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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.


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Lowest-energy structuresof 1BNA, 3BSE, and 2JYK molecules obtainedfrom extended simulatedannealing procedure, superimposed on experimental structures. Theirall-bead RMSDs are 2.1 Å, 3.1 Å, and 4.2 Å, respectively.The reference structures are shown in red. The backbone of the computedstructures is shown in blue and the bases are A (cyan), T (pink),G (green), C (yellow).
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fig10: Lowest-energy structuresof 1BNA, 3BSE, and 2JYK molecules obtainedfrom extended simulatedannealing procedure, superimposed on experimental structures. Theirall-bead RMSDs are 2.1 Å, 3.1 Å, and 4.2 Å, respectively.The reference structures are shown in red. The backbone of the computedstructures is shown in blue and the bases are A (cyan), T (pink),G (green), C (yellow).

Mentions: Figure 10 presents the three lowest-energystructures of tested molecules superimposed on their experimentalstructure. The all-bead RMSDs of 1BNA, 3BSE, and 2JYK molecules with respect to experimentalreferences are 2.1 Å, 3.1 Å, and 4.2 Å, respectively,and as expected, they increase with the length of polymers. All structuresclearly form double-helices, although some discrepancies of the geometryare visible, especially for the longest molecule, for which overestimationof the size of minor groove is clearly visible.


DNA Duplex Formation with a Coarse-Grained Model.

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

Lowest-energy structuresof 1BNA, 3BSE, and 2JYK molecules obtainedfrom extended simulatedannealing procedure, superimposed on experimental structures. Theirall-bead RMSDs are 2.1 Å, 3.1 Å, and 4.2 Å, respectively.The reference structures are shown in red. The backbone of the computedstructures is shown in blue and the bases are A (cyan), T (pink),G (green), C (yellow).
© Copyright Policy
Related In: Results  -  Collection

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

fig10: Lowest-energy structuresof 1BNA, 3BSE, and 2JYK molecules obtainedfrom extended simulatedannealing procedure, superimposed on experimental structures. Theirall-bead RMSDs are 2.1 Å, 3.1 Å, and 4.2 Å, respectively.The reference structures are shown in red. The backbone of the computedstructures is shown in blue and the bases are A (cyan), T (pink),G (green), C (yellow).
Mentions: Figure 10 presents the three lowest-energystructures of tested molecules superimposed on their experimentalstructure. The all-bead RMSDs of 1BNA, 3BSE, and 2JYK molecules with respect to experimentalreferences are 2.1 Å, 3.1 Å, and 4.2 Å, respectively,and as expected, they increase with the length of polymers. All structuresclearly form double-helices, although some discrepancies of the geometryare visible, especially for the longest molecule, for which overestimationof the size of minor groove is clearly visible.

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