title: Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study.
abstract: In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein-ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component.
authors.affiliation: Department of Physical Chemistry, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950, Bydgoszcz, Poland. przemekcz@cm.umk.pl.
authors.forename: Przemysław
authors.initials: P
authors.lastname: Czeleń
authors.affiliation: Department of Inorganic Chemistry, Wrocław Medical University, Borowska 211, 55-556, Wrocław, Poland. zaneta.czyznikowska@gmail.com.
authors.forename: Żaneta
authors.initials: Ż
authors.lastname: Czyżnikowska
keywords: Docking procedure; Intermolecular interaction energy partitioning; Molecular dynamic simulations