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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

One of four model systems used in deriving the bondedpotentials.Model systems for parametrization were created from three-nucleotidechains by removing the bases from the nucleotides at the 5′-and 3′-end and replacing them with methyl groups. The middlenucleotide was left unchanged and can be cytosine (in the figure),thymine, adenine, or guanine.
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fig3: One of four model systems used in deriving the bondedpotentials.Model systems for parametrization were created from three-nucleotidechains by removing the bases from the nucleotides at the 5′-and 3′-end and replacing them with methyl groups. The middlenucleotide was left unchanged and can be cytosine (in the figure),thymine, adenine, or guanine.

Mentions: The parameters of all virtual bond, virtual-bond angle, and virtual-bonddihedral angle degrees of freedom were computed by using four modelsystems, which were obtained from three-nucleotide backbones withmethyl end groups. The base of the middle nucleotide was either adenine,cytosine, guanine, or thymine, for a total of four different modelsystems. One such system with a cytosine base in the middle nucleotideis shown in Figure 3. This is a minimal sizemolecule for which every internal degree of freedom of our coarse-grainedmodel can be defined. Terminal bases were removed to avoid implicitlyincluding electrostatic and van der Waals interactions of bases sinceour model has the nonbonded parameters derived separately.47


DNA Duplex Formation with a Coarse-Grained Model.

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

One of four model systems used in deriving the bondedpotentials.Model systems for parametrization were created from three-nucleotidechains by removing the bases from the nucleotides at the 5′-and 3′-end and replacing them with methyl groups. The middlenucleotide was left unchanged and can be cytosine (in the figure),thymine, adenine, or guanine.
© Copyright Policy
Related In: Results  -  Collection

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

fig3: One of four model systems used in deriving the bondedpotentials.Model systems for parametrization were created from three-nucleotidechains by removing the bases from the nucleotides at the 5′-and 3′-end and replacing them with methyl groups. The middlenucleotide was left unchanged and can be cytosine (in the figure),thymine, adenine, or guanine.
Mentions: The parameters of all virtual bond, virtual-bond angle, and virtual-bonddihedral angle degrees of freedom were computed by using four modelsystems, which were obtained from three-nucleotide backbones withmethyl end groups. The base of the middle nucleotide was either adenine,cytosine, guanine, or thymine, for a total of four different modelsystems. One such system with a cytosine base in the middle nucleotideis shown in Figure 3. This is a minimal sizemolecule for which every internal degree of freedom of our coarse-grainedmodel can be defined. Terminal bases were removed to avoid implicitlyincluding electrostatic and van der Waals interactions of bases sinceour model has the nonbonded parameters derived separately.47

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