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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

Stability of the Verlet-R-RATTLEintegration algorithm over 0.1μs microcanonical simulation of the Drew–Dickerson dodecamerwith time-steps ranging from 10 fs to 28 fs.
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fig5: Stability of the Verlet-R-RATTLEintegration algorithm over 0.1μs microcanonical simulation of the Drew–Dickerson dodecamerwith time-steps ranging from 10 fs to 28 fs.

Mentions: The stabilityof the Verlet-R-RATTLE algorithm was tested on theDrew–Dickerson double-helix. Microcanonical simulations of10 ns length were run with various time-steps: dt = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28 fs. The stability of thetotal energy is shown in Figure 5. The algorithmmaintains good stability up to dt = 22 fs resultingin an order of magnitude speedup compared to the commonly used all-atomtime-step of 2 fs (with SHAKE applied on hydrogens), and shows superiorstability compared to the quaternion-based rigid-body integrationscheme, applied previously19 to the modelof a DNA chain. The drift of the energy over a 20 ns trajectory withdt = 22 fs was only 0.017 kcal/mol, compared to ∼10kcal/mol over 1 ns simulation with the same time-step using a quaternionintegration scheme (see Figure 5 in ref (19)). The drifts of the energyand the RMS fluctuations for various time-steps are collected in Table 6. All canonical simulations and simulated annealingcycles utilized time-step dt = 10 fs.


DNA Duplex Formation with a Coarse-Grained Model.

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

Stability of the Verlet-R-RATTLEintegration algorithm over 0.1μs microcanonical simulation of the Drew–Dickerson dodecamerwith time-steps ranging from 10 fs to 28 fs.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Stability of the Verlet-R-RATTLEintegration algorithm over 0.1μs microcanonical simulation of the Drew–Dickerson dodecamerwith time-steps ranging from 10 fs to 28 fs.
Mentions: The stabilityof the Verlet-R-RATTLE algorithm was tested on theDrew–Dickerson double-helix. Microcanonical simulations of10 ns length were run with various time-steps: dt = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28 fs. The stability of thetotal energy is shown in Figure 5. The algorithmmaintains good stability up to dt = 22 fs resultingin an order of magnitude speedup compared to the commonly used all-atomtime-step of 2 fs (with SHAKE applied on hydrogens), and shows superiorstability compared to the quaternion-based rigid-body integrationscheme, applied previously19 to the modelof a DNA chain. The drift of the energy over a 20 ns trajectory withdt = 22 fs was only 0.017 kcal/mol, compared to ∼10kcal/mol over 1 ns simulation with the same time-step using a quaternionintegration scheme (see Figure 5 in ref (19)). The drifts of the energyand the RMS fluctuations for various time-steps are collected in Table 6. All canonical simulations and simulated annealingcycles utilized time-step dt = 10 fs.

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