Toolbox: structural biology

Duration

20h Th, 15h Pr, 5h AUTR

Number of credits

Lecturer

Christian Damblon, Frédéric Kerff, N..., Loïc Quinton

Coordinator

Frédéric Kerff

Language(s) of instruction

French language

Organisation and examination

Teaching in the second semester

Schedule

Schedule online

Units courses prerequisite and corequisite

Prerequisite or corequisite units are presented within each program

Learning unit contents

This toolbox will cover the various methods for characterising the 3D structure of biological macromolecules, namely X-ray crystallography, nuclear magnetic resonance, electron microscopy, mass spectrometry and modelling. Particular attention will be paid to the advantages/disadvantages and limitations of using each of these methods in order to determine the most appropriate method(s) to answer a given biological question in the context of a research project.

This toolbox will also enable students to learn how to make effective use of the large amount of experimental and modelling structural data available in public databases (Protein Data Bank, Uniprot, etc.).

 

Table of contents of the theoretical courses :

1.General information (Frédéric Kerff)

• 1.1 Detailed introduction on the structure of biological macromolecules.
• 1.2 Presentation of the Protein Data Bank and other structural biology resources available.
• 1.3 Introduction to the use of the PyMOL structure visualisation software.

• 3.1 X-ray sources
• 3.2 Steps in determining the structure of a biological macromolecule by X-ray diffraction
• 3.3 Advantages and limitations of the method

• 4.1 Description of the components of a transmission electron microscope
• 4.2 Determining the structure of a biological macromolecule using the "single particle analysis" method in cryo-electron microscopy
• 4.3 Determining the structure of a biological macromolecule using tomography

• 5.1 Determination of a protein structure by NMR in solution
• 5.2 Characterisation of protein dynamics using NMR
• 5.3 NMR studies of interactions of all kinds
• 5.4 Contribution of NMR to the study of intrinsically disordered proteins and protein folding

• 6.1 Electro-ionisation and fragmentation of biological molecules?
• 6.2 Native mass spectrometry - Analysis of macromolecular protein complexes
• 6.3 Hydrogen-deuterium exchange coupled with mass spectrometry
• 6.4 Cross-linking resolved by mass spectrometry
• 6.5 Mass spectrometry imaging: principles and applications
• 6.6 Basics of ion mobility

Learning outcomes of the learning unit

At the end of the theoretical courses given as part of the Structural Biology toolbox, students will be able to:

• Obtain a model of the three-dimensional structure of a protein from an amino acid sequence;
• Understand the principle of the different stages in the determination of 3D structures by X-ray crystallography, in order to make objective use of crystallographic models;
• Recognise the two main types of 3D structure determination method using transmission electron microscopy (cryo-EM, tomography) for the determination of biological structures with a view to its integration into future research projects;
• Understand how NMR contributes to the understanding of proteins and their function;
• Understand the main mass spectrometry techniques useful in the fields of biology, biochemistry and microbiology;
• As part of a research project, identify the structural biology technique best suited to answering a specific biological question.

• Use open-access structural biology resources (Protein Data Bank, Uniprot, etc.);
• Use the basic functions of the PyMOL software to analyse the three-dimensional structure of biological macromolecules and to prepare figures to illustrate presentations or reports/articles.

Prerequisite knowledge and skills

This module will build on the concepts covered in the following course:

Chemistry of biological macromolecules (BIOC9242-1)

Planned learning activities and teaching methods

• Theoretical courses.?
• Tutorials illustrating the course.?
• Practical work on a personal computer and a practical session in the laboratory.
• Visits to laboratories and discovery of the main instruments.

Mode of delivery (face to face, distance learning, hybrid learning)

Face-to-face course

Recommended or required readings

The slideshows and documents needed for the courses will be available on the e-Campus platform.

Exam(s) in session

Any session

- In-person

oral exam


Additional information:

The BO will be assessed by means of an integrative oral examination in the presence of several module holders.

Work placement(s)

Organisational remarks and main changes to the course

Practical work and/or tutorials are compulsory. The concepts covered may be included in the assessment. Any absence must be justified and, where appropriate, students are required to put their work in order. If a report is required, it must be completed even in the event of absence.

Each student must have a laptop computer with PyMOL software installed (https://pymol.org/2/) and a 3-button mouse. Trackpads are not very suitable for handling this programme.

Contacts

The supervisors are available to answer your questions: either during the lectures/practical sessions given as part of this theme week, or by e-mail (during office hours and no later than 2 days before the examination or submission of the report).

 

Module coordinator :

Dr Kerff Frédéric

Tel: 04/366.36.20
fkerff@uliege.be



Co-tutors :

Prof. Quinton Loic, loic.quinton@uliege.be
Prof. Damblon Christian, c.damblon@uliege.be

Association of one or more MOOCs