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Comparative Molecular Dynamics Studies of Human DNAPolymerase η

View Article: PubMed Central - PubMed

ABSTRACT

High-energyultraviolet radiation damages DNA through the formationof cyclobutane pyrimidine dimers, which stall replication. When thelesion is a thymine–thymine dimer (TTD), human DNA polymeraseη (Pol η) assists in resuming the replication processby inserting nucleotides opposite the damaged site. We performed extensivemolecular dynamics (MD) simulations to investigate the structuraland dynamical effects of four different Pol η complexes withor without a TTD and with either dATP or dGTP as the incoming base.No major differences in the overall structures and equilibrium dynamicswere detected among the four systems, suggesting that the specificityof this enzyme is due predominantly to differences in local interactionsin the binding regions. Analysis of the hydrogen-bonding interactionsbetween the enzyme and the DNA and dNTP provided molecular-level insights.Specifically, the TTD was observed to engage in more hydrogen-bondinginteractions with the enzyme than its undamaged counterpart of twonormal thymines. The resulting greater rigidity and specific orientationof the TTD are consistent with the experimental observation of higherprocessivity and overall efficiency at TTD sites than at analogoussites with two normal thymines. The similarities between the systemscontaining dATP and dGTP are consistent with the experimental observationof relatively low fidelity with respect to the incoming base. Moreover,Q38 and R61, two strictly conserved amino acids across the Pol ηfamily, were found to exhibit persistent hydrogen-bonding interactionswith the TTD and cation-π interactions with the free base, respectively.Thus, these simulations provide molecular level insights into thebasis for the selectivity and efficiency of this enzyme, as well asthe roles of the two most strictly conserved residues.

No MeSH data available.


Active sites of the systems TTD3′-A (A),TTD3′-G(B), N/A-A (C), and TTD5′-A (D). The incoming free nucleotide,dATP or dGTP, is shown in ball-and-stick representation and labeled.The TTD or consecutive normal thymines for N/A-A is displayed in licoricerepresentation with the 3′ and 5′ ends labeled.
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fig1: Active sites of the systems TTD3′-A (A),TTD3′-G(B), N/A-A (C), and TTD5′-A (D). The incoming free nucleotide,dATP or dGTP, is shown in ball-and-stick representation and labeled.The TTD or consecutive normal thymines for N/A-A is displayed in licoricerepresentation with the 3′ and 5′ ends labeled.

Mentions: The complete DNA sequences and numbering are given in Table S1, and the entire complex for each systemis depicted in Figure S1. The differencesbetween these systems are highlighted in Figure 1.


Comparative Molecular Dynamics Studies of Human DNAPolymerase η
Active sites of the systems TTD3′-A (A),TTD3′-G(B), N/A-A (C), and TTD5′-A (D). The incoming free nucleotide,dATP or dGTP, is shown in ball-and-stick representation and labeled.The TTD or consecutive normal thymines for N/A-A is displayed in licoricerepresentation with the 3′ and 5′ ends labeled.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4696480&req=5

fig1: Active sites of the systems TTD3′-A (A),TTD3′-G(B), N/A-A (C), and TTD5′-A (D). The incoming free nucleotide,dATP or dGTP, is shown in ball-and-stick representation and labeled.The TTD or consecutive normal thymines for N/A-A is displayed in licoricerepresentation with the 3′ and 5′ ends labeled.
Mentions: The complete DNA sequences and numbering are given in Table S1, and the entire complex for each systemis depicted in Figure S1. The differencesbetween these systems are highlighted in Figure 1.

View Article: PubMed Central - PubMed

ABSTRACT

High-energyultraviolet radiation damages DNA through the formationof cyclobutane pyrimidine dimers, which stall replication. When thelesion is a thymine–thymine dimer (TTD), human DNA polymeraseη (Pol η) assists in resuming the replication processby inserting nucleotides opposite the damaged site. We performed extensivemolecular dynamics (MD) simulations to investigate the structuraland dynamical effects of four different Pol η complexes withor without a TTD and with either dATP or dGTP as the incoming base.No major differences in the overall structures and equilibrium dynamicswere detected among the four systems, suggesting that the specificityof this enzyme is due predominantly to differences in local interactionsin the binding regions. Analysis of the hydrogen-bonding interactionsbetween the enzyme and the DNA and dNTP provided molecular-level insights.Specifically, the TTD was observed to engage in more hydrogen-bondinginteractions with the enzyme than its undamaged counterpart of twonormal thymines. The resulting greater rigidity and specific orientationof the TTD are consistent with the experimental observation of higherprocessivity and overall efficiency at TTD sites than at analogoussites with two normal thymines. The similarities between the systemscontaining dATP and dGTP are consistent with the experimental observationof relatively low fidelity with respect to the incoming base. Moreover,Q38 and R61, two strictly conserved amino acids across the Pol ηfamily, were found to exhibit persistent hydrogen-bonding interactionswith the TTD and cation-π interactions with the free base, respectively.Thus, these simulations provide molecular level insights into thebasis for the selectivity and efficiency of this enzyme, as well asthe roles of the two most strictly conserved residues.

No MeSH data available.