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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.


Comparison of the RMSFs of the four system from MD simulationsand the B-factor values from the crystal structure 3MR3, which weused as the initial coordinates for the system TTD3′-A.
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fig3: Comparison of the RMSFs of the four system from MD simulationsand the B-factor values from the crystal structure 3MR3, which weused as the initial coordinates for the system TTD3′-A.

Mentions: To locate the flexible regionsof these four systems, we calculatedthe RMSFs of the Cα atoms. Figure 3 features an overlay of the RMSFs from oneMD trajectory per system. The RMSFs for all three trajectories foreach of the four systems are provided in Figure S5. The greatest mobility is found at the loop regions in thepalm (residues 120–180) and little finger (residues 400–420)domains along with the entire thumb domain (residues 240–310),which consists of two longer alpha helices, one short α helix,and loops. The calculated RMSF plots are generally in agreement withthe B-factors detected in the X-ray experiments for the TTD3′-Astructure, as shown in Figure 3. However, the mobility of the thumb region is not as pronouncedand the mobility of the little finger domain is more pronounced inthe experiments than in the MD simulations.


Comparative Molecular Dynamics Studies of Human DNAPolymerase η
Comparison of the RMSFs of the four system from MD simulationsand the B-factor values from the crystal structure 3MR3, which weused as the initial coordinates for the system TTD3′-A.
© Copyright Policy
Related In: Results  -  Collection

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

fig3: Comparison of the RMSFs of the four system from MD simulationsand the B-factor values from the crystal structure 3MR3, which weused as the initial coordinates for the system TTD3′-A.
Mentions: To locate the flexible regionsof these four systems, we calculatedthe RMSFs of the Cα atoms. Figure 3 features an overlay of the RMSFs from oneMD trajectory per system. The RMSFs for all three trajectories foreach of the four systems are provided in Figure S5. The greatest mobility is found at the loop regions in thepalm (residues 120–180) and little finger (residues 400–420)domains along with the entire thumb domain (residues 240–310),which consists of two longer alpha helices, one short α helix,and loops. The calculated RMSF plots are generally in agreement withthe B-factors detected in the X-ray experiments for the TTD3′-Astructure, as shown in Figure 3. However, the mobility of the thumb region is not as pronouncedand the mobility of the little finger domain is more pronounced inthe experiments than in the MD simulations.

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.