X-RAY AND NEUTRON SCATTERING METHODS FOR THE STUDY OF BIOLOGICAL MACROMOLECULES
cod. 1010345

Academic year 2021/22
1° year of course - Second semester
Professor
Martin WEIK
Academic discipline
Fisica applicata (a beni culturali, ambientali, biologia e medicina) (FIS/07)
Field
Attività formative affini o integrative
Type of training activity
Related/supplementary
48 hours
of face-to-face activities
6 credits
hub:
course unit
in ENGLISH

Learning objectives

1. KNOWLEDGE AND UNDERSTANDING
-UNDERSTAND THE FUNDAMENTALS OF THE INTERACTION BETWEEN X-RAYS AND MATTER, WITH SPECIAL EMPHASIS OF BIOLOGICAL MACROMOLECULES.
-EXPLAIN THE MEANING OF THE PHYSICAL QUANTITIES AND THE GENERAL CONCEPTS RELATED WITH THE EXPERIMENTAL TECHNIQUES
-EXAMINE PHYSICAL SYSTEMS TO WHICH THE METHODOLOGIES ADDRESSED CAN BE APPLIED
-RELATE THE EXPERIMENTAL TECHNIQUES DISCUSSED WITHIN THE COURSE WITH BIOLOGICAL MACROMOLECULES.
-UNDERSTAND CONTEXT AND BASIC CONCEPTS OF RECENT LITERATURE THAT USE X-RAY BASED METHODS TO STUDY STRUCTURAL PROPERTIES OF MACROMOLECULES
2. APPLYING KNOWLEDGE AND UNDERSTANDING
-APPLY THE ACQUIRED KNOWLEDGE TO ADDRESS STRUCTURAL AND DYNAMICAL PROPERTIES OF A MACROMOLECULAR SYSTEM
-IDENTIFY THE APPROPRIATE TECHNIQUES FOR THE STUDY OF A PARTICULAR STRUCTURE/DYNAMICS
3. COMMUNICATION SKILLS
-KNOW HOW TO COMMUNICATE IDEAS-PROBLEMS-SOLUTIONS ABOUT MOLECULAR STRUCTURE AND DYNAMICS IN A CLEAR, SYNTHETIC AND EFFECTIVE WAY
-KNOW HOW TO DESCRIBE THE PHASES OF A MEASUREMENT APPROPRIATELY
-ABLE TO EXPLAIN TO THE GROUP MATES AND THE TEACHER THE VARIOUS EXPERIMENTAL ISSUES
4. MAKING JUDGEMENTS
-ABLE TO ANALYZE FROM A QUANTITATIVE POINT OF VIEW RELEVANT STRUCTURAL AND DYNAMICAL EVENT IN MACROMOLECULES BOTH AT THE THEORETICAL AND EXPERIMENTAL LEVEL
-ABLE TO EVALUATE LIMITS AND POTENTIAL OF THE TECHNIQUES DESCRIBED DURING THE COURSE.
-ABLE TO EVALUATE CRITICALLY THE VALIDITY LIMITS OF THE DEVELOPED MODELS, AND THE ANALOGIES AND DIFFERENCES BETWEEN THE PHYSICAL SYSTEMS STUDIED
5. LEARNING SKILLS
-LINK THE DIFFERENT TOPICS DISCUSSED IN THE COURSE AND THOSE DEALT WITH IN OTHER COURSES (EG PHYSICS OF MATTER, QUANTUM MECHANICS, CHEMISTRY)
-KNOW HOW TO CHANGE YOUR CONCEPTUAL FRAMEWORK OR THE PLAN OF AN EXPERIMENTAL MEASURE IN RESPONSE TO NEW INPUTS BY DEVELOPING ALTERNATIVE SOLUTIONS AND METHODOLOGIES

Prerequisites

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Course unit content

ITALY IS A MEMBER COUNTRY OF ALL EUROPEAN NEUTRON AND X-RAY LARGE SCALE FACILITIES, I.E. OF THE EUROPEAN SYNCHROTRON RADIATION FACILITY (ESRF) AND THE INSTITUT LAUE LANGEVIN (ILL) NEUTRON FACILITY IN GRENOBLE, FRANCE, THE EUROPEAN X-RAY FREE ELECTRON LASER (EUXFEL) IN HAMBURG, GERMANY AND THE EUROPEAN SPALLATION SOURCE (ESS) IN LUND, SWEDEN. THESE FACILITIES OFFER UNIQUE OPPORTUNITIES TO STUDY THE STRUCTURE AND DYNAMICS OF BIOLOGICAL MACROMOLECULES, INCLUDING PROTEINS AND DNA, A RESEARCH TOPIC OF BOTH ACADEMIC AND MEDICAL INTEREST. THE COURSE INTENDS TO EQUIP ADVANCED PHYSICS STUDENTS FOR A
MASTER OR PHD THESIS AT OR IN COLLABORATION WITH EUROPEAN X-RAY AND NEUTRON LARGE SCALE FACILITIES TO STUDY BIOLOGICAL MACROMOLECULES. BESIDES ITS FOCUS ON X-RAY AND NEUTRON BASED METHODS, THE COURSE WILL PROVIDE A SURVEY OF COMPLEMENTARY BIOPHYSICAL METHODS, INCLUDING SINGLE PARTICLE CRYO ELECTRON MICROSCOPY, ELECTRONIC AND VIBRATIONAL SPECTROSCOPIES, NMR, AFM, ETC. THE COURSE IS INTENDED TO BE EMBEDDED INTO AN EXCHANGE PROGRAM BETWEEN THE UNIVERSITY OF PARMA AND THE INSTITUT DE BIOLOGIE STRUCTURALE AND ITS ESRF AND ILL PARTNERS AT THE EUROPEAN PHOTON NEUTRON CAMPUS IN GRENOBLE THAT PROF. CRISTIANO VIAPPIANI AND DR. MARTIN WEIK INTEND TO INITIATE.
COURSE OUTLINE :
PART I (TEACHING – 26 HRS)
- INTRODUCTION TO THE STRUCTURE AND DYNAMICS OF BIOLOGICAL MACROMOLECULES (4 HRS)
- INTERACTION OF X-RAYS AND NEUTRONS WITH MATTER (2 HRS)
- LARGE SCALE X-RAY FACILITIES (SYNCHROTRON, XFEL) (2 HRS)
- LARGE SCALE NEUTRON FACILITIES (REACTOR, SPALLATION SOURCE) (2 HRS)
- CONVENTIONAL X-RAY CRYSTALLOGRAPHY (CRYSTALLIZATION, DATA COLLECTION, ANALYSIS) (4 HRS)
- SERIAL X-RAY CRYSTALLOGRAPHY AT SYNCHROTRONS AND XFELS (2 HRS)
- TIME-RESOLVED X-RAY CRYSTALLOGRAPHY (2 HRS)
- SMALL ANGLE NEUTRON AND X-RAY SCATTERING (2 HRS)
- NEUTRON CRYSTALLOGRAPHY, REFLECTOMETRY AND SPECTROSCOPY (2 HRS)
- COMPLEMENTARY BIOPHYSICAL TECHNIQUES (4 HRS)
PART II (22 HRS)
- VIRTUAL TOUR OF A SYNCHROTRON/XFEL/NEUTRON FACILITY
- REMOTE CRYSTALLOGRAPHY DATA COLLECTION AT ESRF (ASSUMING ESRF TO BE SUPPORTIVE)
- CRYSTALLOGRAPHY DATA PROCESSING AND ANALYSIS
- REPRESENTATION OF PROTEIN STRUCTURES (PYMOL)
- PRESENTATION OF CURRENT STATE-OF-THE-ART RESEARCH PUBLICATIONS BY STUDENTS
- QUIZZES
- PRESENTATION OF COLLABORATIVE (U PARMA / IBS) RESEARCH PROJECTS THE STUDENTS COULD GET INVOLVED IN

Full programme

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Bibliography

Zaccai N., Serdyuk I., Zaccai G. (2017) Methods in Molecular Biophysics: Structure, Dynamics, Function for Biology and Medicine - 2nd Edition. Cambridge University Press.
X-ray Free Electron Lasers: A Revolution in Structural Biology, Boutet S, Fromme P, Hunter MS (eds) pp 331-356. Cham: Springer International Publishing
Neutrons & Biology (2020) EPJ Web Conf., 236

Teaching methods

THE COURSE CONSISTS IN A SERIES OF LECTURES COVERING THE FUNDAMENTALS OF THE X-RAY BASED METHODS TO STUDY STRUCTURAL AND DYNAMICAL PROPERTIES OF MACROMOLECULES.
SPECIFIC EXAMPLES WILL BE DISCUSSED IN DETAIL. REMOTE SESSIONS FROM GRENOBLE WILL PROVIDE DIRECT VIEW OF EXPERIMENTAL FACILITIES AT A SYNCHROTRON SOURCE. A REPRESENTATIVE EXPERIMENT WILL BE PERFORMED
IN CASE THE CURRENT PANDEMIC ALLOWS IT, THE COURSE IS INTENDED TO BE DELIVERED IN PRESENCE

Assessment methods and criteria

STUDENTS WILL BE ASSIGNED A TOPIC AMONG THOSE TOUCHED DURING THE CLASSES. THE STUDENTS WILL ELABORATE A PRESENTATION THAT WILL BE DELIVERED TO THE CLASS AND THE TEACHER, FOLLOWED BY DISCUSSION

Other information

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