Modeling biochemical systems : from QM/MM methods to metadynamics

Les structures cristallographiques de macromolécules comme les protéines, obtenues par la biologie structurale sont des modèles statiques. Or, c'est la flexibilité et la dynamique de ces macromolécules qui sont généralement responsables de leurs fonctions. La simulation permet d'explorer cette flexibilité lors de différents phénomènes qui ont lieu dans ces systèmes : une réaction chimique, des interactions avec une petite molécule… Simuler de tels phénomènes est un défi car la dynamique moléculaire classique ne permet pas de les observer. Des algorithmes permettent d'accélérer l'échantillonnage des dynamiques pour lever cette limitation et de calculer les barrières d'activation pour de tels phénomènes. Simultanément, le choix du niveau de calcul est crucial car il faut concilier la taille importante des systèmes, la nature des interactions et les phénomènes électroniques impliqués. Dans ce travail, différentes méthodes, dont principalement la métadynamique soit au niveau classique ou quantique, ou encore en combinant les deux niveaux quantique/classique, seront utilisées pour modéliser quatre processus complexes : des changements de conformations d'une protéine, des interactions entre métalloprotéine et inhibiteur, des réactions en solution et dans une enzyme.Crystallographic structures of macromolecules, such as proteins, obtained by structural biology are static models. However, flexibility and dynamics of macromolecules are generally responsible for their functions. Modeling allows us to explore this flexibility in different phenomena that take place in these systems: a chemical reaction, interaction with a small molecule... Modeling such phenomena is a challenge because they cannot be observed by classical molecular dynamics. Algorithms can accelerate sampling of dynamics to simulate these events and calculate their activation barriers. Simultaneously, the choice of the level of calculation is crucial because it must merge with the size of the systems, the nature of interactions and the electronic phenomena involved.In this thesis, some methods, mainly metadynamics at classical level, quantum or the hybrid quantum/classical level, will be used to model four complex processes: conformational changes of proteins, metalloprotein/inhibitor interactions, reactivity in solution and enzymatic reactivity

Conformational Flexibility of Human Casein Kinase Catalytic Subunit Explored by Metadynamics

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Density Functional Theory Study of Monoethanolamine Adsorption on Hydroxylated Cr2O3 Surfaces

International audienceThe adsorption of monoethanolamine (MEA), a well-known CO2 capture amine, on the hydroxylated (0001)-Cr2O3 surface was investigated by periodic density functional theory calculations and complementary ab initio molecular dynamics. Two different adsorption modes were investigated: adsorption of MEA above the hydroxylated surface and substitution of a surface water molecule by MEA. Several MEA coverages were studied from 0.25 to 1 monolayer. An atomistic thermodynamic approach was used to take into account the effects of temperature and solvation on the MEA adsorption process in aqueous solution. MEA can adsorb on the surface in a parallel orientation, and H-bonds are formed between amine and alcohol groups and different (H)OH groups at the surface. In the gas phase at 0 K, the formation of a monolayer (ML) of MEA above the surface is the most favorable adsorption mode. In aqueous solution at 298.15K, calculations have suggested that MEA adsorbs above the hydroxylated Cr2O3 surface with a density of 2.37 MEA/nm2 (0.5 ML). However, the substitution process was found to be endothermic at temperatures above 298.15 K

Investigation of Binding-Site Homology between Mushroom and Bacterial Tyrosinases by Using Aurones as Effectors

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