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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

Relations between global coordinates (R,Q) and distances between beads for interactions of (a) two sphericalrigid-bodies, where there is only one distance rij = /Rij/; (b) spherical and planar rigid body, where distances between interactingbeads are functions of global coordinates given by eq 9; and (c) two planar rigid-bodies, where distances betweeninteracting beads are given by eq 13.
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fig2: Relations between global coordinates (R,Q) and distances between beads for interactions of (a) two sphericalrigid-bodies, where there is only one distance rij = /Rij/; (b) spherical and planar rigid body, where distances between interactingbeads are functions of global coordinates given by eq 9; and (c) two planar rigid-bodies, where distances betweeninteracting beads are given by eq 13.

Mentions: Each chemical unit in the coarse-grained approximation constitutesa rigid body. The origin of the local coordinate frame of each rigidbody is located at its center of mass, and its axes are aligned withthe principal axes of the moment of inertia tensor. The position andorientation of each rigid body with respect to the global coordinateframe is described by a vector–tensor pair (R,Q), where R is the position of the center ofmass and Q is the rotation matrix. In the model, twotypes of rigid bodies can be distinguished—spherical (P andS) and planar (A,T,G,C). The spherical rigid bodies interact withother particles only by central forces (see “Potential Energy Function”), and their orientationis irrelevant; therefore, a constant rotation matrix Qsphere = const is assigned to them. The orientation ofeach planar rigid body is described by a 3 × 2 rotation matrix Qplanar and varies as the rigid body changes itsorientation during a simulation run. The geometry of the chain isdefined in vector–tensor space (Ri,Qi) where i = 1,...,N and N is thenumber of rigid bodies. The relations between global coordinates (Ri, Qi) and distances between various beads, used for definitionsof nonbonded interactions, are shown in Figure 2.


DNA Duplex Formation with a Coarse-Grained Model.

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

Relations between global coordinates (R,Q) and distances between beads for interactions of (a) two sphericalrigid-bodies, where there is only one distance rij = /Rij/; (b) spherical and planar rigid body, where distances between interactingbeads are functions of global coordinates given by eq 9; and (c) two planar rigid-bodies, where distances betweeninteracting beads are given by eq 13.
© Copyright Policy
Related In: Results  -  Collection

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

fig2: Relations between global coordinates (R,Q) and distances between beads for interactions of (a) two sphericalrigid-bodies, where there is only one distance rij = /Rij/; (b) spherical and planar rigid body, where distances between interactingbeads are functions of global coordinates given by eq 9; and (c) two planar rigid-bodies, where distances betweeninteracting beads are given by eq 13.
Mentions: Each chemical unit in the coarse-grained approximation constitutesa rigid body. The origin of the local coordinate frame of each rigidbody is located at its center of mass, and its axes are aligned withthe principal axes of the moment of inertia tensor. The position andorientation of each rigid body with respect to the global coordinateframe is described by a vector–tensor pair (R,Q), where R is the position of the center ofmass and Q is the rotation matrix. In the model, twotypes of rigid bodies can be distinguished—spherical (P andS) and planar (A,T,G,C). The spherical rigid bodies interact withother particles only by central forces (see “Potential Energy Function”), and their orientationis irrelevant; therefore, a constant rotation matrix Qsphere = const is assigned to them. The orientation ofeach planar rigid body is described by a 3 × 2 rotation matrix Qplanar and varies as the rigid body changes itsorientation during a simulation run. The geometry of the chain isdefined in vector–tensor space (Ri,Qi) where i = 1,...,N and N is thenumber of rigid bodies. The relations between global coordinates (Ri, Qi) and distances between various beads, used for definitionsof nonbonded interactions, are shown in Figure 2.

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