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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.


Histogramsdepicting the number of hydrogen bonds formed withinthe nucleic acids obtained from one of the three independent trajectoriesof the systems TTD3′-A (black), TTD3′-G (red), N/A-A(green), and TTD5′-A (blue). Hydrogen bonds were defined witha donor–acceptor heavy-atom distance cutoff of 3.5 Å anda donor–hydrogen–acceptor angle cutoff of 135°.The analogous data obtained from all trajectories are provided in Figure S12.
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fig7: Histogramsdepicting the number of hydrogen bonds formed withinthe nucleic acids obtained from one of the three independent trajectoriesof the systems TTD3′-A (black), TTD3′-G (red), N/A-A(green), and TTD5′-A (blue). Hydrogen bonds were defined witha donor–acceptor heavy-atom distance cutoff of 3.5 Å anda donor–hydrogen–acceptor angle cutoff of 135°.The analogous data obtained from all trajectories are provided in Figure S12.

Mentions: To characterize thesignificant interactionsin these systems, we examined the number of hydrogen bonds formedwithin the nucleic acid subsystem, namely within the subsystem comprisedof the DNA primer/template and the dNTP. To compare these numbers, Figures 7 and S12 depict histograms of the number of hydrogenbonds within the nucleic acid subsystem. Figure 7 illustrates that the nucleic acid constructin the TTD3′-A system forms the largest number of hydrogenbonds, suggesting stronger interactions between the DNA primer/templatestructure and the dNTP molecule. Interestingly, the smallest numberof hydrogen bonds is found in the N/A-A system without a TTD.


Comparative Molecular Dynamics Studies of Human DNAPolymerase η
Histogramsdepicting the number of hydrogen bonds formed withinthe nucleic acids obtained from one of the three independent trajectoriesof the systems TTD3′-A (black), TTD3′-G (red), N/A-A(green), and TTD5′-A (blue). Hydrogen bonds were defined witha donor–acceptor heavy-atom distance cutoff of 3.5 Å anda donor–hydrogen–acceptor angle cutoff of 135°.The analogous data obtained from all trajectories are provided in Figure S12.
© Copyright Policy
Related In: Results  -  Collection

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

fig7: Histogramsdepicting the number of hydrogen bonds formed withinthe nucleic acids obtained from one of the three independent trajectoriesof the systems TTD3′-A (black), TTD3′-G (red), N/A-A(green), and TTD5′-A (blue). Hydrogen bonds were defined witha donor–acceptor heavy-atom distance cutoff of 3.5 Å anda donor–hydrogen–acceptor angle cutoff of 135°.The analogous data obtained from all trajectories are provided in Figure S12.
Mentions: To characterize thesignificant interactionsin these systems, we examined the number of hydrogen bonds formedwithin the nucleic acid subsystem, namely within the subsystem comprisedof the DNA primer/template and the dNTP. To compare these numbers, Figures 7 and S12 depict histograms of the number of hydrogenbonds within the nucleic acid subsystem. Figure 7 illustrates that the nucleic acid constructin the TTD3′-A system forms the largest number of hydrogenbonds, suggesting stronger interactions between the DNA primer/templatestructure and the dNTP molecule. Interestingly, the smallest numberof hydrogen bonds is found in the N/A-A system without a TTD.

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.