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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.


Surface areas for theconsensus active site for all three independenttrajectories of the four systems, TTD3′-A (A), TTD3′-G(B), N/A-A (C), and TTD5′-A (D), are shown as transparent lines,whereas the Akima spline interpolations of these are shown as thicker,opaque lines for better visibility of the trends. Black, red, andgreen represent the profiles for three independent trajectories.
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fig4: Surface areas for theconsensus active site for all three independenttrajectories of the four systems, TTD3′-A (A), TTD3′-G(B), N/A-A (C), and TTD5′-A (D), are shown as transparent lines,whereas the Akima spline interpolations of these are shown as thicker,opaque lines for better visibility of the trends. Black, red, andgreen represent the profiles for three independent trajectories.

Mentions: For a morecomprehensive analysis, the definition of active sitewas modified to include all residues that are within 5 Å fromthe dNTP nucleotide or the TTD lesion (Table S2). These residues were inferred from three frames extracted fromeach of the TTD3′-A, TTD3′-G, and TTD5′-A MDtrajectories. The identified residues for each system were combinedto form a consensus active site, and the associated surface area wascalculated for all 12 independent MD trajectories. The results aredepicted in Figure 4. All of these trajectories initially exhibit a surface area valueof approximately 750 Å2. The TTD3′-A, TTD3′-G,and N/A-A trajectories oscillate about this value with minor fluctuations,with TTD3′-A remaining the most consistent. Two of the N/A-Atrajectories exhibit a slightly more closed active site, which couldbe attributed to the absence of the distortion created by the TTDlesion. However, the difference is relatively small, thereby stillconsistent with a rather open active site spacious enough to accommodatedistorted DNA.15,21


Comparative Molecular Dynamics Studies of Human DNAPolymerase η
Surface areas for theconsensus active site for all three independenttrajectories of the four systems, TTD3′-A (A), TTD3′-G(B), N/A-A (C), and TTD5′-A (D), are shown as transparent lines,whereas the Akima spline interpolations of these are shown as thicker,opaque lines for better visibility of the trends. Black, red, andgreen represent the profiles for three independent trajectories.
© Copyright Policy
Related In: Results  -  Collection

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

fig4: Surface areas for theconsensus active site for all three independenttrajectories of the four systems, TTD3′-A (A), TTD3′-G(B), N/A-A (C), and TTD5′-A (D), are shown as transparent lines,whereas the Akima spline interpolations of these are shown as thicker,opaque lines for better visibility of the trends. Black, red, andgreen represent the profiles for three independent trajectories.
Mentions: For a morecomprehensive analysis, the definition of active sitewas modified to include all residues that are within 5 Å fromthe dNTP nucleotide or the TTD lesion (Table S2). These residues were inferred from three frames extracted fromeach of the TTD3′-A, TTD3′-G, and TTD5′-A MDtrajectories. The identified residues for each system were combinedto form a consensus active site, and the associated surface area wascalculated for all 12 independent MD trajectories. The results aredepicted in Figure 4. All of these trajectories initially exhibit a surface area valueof approximately 750 Å2. The TTD3′-A, TTD3′-G,and N/A-A trajectories oscillate about this value with minor fluctuations,with TTD3′-A remaining the most consistent. Two of the N/A-Atrajectories exhibit a slightly more closed active site, which couldbe attributed to the absence of the distortion created by the TTDlesion. However, the difference is relatively small, thereby stillconsistent with a rather open active site spacious enough to accommodatedistorted DNA.15,21

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.