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DNA Duplex Formation with a Coarse-Grained Model.

Maciejczyk M, Spasic A, Liwo A, Scheraga HA - J Chem Theory Comput (2014)

Bottom Line: Chem. 2010, 31, 1644].Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model.It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

View Article: PubMed Central - PubMed

Affiliation: Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury , 11-041 Olsztyn, Poland.

ABSTRACT
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem. 2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

No MeSH data available.


Related in: MedlinePlus

Same as Figure 7 but for the 3BSE hexadecamer.
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fig8: Same as Figure 7 but for the 3BSE hexadecamer.

Mentions: The folding efficiency oflonger polymers decreases as the dimensionalityof phases spaces increases (see Table 5). 16%of long trajectories of 3BSE molecule led to final structures with more than 75%of native contacts (13–16 contacts). For the 2JYK molecule, the foldingrate is almost the same as that for 3BSE and equals 15%. Nevertheless, the energyvs RMSD graphs (Figures 8 and 9) are qualitatively similar to these obtained for 1BNA molecule(Figure 7). In both cases, two clusters ofantiparallel and parallel dsDNAs are clearly visible and correct—antiparallelcluster has mean potential energy around 20 kcal/mol lower than thisof incorrect—parallel dsDNA cluster. These values should effectivelydiscriminate misfolded structures in the real-, long-time foldingprocess. This mean-energy difference increases to 22 kcal/mol forthe longest 2JYK molecule. The energy-minimized reference structures, marked by biggerdot in Figures 8 and 9, have RMSD only 0.6 Å away from original structure. In bothcases, the reference structures have potential energy around 10 kcal/mollower than these obtained from simulated annealing procedure. Thisobservation suggests that longer cooling process should lead to improvementsin geometry of final structures, as the minimum of potential energywas not reached by any simulated annealing cycle for longer modelsystems.


DNA Duplex Formation with a Coarse-Grained Model.

Maciejczyk M, Spasic A, Liwo A, Scheraga HA - J Chem Theory Comput (2014)

Same as Figure 7 but for the 3BSE hexadecamer.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230386&req=5

fig8: Same as Figure 7 but for the 3BSE hexadecamer.
Mentions: The folding efficiency oflonger polymers decreases as the dimensionalityof phases spaces increases (see Table 5). 16%of long trajectories of 3BSE molecule led to final structures with more than 75%of native contacts (13–16 contacts). For the 2JYK molecule, the foldingrate is almost the same as that for 3BSE and equals 15%. Nevertheless, the energyvs RMSD graphs (Figures 8 and 9) are qualitatively similar to these obtained for 1BNA molecule(Figure 7). In both cases, two clusters ofantiparallel and parallel dsDNAs are clearly visible and correct—antiparallelcluster has mean potential energy around 20 kcal/mol lower than thisof incorrect—parallel dsDNA cluster. These values should effectivelydiscriminate misfolded structures in the real-, long-time foldingprocess. This mean-energy difference increases to 22 kcal/mol forthe longest 2JYK molecule. The energy-minimized reference structures, marked by biggerdot in Figures 8 and 9, have RMSD only 0.6 Å away from original structure. In bothcases, the reference structures have potential energy around 10 kcal/mollower than these obtained from simulated annealing procedure. Thisobservation suggests that longer cooling process should lead to improvementsin geometry of final structures, as the minimum of potential energywas not reached by any simulated annealing cycle for longer modelsystems.

Bottom Line: Chem. 2010, 31, 1644].Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model.It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

View Article: PubMed Central - PubMed

Affiliation: Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury , 11-041 Olsztyn, Poland.

ABSTRACT
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem. 2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

No MeSH data available.


Related in: MedlinePlus