Abstract:
This research compares the accuracy and efficiency of the Kirkwood-Buff force field
(KBFF), a less common force field in applications, with the widely used CHARMM36
force field. The study focuses on the stability variations of human uracil DNA
glycosylase (hUNG) enzyme in its wild form and when complexed with toxic metal
ions Cd(II), Pb(II), and Ni(II). Four systems were considered, including the free
enzyme and the enzyme complexed with each mentioned toxic ion. Utilizing the
CavityPlus server, the binding pockets for the metal ions were identified, and molecular
dynamics simulations were conducted for 100 ns with repetition using both KBFF and
CHARMM36 force fields. The enzyme stability in each system was analyzed using root
mean square deviation and radius of gyration methods. Results revealed that
irrespective of the force field, Cd(II), Ni(II), and Pb(II) ions consistently stabilized the
hUNG enzyme compared to the free enzyme. These findings highlight the efficiency of
both force fields in capturing the stabilizing interactions between toxic metal ions and
the enzyme, showcasing the reliability of KBFF in biomolecular simulations.
Consequently, this study suggests that KBFF can be considered an efficient and
accurate force field for investigating the dynamics of biomolecular systems.
