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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

Coarse-grained representation of fragments of the DNA chain superimposedon the atomic representation. Four basic building blocks A, T, G,C attached to small fragments of backbones are shown. Charged beads,which replace phosphate groups, are marked red; neutral beads, whichreplace deoxyriboses, are marked dark blue. Dipolar beads have differentcolors for different bases: A, pink; G, green; T, cyan; and C, yellow.Dipolar beads symbols are defined for all building blocks. The internaldegrees of freedom used for the definition of the bonded part of thepotential energy function (eq 2) are definedin Tables 1–4. For clarity, symbols of beads used for definition of bonded potentialsof the backbone are shown for thymine only. The longer fragment ofcoarse-grained strand of DNA with ATGC sequence overlapped on theatomic model is shown in the right panel. Sequential numbers of consecutivebuilding blocks are assigned.
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fig1: Coarse-grained representation of fragments of the DNA chain superimposedon the atomic representation. Four basic building blocks A, T, G,C attached to small fragments of backbones are shown. Charged beads,which replace phosphate groups, are marked red; neutral beads, whichreplace deoxyriboses, are marked dark blue. Dipolar beads have differentcolors for different bases: A, pink; G, green; T, cyan; and C, yellow.Dipolar beads symbols are defined for all building blocks. The internaldegrees of freedom used for the definition of the bonded part of thepotential energy function (eq 2) are definedin Tables 1–4. For clarity, symbols of beads used for definition of bonded potentialsof the backbone are shown for thymine only. The longer fragment ofcoarse-grained strand of DNA with ATGC sequence overlapped on theatomic model is shown in the right panel. Sequential numbers of consecutivebuilding blocks are assigned.

Mentions: The DNA chain is built of six types of chemical units:phosphate group (P), deoxyribose (S), adenine (A), thymine (T), guanine(G), and cytosine (C). In the coarse-grained approximation, atomsthat constitute each unit are replaced by the three types of beadsdefined above. The deoxyribose ring is replaced by one neutral bead,the phosphate group is replaced by one charged bead and each baseis replaced by a set of dipolar beads. The distances between the dipolarbeads of each base are fixed.47 A schematicrepresentation of the coarse-grained units overlapped on their atomicrepresentation is shown in Figure 1. The parametrizationof the bead model is described in the Parametrization section.


DNA Duplex Formation with a Coarse-Grained Model.

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

Coarse-grained representation of fragments of the DNA chain superimposedon the atomic representation. Four basic building blocks A, T, G,C attached to small fragments of backbones are shown. Charged beads,which replace phosphate groups, are marked red; neutral beads, whichreplace deoxyriboses, are marked dark blue. Dipolar beads have differentcolors for different bases: A, pink; G, green; T, cyan; and C, yellow.Dipolar beads symbols are defined for all building blocks. The internaldegrees of freedom used for the definition of the bonded part of thepotential energy function (eq 2) are definedin Tables 1–4. For clarity, symbols of beads used for definition of bonded potentialsof the backbone are shown for thymine only. The longer fragment ofcoarse-grained strand of DNA with ATGC sequence overlapped on theatomic model is shown in the right panel. Sequential numbers of consecutivebuilding blocks are assigned.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Coarse-grained representation of fragments of the DNA chain superimposedon the atomic representation. Four basic building blocks A, T, G,C attached to small fragments of backbones are shown. Charged beads,which replace phosphate groups, are marked red; neutral beads, whichreplace deoxyriboses, are marked dark blue. Dipolar beads have differentcolors for different bases: A, pink; G, green; T, cyan; and C, yellow.Dipolar beads symbols are defined for all building blocks. The internaldegrees of freedom used for the definition of the bonded part of thepotential energy function (eq 2) are definedin Tables 1–4. For clarity, symbols of beads used for definition of bonded potentialsof the backbone are shown for thymine only. The longer fragment ofcoarse-grained strand of DNA with ATGC sequence overlapped on theatomic model is shown in the right panel. Sequential numbers of consecutivebuilding blocks are assigned.
Mentions: The DNA chain is built of six types of chemical units:phosphate group (P), deoxyribose (S), adenine (A), thymine (T), guanine(G), and cytosine (C). In the coarse-grained approximation, atomsthat constitute each unit are replaced by the three types of beadsdefined above. The deoxyribose ring is replaced by one neutral bead,the phosphate group is replaced by one charged bead and each baseis replaced by a set of dipolar beads. The distances between the dipolarbeads of each base are fixed.47 A schematicrepresentation of the coarse-grained units overlapped on their atomicrepresentation is shown in Figure 1. The parametrizationof the bead model is described in the Parametrization section.

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