First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
INDUSTRIAL BIOTECHNOLOGY
Course unit
PROTEIN STRUCTURE
SCP9088036, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2019/20

Information on the course unit
Degree course Second cycle degree in
INDUSTRIAL BIOTECHNOLOGY
SC1731, Degree course structure A.Y. 2014/15, A.Y. 2019/20
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Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination PROTEIN STRUCTURE
Website of the academic structure http://biotecnologie.scienze.unipd.it/2019/laurea_magistrale
Department of reference Department of Biology
Mandatory attendance
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge ROBERTO BATTISTUTTA CHIM/06
Other lecturers STEFANO MAMMI CHIM/04

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines CHIM/06 Organic Chemistry 2.0
Core courses CHIM/05 Science and Technology of Polymeric Materials 2.0
Core courses CHIM/06 Organic Chemistry 2.0

Course unit organization
Period Second semester
Year 1st Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Lecture 6.0 48 102.0 No turn

Calendar
Start of activities 02/03/2020
End of activities 12/06/2020
Show course schedule 2019/20 Reg.2014 course timetable

Examination board
Board From To Members of the board
1 STRUTTURA DI PROTEINE 2019-2020 01/10/2019 27/11/2020 BATTISTUTTA ROBERTO (Presidente)
MAMMI STEFANO (Membro Effettivo)
BELLANDA MASSIMO (Supplente)

Syllabus
Prerequisites: None beyond the requisites for admission to the Master's program.
Target skills and knowledge: The course describes the biophysical techniques aimed at the determination of the 3D structure and dynamics of proteins and their assemblies to understand how they function, how they evolve, and how they can be modulated. The following techniques will be illustrated: nuclear magnetic resonance (NMR) spectroscopy, x-ray crystallography, electron cryo-microscopy (Cryo-EM), and small-angle x-ray scattering (SAXS). The course will benefit from examples of structure determination and analysis of relevant proteins, and from the guided reading of recent scientific papers on advanced topics.
Examination methods: The exam (oral) consists in a guided discussion on topics related to the content of the course.
Assessment criteria: The acquisition of the knowledge and of the abilities relative to the content described below will be evaluated.
Course unit contents: Review of the basic principles of NMR: chemical shift, scalar coupling, dipolar coupling, nuclear Overhauser effect. Instrumentation.
Introduction to two-dimensional NMR spectroscopy. Homonuclear 2D experiments: COSY, TOCSY, NOESY. Heteronuclear correlation spectroscopy. Homonuclear and heteronuclear 3D experiments.
Use of the NMR parameters to solve the structure of proteins. Characteristic patterns of specific secondary structures.
Computational methods: distance geometry, molecular dynamics.
RDC, use of chemical shifts. Protein-protein interactions, protein-small molecule interactions. NMR relaxation and dynamic processes. Solid-State NMR.

Overview of protein crystallography. Crystallization techniques, properties of crystals, symmetries and space groups. Geometric principles of diffraction, Bragg law and Ewald sphere. Instrumentation, data collection and data reduction. Diffraction basics: scattering of X-rays; atomic scattering factor, structure factor and B-factor. From diffraction data to electron density. Fourier transform and diffraction. The phase problem. Patterson function. Experimental phasing for macromolecules: isomorphous replacement (MIR, SIR), anomalous scattering (SAD, MAD), SIRAS, direct methods, molecular replacement. Improvement of phases, density modification techniques.

The resolution revolution: recent crucial advances in Cryo-EM. Comparison between x.-ray crystallography and Cryo-EM. Interaction of electrons with matter, principles of electron scattering and diffraction. Transmission electron microscope (TEM) basic anatomy. Image formation by amplitude contrast or phase contrast. TEM of biological specimens. Weak-phase-object approximation for weak electron scatters. Defocusing and lens aberrations for increasing contrast. Fourier transform and image formation in TEM. Point spread function (PSF) and contrast transfer function (CTF). Single particle analysis. Sample preparation. From 2D images to the 3D structure: image reconstruction. Resolution in crystallography and Cryo-EM.
Model building and refinement in X-ray crystallography and in Cryo-EM: principles and practice.

Structure validation and analysis: quality of the final refined 3D models derived by X-ray crystallography and Cryo-EM.

Small Angle X-ray Scattering (SAXS) in structural biology: principle and basics. The SAXS experiment: scattering of particles in solution vs scattering in a crystal. SAXS curves and particle shapes: Guinier plot and distance distribution function, radius of gyration and maximun particle size, Porod volume, Kratky plot for globular and unfolded proteins. Interpolation of SAXS data with 3D protein models.

Examples of protein structure determination. Reading a structural biology paper.
Planned learning activities and teaching methods: Lectures
Additional notes about suggested reading: http://www.cis.rit.edu/htbooks/nmr
https://qshare.queensu.ca/Users01/sauriolf/www/webcourse/index.htm
Grant Jensen, Getting Started in Cryo-EM, http://cryo-em-course.caltech.edu.
Part of the material will be provided in class.
Textbooks (and optional supplementary readings)
  • J. Cavanagh, Protein NMR spectroscopy: principles and practice. Amsterdam: Elsevier, 2007. Cerca nel catalogo
  • Bernhard Rupp, Biomolecular crystallography. New York: Garland Science, 2010. Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Lecturing
  • Problem based learning
  • Case study
  • Working in group
  • Problem solving
  • Active quizzes for Concept Verification Tests and class discussions
  • Use of online videos
  • Loading of files and pages (web pages, Moodle, ...)

Innovative teaching methods: Software or applications used

Sustainable Development Goals (SDGs)
Quality Education