Tesis Doctorado
Understanding the phosphoryl transfer mechanisms in protein kinases through QM/MM hybrid methods
Autor
Recabarren-Hurtado, Rodrigo Hernán
Institución
Resumen
In the present doctoral thesis, the main focus was the study of the phosphoryl transfer mechanism in the protein cyclin-dependent kinase 2 (CDK2). For this, different computational methods such as molecular dynamics (MD) simulations, quantum chemical calculations, and in particular hybrid QM/MM (quantum mechanics/molecular mechanics) calculations were used. CDKs are well known as the master regulators of the eukaryotic cell cycle, and for many years have been the subject of extensive research due their potential use as therapeutic targets in cancer treatment. In this context, the precise knowledge of the reaction mechanisms could help to propose new strategies for their inhibition. CDK2 arises like one of the most studied kinases and the availability of many crystallographic structures makes it an attractive study system. With respect to CDK2, two main questions were addressed: the first one related to which is the most favorable mechanistic pathway for the phosphoryl transfer reaction when one Mg2+ ion is present at the active site (Manuscript 1); a second question was how a second Mg2+ ion at the active site affects the reaction mechanism and its associated free energy barrier (Manuscript 2); and in a third part (Manuscript 3), the effect of replacing Mg2+ by Ca2+ in the product state of protein kinase A (PKA) was studied, contributing to the understanding of the inhibitory effect that Ca2+ exerts in catalysis. Altogether, the results of the present doctoral thesis help to deepen the understanding of the reaction mechanisms in protein kinases and give new insights into how metal cofactors act in the enzymatic reaction. PFCHA-Becas Hay artículos en la tesis que aún no han sido publicados. PFCHA-Becas