This dissertation details the use of computational methods to understand the effect that cancer-related mutations have on proteins that complex with nucleic acids. Firstly, we perform molecular dynamics (MD) simulations of various mutations in DNA polymerase κ (pol κ). Through an experimental collaboration, we classify the mutations as more or less active than the wild type complex, depending upon the incoming nucleotide triphosphate. From these classifications we use quantum mechanics/molecular mechanics (QM/MM) to explore the reaction mechanism. Preliminary analysis points to a novel method for nucleotide addition in pol κ. Secondly, we study the ten-eleven translocation 2 (TET2) enzyme in various contexts. We find that the identities of both the substrate and complementary strands (or lack thereof) are crucial for maintaining the complex structure. Separately, we find that point mutations within the protein can affect structural features throughout the complex, only at distal sites, or only within the active site. The mutation's position within the complex alone is not indicative of its impact. Thirdly, we share a new method that combines direct coupling analysis and MD to predict potential rescue mutations using poly(ADP-ribose) polymerase 1 as a model enzyme. Fourthly, we perform MD simulations of mutations in the protection of telomeres 1 (POT1) enzyme. The investigated variants modify the POT1-ssDNA complex dynamics and protein—DNA interactions. Fifthly, we investigate the incorporation of remdesivir and other nucleotide analogue prodrugs into the protein-RNA complex of severe acute respiratory syndrome-coronavirus 2 RNA-dependent RNA polymerase. We find evidence for destabilization throughout the complex and differences in inter-subunit communication for most of the incorporation patterns studied. Finally, we share a method for determining a minimum active region for QM/MM simulations. The method is validated using 4-oxalocrotonate, TET2, and DNA polymerase λ as test cases.

Dans cette thèse, des particules de polymère fonctionnalisées en surface avec des groupes poly (éthylène glycol) (PEG) ont été synthétisées pour favoriser leur interaction avec les dérivés cellulosique via liaisons hydrogène intermoléculaires. Deux voies de synthèse ont été proposées pour obtenir ses composites cellulose/latex.La première voie est basée sur l'auto-assemblage induit par polymérisation (PISA) pour former des nanoparticules fonctionnalisées avant leur adsorption sur un substrat cellulosique. La PISA tire profit de la formation de copolymères blocs amphiphiles dans l'eau en combinant la polymérisation en émulsion avec les techniques de polymérisation radicalaire contrôlées (RDRP). Ces dernières sont utilisées pour synthétiser des polymères hydrophiles agissant à la fois comme précurseur pour la polymerization en émulsion d'un monomère hydrophobe, et comme stabilisant des particules de latex obtenues. Deux techniques de RDRP ont été étudiées : les polymérisations RAFT et SET-LRP. Des polymères hydrophiles à base de PEG de faible masse molaire ont été synthétisés en utilisant ses deux techniques qui sont ensuite utilisés pour la polymérisation d'un bloc hydrophobe dans l'eau. Le transfert de l'agent de contrôle au site de la polymérisation était difficile en utilisant la SET-LRP en émulsion, conduisant à la formation de larges particules. En utilisant la RAFT en émulsion, des particules nanométriques ont été obtenues, avec un changement morphologique observé en fonction de la taille du segment hydrophobe, puis adsorbées sur des nanofibrilles de cellulose (CNF).La seconde voie utilise la polymérisation en émulsion classique réalisée en présence de nanocristaux de cellulose (CNC) conduisant à une stabilisation Pickering des particules de polymère. L'interaction cellulose/particule est assurée grâce à l'ajout d’un comonomère à type PEG. Une organisation a été visualisé dans laquelle plusieurs particules de polymère recouvrent chaque CNC / In this thesis, polymer particles surface-functionalized with poly(ethylene glycol) (PEG) groups were synthesized to promote their interaction with cellulose derivatives via intermolecular hydrogen bond. Two synthetic routes were proposed to obtain such cellulose/latex composites.The first route was based on the polymerization-induced self-assembly (PISA) to form functionalized polymer nanoparticles prior to adsorption onto cellulosic substrate. PISA takes advantage of the formation of amphiphilic block copolymers in water by combining emulsion polymerization with reversible-deactivation radical polymerization (RDRP) techniques. The latter were used to synthesize well-controlled hydrophilic polymer chains, acting as both precursor for the emulsion polymerization of a hydrophobic monomer, and stabilizer of the final latex particles. Two RDRP techniques were investigated: reversible addition-fragmentation chain transfer (RAFT), and single electron transfer-living radical polymerization (SET-LRP). Low molar mass PEG-based hydrophilic polymers have been synthesized using both techniques, used for the polymerization of a hydrophobic block in water. The transfer of controlling agent at the locus of the polymerization was challenging for SET-LRP in emulsion conditions leading to surfactant-free large particles. Nanometric latex particles were obtained via RAFT-mediated emulsion polymerization, with morphology change from sphere to fibers observed depending on the size of the hydrophobic segment, which were then able to be adsorbed onto cellulose nanofibrils (CNFs).The second route used conventional emulsion polymerization performed directly in presence of cellulose nanocrystals (CNCs) leading to Pickering-type stabilization of the polymer particles. Cellulose/particle interaction was provided thanks to the addition of PEG-based comonomer. Original organization emerged where CNCs were covered by several polymer particles

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