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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.


Time evolution of the radius of gyration(lower curves) and thelargest distance between any two protein atoms (upper curves) forthe systems TTD3′-A (black), TTD5′-G (red), N/A-A (green),and TTD5′-A (blue) obtained from one of the three independenttrajectories for each system. The analogous data obtained from alltrajectories are provided in Figure S5.
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fig5: Time evolution of the radius of gyration(lower curves) and thelargest distance between any two protein atoms (upper curves) forthe systems TTD3′-A (black), TTD5′-G (red), N/A-A (green),and TTD5′-A (blue) obtained from one of the three independenttrajectories for each system. The analogous data obtained from alltrajectories are provided in Figure S5.

Mentions: After investigating the activesite surface area, we examined theoverall compactness of the enzyme. For this purpose, we calculatedthe time evolution of the radius of gyration, as well as the largestdistance between any two protein atoms, for the MD trajectories. Asshown in Figure 5,all four systems exhibit similar behavior with respect to these properties.The analogous data for all trajectories are provided in Figure S8. The compactness of these systems remainsconsistent throughout the trajectories with an approximate radiusof gyration of 25 Å. The maximum interatomic distance is lessmeaningful than the radius of gyration because of the loop motions,but even this quantity remains mostly unchanged during the trajectoriesexcept for minor fluctuations.


Comparative Molecular Dynamics Studies of Human DNAPolymerase η
Time evolution of the radius of gyration(lower curves) and thelargest distance between any two protein atoms (upper curves) forthe systems TTD3′-A (black), TTD5′-G (red), N/A-A (green),and TTD5′-A (blue) obtained from one of the three independenttrajectories for each system. The analogous data obtained from alltrajectories are provided in Figure S5.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Time evolution of the radius of gyration(lower curves) and thelargest distance between any two protein atoms (upper curves) forthe systems TTD3′-A (black), TTD5′-G (red), N/A-A (green),and TTD5′-A (blue) obtained from one of the three independenttrajectories for each system. The analogous data obtained from alltrajectories are provided in Figure S5.
Mentions: After investigating the activesite surface area, we examined theoverall compactness of the enzyme. For this purpose, we calculatedthe time evolution of the radius of gyration, as well as the largestdistance between any two protein atoms, for the MD trajectories. Asshown in Figure 5,all four systems exhibit similar behavior with respect to these properties.The analogous data for all trajectories are provided in Figure S8. The compactness of these systems remainsconsistent throughout the trajectories with an approximate radiusof gyration of 25 Å. The maximum interatomic distance is lessmeaningful than the radius of gyration because of the loop motions,but even this quantity remains mostly unchanged during the trajectoriesexcept for minor fluctuations.

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.