An Abridged Transition
State Model To Derive Structure, Dynamics, and Energy Components of
DNA Polymerase β Fidelity
Martin Klvaňa
Petr Jeřábek
Myron F. Goodman
Jan Florián
10.1021/bi200790s.s001
https://acs.figshare.com/articles/journal_contribution/An_Abridged_Transition_State_Model_To_Derive_Structure_Dynamics_and_Energy_Components_of_DNA_Polymerase_Fidelity/2623192
We show how a restricted reaction surface can be used
to facilitate the calculation of biologically important contributions
of active site geometries and dynamics to DNA polymerase fidelity.
Our analysis, using human DNA polymerase beta (pol β), is performed
within the framework of an electrostatic linear free energy response
(EFER) model. The structure, dynamics, and energetics of pol β-DNA–dNTP
interactions are computed between two points on the multidimensional
reaction free energy surface. “Point 1” represents a
ground state activation intermediate (GSA), which is obtained by deprotonating
the terminal 3′OH group of the primer DNA strand. “Point
2” is the transition state (PTS) for the attack of the 3′O<sup>–</sup> (O<sub>nuc</sub>) on the P<sub>α</sub> atom
of dNTP substrate, having the electron density of a dianionic phosphorane
intermediate. Classical molecular dynamics simulations are used to
compute the geometric and dynamic contributions to the formation of
right and wrong O<sub>nuc</sub>–P chemical bonds. Matched dCTP·G
and mismatched dATP·G base pairs are used to illustrate the analysis.
Compared to the dCTP·G base pair, the dATP·G mismatch has
fewer GSA configurations with short distances between O<sub>nuc</sub> and P<sub>α</sub> atoms and between the oxygen in the scissile
P–O bond (O<sub>lg</sub>) and the nearest structural water.
The thumb subdomain conformation of the GSA complex is more open for
the mismatch, and the H-bonds in the mispair become more extended
during the nucleophilic attack than in the correct pair. The electrostatic
contributions of pol β and DNA residues to catalysis of the
right and wrong P–O<sub>nuc</sub> bond formation are 5.3 and
3.1 kcal/mol, respectively, resulting in an 80-fold contribution to
fidelity. The EFER calculations illustrate the considerable importance
of Arg183 and an O<sub>lg</sub>-proximal water molecule to pol β
fidelity.
2011-08-16 00:00:00
electron density
energy response
energy surface
OH
PTS
DNA Polymerase β FidelityWe show
thumb subdomain conformation
bond
site geometries
Onuc
transition state
DNA polymerase beta
P α atoms
primer DNA strand
dianionic phosphorane
contribution
Abridged Transition State Model
Arg 183
pol β
dNTP substrate
DNA residues
nucleophilic attack
pol β fidelity
EFER calculations
GSA configurations
reaction surface
Derive Structure
ground state activation
DNA polymerase fidelity
P α atom
Energy Components
dynamics simulations