First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
INDUSTRIAL BIOTECHNOLOGY
Course unit
PROTEIN STRUCTURE
SCN1037636, A.A. 2018/19

Information concerning the students who enrolled in A.Y. 2018/19

Information on the course unit
Degree course Second cycle degree in
INDUSTRIAL BIOTECHNOLOGY
SC1731, Degree course structure A.Y. 2014/15, A.Y. 2018/19
N0
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Number of ECTS credits allocated 8.0
Type of assessment Mark
Course unit English denomination PROTEIN STRUCTURE
Website of the academic structure http://biotecnologie.scienze.unipd.it/2018/laurea_magistrale
Department of reference Department of Biology
E-Learning website https://elearning.unipd.it/biologia/course/view.php?idnumber=2018-SC1731-000ZZ-2018-SCN1037636-N0
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 STEFANO MAMMI CHIM/04
Other lecturers ROBERTO BATTISTUTTA CHIM/06

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses CHIM/05 Science and Technology of Polymeric Materials 4.0
Core courses CHIM/11 Chemistry and Biotechnology of Fermentations 4.0

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

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Laboratory 1.0 16 9.0 No turn
Lecture 7.0 56 119.0 No turn

Calendar
Start of activities 25/02/2019
End of activities 14/06/2019
Show course schedule 2019/20 Reg.2014 course timetable

Examination board
Board From To Members of the board
7 STRUTTURE DI PROTEINE 2018-2019 01/10/2018 30/11/2019 MAMMI STEFANO (Presidente)
BATTISTUTTA ROBERTO (Membro Effettivo)
BELLANDA MASSIMO (Supplente)
6 STRUTTURE DI PROTEINE 2017/2018 01/10/2017 25/11/2018 MAMMI STEFANO (Presidente)
BATTISTUTTA ROBERTO (Membro Effettivo)
BELLANDA MASSIMO (Supplente)

Syllabus
Prerequisites: None beyond the requisites for admission to the Master's program.
Target skills and knowledge: The course deals with the modern methodologies for the determination of the 3D atomic structure of small molecules, both organic and inorganic, and biological macromolecules by X-ray diffraction techniques on single crystals. The basics of diffraction and molecular structure determination will be presented, with particular emphasis on most recent advances mainly in the field of macromolecular crystallography. The course will benefit from examples of structure determination of particular interest, and from the guided reading of recent scientific papers on advanced crystallographic topics.
NMR: This portion of the course describes the experimental methods and the practical applications of NMR spectroscopy to determine the solution structure of peptides and proteins. Computational methods useful to interpret the experimental data will also be described. During the laboratory practice, the students will use computer programs to analyze two- and three-dimensional spectra.
Examination methods: The written test consists in 7-8 open questions for a total of 60 points and 6 closed questions (1 point each). The grade is half the points obtained.
The oral test consists in a guided discussion on topics related to the content of the course.
The final grade is the average of the grades obtained in the two tests.
Assessment criteria: The acquisition of the knowledge and of the abilities relative to the content described below will be evaluated.
Course unit contents: NMR - Lectures:
1. Review of the basic principles of NMR: chemical shift, scalar coupling, dipolar coupling, nuclear Overhauser effect.
Practical aspects: instrumentation, acquisition and processing of the FID.
2. Introduction to two-dimensional NMR spectroscopy.
3. Homonuclear 2D experiments: COSY, TOCSY, NOESY.
4. Use of the NMR parameters to solve the structure of peptides and proteins. Characteristic patterns of specific secondary structures.
5. Computational methods: distance geometry, molecular dynamics.
6. Inverse heteronuclear correlation spectroscopy.
7. Homonuclear and heteronuclear 3D experiments.
8. Advanced methodologies (outline): protein-protein interactions, protein-small molecule interactions.
NMR - Lab:
1. Assignment of the 2D spectra of a small peptide.
2. Assignment of the HSQC spectrum of a small protein using 3D spectra.
3. Identification of the binding site between two proteins using chemical shift mapping.
Biomolecular crystallography:
Overview of protein crystallography: crystals, X-ray diffraction and the mathematics of crystallography. Protein crystallization: properties, growth and quality of protein crystals; crystallization techniques and strategies.
Crystal geometry: periodic lattices and symmetry in 3D; space groups; reciprocal lattice and reciprocal space symmetry; systematic absences.
Diffraction basics: scattering of X-rays; atomic scattering factors, structure factor and B-factor; geometric principles of diffraction, Bragg law, Ewald sphere and Friedel pairs; anomalous scattering and Bijvoet pairs.
Instrumentation and data collection techniques: overview, data reduction.
From diffraction data to electron density: introduction; Fourier sums and Fourier transform, Fourier mathematics and diffraction, meaning of the Fourier equations; the phase problem; Patterson function and Patterson maps.
Experimental phasing: solving the phase problem; marker atom substructure methods; isomorphous replacement (MIR, SIR), anomalous scattering (SAD, MAD), SIRAS, direct methods, molecular replacement; improvement of phases, density modification techniques.
Model building and refinement: principles and practice.
Structure validation and analysis: judging the molecular model, judging the quality and usefulness of the refined model.
Examples of protein structure determination by macromolecular crystallography.
Reading a crystallographic paper.
Planned learning activities and teaching methods: NMR: Lectures (3 CFU) and Laboratory (1 CFU).
Crystallography: Lectures (4 CFU).
Additional notes about suggested reading: http://www.cis.rit.edu/htbooks/nmr
https://qshare.queensu.ca/Users01/sauriolf/www/webcourse/index.htm
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
  • T. D. W. Claridge, High-Resolution NMR Techniques in Organic Chemistry. Amsterdam: Pergamon Press, 1999. Cerca nel catalogo
  • A. E. Derome, Modern NMR Techniques for Chemistry Research. Oxford: Pergamon Press, 1987. Cerca nel catalogo
  • Bernhard Rupp, Biomolecular crystallography. --: Garland Sciences, --. Cerca nel catalogo
  • Gale Rhodes, Crystallography made crystal clear. --: Academic Press, --. Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Lecturing
  • Laboratory
  • Problem solving
  • Active quizzes for Concept Verification Tests and class discussions
  • Loading of files and pages (web pages, Moodle, ...)

Innovative teaching methods: Software or applications used
  • Moodle (files, quizzes, workshops, ...)
  • Kahoot

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