NMR Spectroscopy. WILEY.
3. Cavanagh, Fairbrother, Palmer, Rance, Skelton. Protein NMR spectroscopy: Principles and Practice. Elsevier Academic Press.
2. Keeler. Understanding NMR Spectroscopy. WILEY.
3. Cavanagh, Fairbrother, Palmer, Rance, Skelton. Protein NMR spectroscopy: Principles and Practice. Elsevier Academic Press.
Contenuti
Session 1: Introduction to NMR (Overview of biomolecular NMR applications, nuclear spins, gyromagnetic ratios and magnetic moments, interaction of nuclear spins with external magnetic fields, Zeeman energy levels, Boltzmann magnetization, Larmor frequency, resonance, RF pulses, brief history of NMR, spin-1/2 nuclei useful for biomolecular NMR, isotope labeling of proteins for NMR studies).
Session 2: Basic 1D experiments (vector model, Bloch equation, T1 relaxation, T2 relaxation, NMR frequencies and chemical shifts, NMR signal linewidths, scalar (J) coupling, splitting, introduction of sensitivity and resolution, basic pulse-acquire experiment, FID detection, spin echo, signal saturation, overview of NMR hardware, frequency locking, probe tuning and matching, magnetic field shimming, RF pulses: hard and soft; pulse optimization, T1 and T2 experiments).
Session 3: Basic NMR theory: Quantum mechanics of one-spin and two-spin systems
(spin state, density matrix, populations, coherences, Liouville-Von Neumann equation, NMR Hamiltonians, product operator formalism, quantum mechanical description of the pulse-acquire experiment in one-spin and two-spin systems).
Session 4: 2D and multidimensional NMR experiments: homonuclear and heteronuclear
(general scheme of 2D experiments: preparation, evolution, mixing, detection; through-bond coherence transfer: COSY, TOCSY;
Through-space coherence transfer: NOESY, ROESY; heteronuclear through-bond transfer: HMQC, HSQC, TROSY).
Sessions 5-6: NMR resonance assignment
(resonance assignment in small molecules, sequential assignment approach for unlabeled proteins, production of singly labeled (15N or 13C) proteins, heteronuclear-edited assignment for singly labeled proteins, production of double labeled (15N, 13C) proteins, triple resonance approach for double-labeled proteins, production of triple labeled (2H, 15N, 13C) labeled large proteins, triple resonance approach for triple labeled larger proteins resonance assignment in intrinsically disordered proteins, fast data acquisition methods, automated assignment, exercise)
Session 7: Monitoring protein-ligand interactions by NMR
(Binding: interface, kinetics, thermodynamics; NMR chemical shift timescale: fast, intermediate and slow exchange processes, protein-observed methods: NMR titration assays, chemical shift and intensity perturbation mapping methods, soft-docking methods, cross-saturation methods; Ligand-observed methods: STD-NMR, transfer NOE, Water-LOGSY; binding mechanism: induced fit vs conformational selection)
Sessions 8-9: Structure-determination by NMR
(structural information contained in NMR data: chemical shifts, scalar couplings, NOEs, residual dipolar coupling, water-amide proton exchange; NMR experiments required for collection of conformational (distance, angle and hydrogen bond) constraints; identification of regular secondary structures, structure calculation and refinement, structure evaluation, comparison between NMR and other structural biology techniques)
Sessions 10-11: Protein dynamics by NMR (physical basis of protein motions, NMR spin relaxation mechanisms, basic 15N relaxation theory, 15N relaxation rate measurements (T1, T2 and heteronuclear NOE), dynamical analysis of 15N relaxation rates in proteins: spectral density mapping, model-based, model-free and detector-based approaches; quantification of conformational exchange dynamics in proteins, supra-tauc motions in proteins, protein dynamics in IDPs, integration with other techniques)
Session 12: NMR in drug discovery
(Fragment screening and fragment-based drug discovery, structure-activity relations, case studies)
Session 2: Basic 1D experiments (vector model, Bloch equation, T1 relaxation, T2 relaxation, NMR frequencies and chemical shifts, NMR signal linewidths, scalar (J) coupling, splitting, introduction of sensitivity and resolution, basic pulse-acquire experiment, FID detection, spin echo, signal saturation, overview of NMR hardware, frequency locking, probe tuning and matching, magnetic field shimming, RF pulses: hard and soft; pulse optimization, T1 and T2 experiments).
Session 3: Basic NMR theory: Quantum mechanics of one-spin and two-spin systems
(spin state, density matrix, populations, coherences, Liouville-Von Neumann equation, NMR Hamiltonians, product operator formalism, quantum mechanical description of the pulse-acquire experiment in one-spin and two-spin systems).
Session 4: 2D and multidimensional NMR experiments: homonuclear and heteronuclear
(general scheme of 2D experiments: preparation, evolution, mixing, detection; through-bond coherence transfer: COSY, TOCSY;
Through-space coherence transfer: NOESY, ROESY; heteronuclear through-bond transfer: HMQC, HSQC, TROSY).
Sessions 5-6: NMR resonance assignment
(resonance assignment in small molecules, sequential assignment approach for unlabeled proteins, production of singly labeled (15N or 13C) proteins, heteronuclear-edited assignment for singly labeled proteins, production of double labeled (15N, 13C) proteins, triple resonance approach for double-labeled proteins, production of triple labeled (2H, 15N, 13C) labeled large proteins, triple resonance approach for triple labeled larger proteins resonance assignment in intrinsically disordered proteins, fast data acquisition methods, automated assignment, exercise)
Session 7: Monitoring protein-ligand interactions by NMR
(Binding: interface, kinetics, thermodynamics; NMR chemical shift timescale: fast, intermediate and slow exchange processes, protein-observed methods: NMR titration assays, chemical shift and intensity perturbation mapping methods, soft-docking methods, cross-saturation methods; Ligand-observed methods: STD-NMR, transfer NOE, Water-LOGSY; binding mechanism: induced fit vs conformational selection)
Sessions 8-9: Structure-determination by NMR
(structural information contained in NMR data: chemical shifts, scalar couplings, NOEs, residual dipolar coupling, water-amide proton exchange; NMR experiments required for collection of conformational (distance, angle and hydrogen bond) constraints; identification of regular secondary structures, structure calculation and refinement, structure evaluation, comparison between NMR and other structural biology techniques)
Sessions 10-11: Protein dynamics by NMR (physical basis of protein motions, NMR spin relaxation mechanisms, basic 15N relaxation theory, 15N relaxation rate measurements (T1, T2 and heteronuclear NOE), dynamical analysis of 15N relaxation rates in proteins: spectral density mapping, model-based, model-free and detector-based approaches; quantification of conformational exchange dynamics in proteins, supra-tauc motions in proteins, protein dynamics in IDPs, integration with other techniques)
Session 12: NMR in drug discovery
(Fragment screening and fragment-based drug discovery, structure-activity relations, case studies)
Lingua Insegnamento
INGLESE
Corsi
Corsi
MEDICAL AND PHARMACEUTICAL BIOTECHNOLOGIES
Laurea Magistrale
2 anni
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