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An Abridged Transition State Model To Derive Structure, Dynamics, and Energy Components of DNA Polymerase β Fidelity
journal contribution
posted on 2011-08-16, 00:00 authored by Martin Klvaňa, Petr Jeřábek, Myron F. Goodman, Jan FloriánWe 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– (Onuc) on the Pα 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 Onuc–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 Onuc and Pα atoms and between the oxygen in the scissile
P–O bond (Olg) 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–Onuc 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 Olg-proximal water molecule to pol β
fidelity.
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electron densityenergy responseenergy surfaceOHPTSDNA Polymerase β FidelityWe showthumb subdomain conformationbondsite geometriesOnuctransition stateDNA polymerase betaP α atomsprimer DNA stranddianionic phosphoranecontributionAbridged Transition State ModelArg 183pol βdNTP substrateDNA residuesnucleophilic attackpol β fidelityEFER calculationsGSA configurationsreaction surfaceDerive Structureground state activationDNA polymerase fidelityP α atomEnergy Componentsdynamics simulations
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