The course is organized over two weeks at the Biochemistry laboratory of Ecole Polytechnique.

During the first week, you will conduct a mini research project aimed at characterizing the active site of an essential enzymatic protein and performing a thorough study of the function of several amino acids in catalysis.

The purpose of this course is to introduce an experimental approach used to carry out a research project, to discover new methods, to discuss the merits of the use of these methods, their advantages and their limits. This course therefore provides useful tools in all areas of the molecular studies of biological processes.

Experimental work: site-directed mutagenesis, gene sequencing, protein purification, characterization of mutant proteins by in-depth study of their catalytic mechanisms, biophysical methods.

During the second week you will attend a series of lectures directly related to the experimental study of the first week.

A half-day will be devoted to the use of computer tools for the study of the phylogeny of RNAs and proteins and for the engineering of protein:ligand interactions.

Finally, three days will be devoted to electron microscopy applied to ribosomal complexes. The preparation of samples for electron microscopy and cryo-micoscopy will be introduced. You will be able to observe the grids prepared on one of the two microscopes available at Ecole polytechnique. Finally, you will also attend an introduction to the collection and processing of cryo-electron microscopy images to obtain the three-dimensional structure of your object of study. The advantages and limitations of this technique will be discussed throughout this training.

Structural bioinformatics. Lecturers: Thomas Gaillard and Thomas Simonson; 6 ECTS; 40 hours; lectures and practicals

Many aspects of the structure, dynamics, function, and engineering of biomolecules (proteins but also RNA and DNA) will be discussed. The bases of their stability will be recalled; the main properties of the solvent; the effects that govern refolding and molecular recognition. We will discuss basic modeling tools: sequence alignment, homology modeling, molecular dynamics, docking. In addition to the theoretical bases (course + TD), we will manipulate these tools through mini-projects or TPs, in a linux environment. The softwares used have a very general interest in structural biology; some have been co-developed by the teachers.


Bioinformatique structurale – Lieu : Ecole polytechnique

On abordera de nombreux aspects de la structure, la dynamique, la fonction, et l'ingénierie des biomolécules (protéines mais aussi ARN et ADN). On rappellera les bases de leur stabilité; les principales propriétés du solvant; les effets qui gouvernent le repliement et la reconnaissance moléculaire. On abordera des outils de base de modélisation: alignement de séquences, modélisation par homologie, dynamique moléculaire, docking. Outre les bases théoriques (cours + TD), on manipulera ces outils à travers des mini-projets ou TPs, dans un environnement linux. Les logiciels utilisés ont un intérêt très général en biologie structurale; certains ont été co-développées par les enseignants.


Nature-based solutions to substitute fossile resources and address global change


Lecturer: Benoît Gabrielle - Agro-ParisTech

Natural ecosystems and the services they provide are a key to address current environmental challenges, such as climate change, the preservation of air and water quality, and the transition toward a low-carbon economy. Engineering these services via the management of ecosystems, land-use planning or the integration of plants in urban environments can « pave the way towards a more resource efficient, competitive and greener economy » (EU Research Agenda, 2015). Nature-based solutions include for example the production of bio-based alternatives to fossile-based products, the mitigation of heat waves in cities via the presence of vegetation, the enhacement of carbon storage in ecosystems or the management of watersheds to reduce flood risks.

The aim of the course is to raise the awareness of these solutions, with a particular focus on biomass production and transformation into fuels, materials and chemicals to substitute fossile resources, and to equip them with key concepts and know-hows on the design and assessment of such solutions. The course will provide students with a detailed understanding of the issues associated with the development of nature-based solutions to meet our needs for food and energy, mitigate climate change or air pollution, and methods to their sustainability along the environmental and economic dimensions.


Langue du cours : Anglais

Credits ECTS : 4

Synthetic biology. Lecturers: Thomas Gaillard, Hannu Myllykallio, Yves Mechulam; 6 ECTS; 40 hours; lectures.

This course will present the main bioinformatics and molecular biology concepts used to build new biological systems of therapeutic or industrial interest. It will deal in particular with synthetic regulatory circuits, new biofuels, proteins containing non-canonical amino acids, …

Molecular structures of the cell. Lecturer: Anna Polesskaya; 6 ECTS; 40 hours; lectures.

This course will present several examples of central cellular structures, including the cytoskeleton.

Grant application. Lecturer: Researcher depending on the project; 6 ECTS; 40 hours; personal project.

Students will prepare a scientific project in the form of an application for a research grant.

BIO658 : Biocristallographie.
Responsable : Nicolas Leulliot

L'enseignement est organisé sous forme de cours hebdomadaires, à la faculté de pharmacie de Paris. Il comporte également des Travaux pratiques : Cristallogenèse, Phasage par remplacement moléculaire et/ou par méthodes expérimentales. Reconstruction du modèle dans la carte de densité électronique. Des travaux pratiques sur la collecte de données sont effectués en collaboration avec l'équipe de la ligne de lumière Proxima2 au synchrotron SOLEIL. Il est proposé à tous les étudiants qui en ressentent le besoin de suivre un programme préalable d'une semaine de remise à niveau pour se familiariser avec les concepts et outils mathématiques utilisés en cristallographie et spectroscopie.

BIO659 : Protéomique
Responsable : Virginie Redeker

1- Etat des lieux des analyses protéomiques.

2- Méthodes de spectrométrie de masse adaptées à l’analyse des peptides et protéines
-Principe des modes d’ionisation (MALDI, ESI)
-Principe des analyseurs de masse simples et hybrides (TOF-TOF, Q-TOF, Trappe, Orbitrap, FTICR...)
-Comparaison de leurs spécificités et utilités.

3- Stratégies protéomiques
-Identifications de protéines peu abondantes dans des mélanges très complexes
-Caractérisations des modifications post-traductionnelles connues ou inconnues.
-Quantification: méthodes globales ou ciblées.
-Interactions protéine-protéine
-Informations structurales: interactions non covalentes et caractérisation de déterminants stucturaux

4- Méthodes de préparation, séparation et enrichissement des protéines et peptides
-Préparations classiques des échantillons, électrophorèse, chromatographie.
-Cas des modifications post-traductionnelles (modifications classiques, glycosylations, phosphorylations, nouvelles modifications, …)
-Cas des protéines membranaires.
-Méthodes d’enrichissement.

5- Analyses de spectres (cours et TD)
-Mesures de masse d'une protéine, d'un mélange de peptides
-Fragmentation de peptides et protéines : principe et analyse de spectres de fragmentation
-Cas pratiques

6- Visite d’une plateforme de protéomique avec ateliers de mesures de masse et d’identification de protéines.