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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.


RMSFs of the P atoms in the DNA constructs in systemsTTD3′-A(black), TTD3′-G (red), N/A-A (green), and TTD5′-A (blue)from one of the three independent trajectories. The primer strandsare represented as solid lines and the template strands are representedas dashed lines. P atoms 447 and 448 represent the P atoms of theTTD in the TTD3′-A and TTD3′-G systems, while P atoms448 and 449 constitute the TTD in the TTD5′-A and the normalTT in the N/A-A systems. The analogous data for all trajectories aredepicted in Figure S17.
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fig10: RMSFs of the P atoms in the DNA constructs in systemsTTD3′-A(black), TTD3′-G (red), N/A-A (green), and TTD5′-A (blue)from one of the three independent trajectories. The primer strandsare represented as solid lines and the template strands are representedas dashed lines. P atoms 447 and 448 represent the P atoms of theTTD in the TTD3′-A and TTD3′-G systems, while P atoms448 and 449 constitute the TTD in the TTD5′-A and the normalTT in the N/A-A systems. The analogous data for all trajectories aredepicted in Figure S17.

Mentions: Finally, we performed an analysis of the atomicfluctuations ofthe phosphorus atoms of the DNA backbone to investigate the relativemobilities of the nucleotides in the DNA strands. Note that the 5′-terminalnucleotides are exempt from this analysis because of their lack ofphosphate groups. In the template strand, the mobility is consistentlylow in the region around the TTD, as depicted in Figures 10 and S17. In general, the nucleotides toward the strand ends aremore mobile. Overall, the residues that are closer to the active siteare less mobile, as they are embedded in a more extended hydrogen-bondingnetwork involving not only their phosphate groups, but also the thyminebases themselves. Additionally, covalent bonding enforces restraintson the motions of the thymines of the TTD, as illustrated by the typicallylower mobilities of the P1 and P2 atoms of the TTD3′-A, TTD3′-G,and TTD5′-A systems compared to the P atoms of residues 448and 449 in the N/A-A system (Figure S17).


Comparative Molecular Dynamics Studies of Human DNAPolymerase η
RMSFs of the P atoms in the DNA constructs in systemsTTD3′-A(black), TTD3′-G (red), N/A-A (green), and TTD5′-A (blue)from one of the three independent trajectories. The primer strandsare represented as solid lines and the template strands are representedas dashed lines. P atoms 447 and 448 represent the P atoms of theTTD in the TTD3′-A and TTD3′-G systems, while P atoms448 and 449 constitute the TTD in the TTD5′-A and the normalTT in the N/A-A systems. The analogous data for all trajectories aredepicted in Figure S17.
© Copyright Policy
Related In: Results  -  Collection

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

fig10: RMSFs of the P atoms in the DNA constructs in systemsTTD3′-A(black), TTD3′-G (red), N/A-A (green), and TTD5′-A (blue)from one of the three independent trajectories. The primer strandsare represented as solid lines and the template strands are representedas dashed lines. P atoms 447 and 448 represent the P atoms of theTTD in the TTD3′-A and TTD3′-G systems, while P atoms448 and 449 constitute the TTD in the TTD5′-A and the normalTT in the N/A-A systems. The analogous data for all trajectories aredepicted in Figure S17.
Mentions: Finally, we performed an analysis of the atomicfluctuations ofthe phosphorus atoms of the DNA backbone to investigate the relativemobilities of the nucleotides in the DNA strands. Note that the 5′-terminalnucleotides are exempt from this analysis because of their lack ofphosphate groups. In the template strand, the mobility is consistentlylow in the region around the TTD, as depicted in Figures 10 and S17. In general, the nucleotides toward the strand ends aremore mobile. Overall, the residues that are closer to the active siteare less mobile, as they are embedded in a more extended hydrogen-bondingnetwork involving not only their phosphate groups, but also the thyminebases themselves. Additionally, covalent bonding enforces restraintson the motions of the thymines of the TTD, as illustrated by the typicallylower mobilities of the P1 and P2 atoms of the TTD3′-A, TTD3′-G,and TTD5′-A systems compared to the P atoms of residues 448and 449 in the N/A-A system (Figure S17).

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.