Etude de l'ADN gyrase B: Liaison de ligands et flexibilité moléculaire

L ADN gyrase est une enzyme vitale pour la bactérie grâce à sa capacité de manipuler les molécules d ADN dans la cellule vivante. Cette capacité fait de l ADN gyrase une cible idéale pour des composés anti-infectieux. Dans ce travail, l ADN gyrase a été étudié par des méthodes de modélisatoin moléculaire. Une approche de conception de ligands basée sur la structure a été entreprise sur le sous-domaine N-terminal de 24 kDa de l ADN gyrase B (domaine GHKL). La flexibilité de deux boucles du site actif du domaine GHKL a été étudiée par des simulations de dynamiques moléculaires en présence de différents ligands. Dans une dernière partie, une analyse des modes normaux du dimère du domaine N-terminal de 43 kDa a été entreprise.DNA gyrase is a vital bacterial enzyme necessary for the handling of the large DNA molecules in the living cell. Therefore DNA gyrase is an ideal target enzyme for anti-infectious compounds. In this work DNA gyrase has been studied by molecular modelling methods. A computational structure-based ligand design approach has been carried out on the N-terminal 24 kDa subdomain of DNA gyrase B (GHKL domain). To further examine the flexibility of two active site loops, molecular dynamics simulations have been carried out on the GHKL domain in different ligand binding conditions. In a final part, normal mode analysis has been carried out on the dimer of the 43 kDa domain of DNA gyrase B.STRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF

Effects of loop conformation on pKa and ligand binding in DNA gyrase B

Molecular dynamics simulations of the adenosine triphosphatase (ATPase) subdomain of DNA gyrase B were done to characterize the flexibility of two loops implicated in ligand binding. The simulations show that bound adenosine triphosphate (ATP) stabilizes the conformation of the two loops. Simulations of the ATPase subdomain without ATP show that the loops are more flexible and can assume alternative conformations. We further investigated the dependence of histidine pKa on the loop conformations using continuum dielectric calculations. Using multiple conformations, we showed that the protonation states of titratable groups in the flexible loops can depend on the loop conformation. This, in turn, will affect ligand binding and calculations such as the multiple copy simultaneous search (MCSS) method for small functional group binding. This illustrates the importance of accurately determining the protonation state of the protein prior to the calculation