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Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA.

Benítez AA, Hernández Cifre JG, Díaz Baños FG, de la Torre JG - BMC Biophys (2015)

Bottom Line: The general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution.Our simulation results also compare quite well with other numerical data.An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Química Física, Universidad de Murcia, Murcia, 30100 Spain.

ABSTRACT

Background: The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. The elastic interactions are modeled by a set of Hooke springs that form a minimalist elastic network. The Brownian dynamics technique is employed to simulate the time evolution of the RNA conformations.

Results: That scheme is applied to the 5S ribosomal RNA of E. Coli and the yeast phenylalanine transfer RNA. From the Brownian trajectory, several solution properties (radius of gyration, translational diffusion coefficient, and a rotational relaxation time) are calculated. For the case of yeast phenylalanine transfer RNA, the time evolution and the probability distribution of the inter-arm angle is also computed.

Conclusions: The general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution. Our simulation results also compare quite well with other numerical data. An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics.

No MeSH data available.


Related in: MedlinePlus

Double-helical model for RNA. a All the connectors supported by a given bead i (beads connected to i are labeled using i as reference). b All the connectors between first neighbors beads along each helix piece (i.e. connectors between each bead i and beads i±1). Beads appear smaller than in the real model (where they are tangent) for the sake of a better visualization of the connectors
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Fig2: Double-helical model for RNA. a All the connectors supported by a given bead i (beads connected to i are labeled using i as reference). b All the connectors between first neighbors beads along each helix piece (i.e. connectors between each bead i and beads i±1). Beads appear smaller than in the real model (where they are tangent) for the sake of a better visualization of the connectors

Mentions: Beads are the model elements where the friction and the intra-molecular interactions take place. There are two types of intra-molecular interactions in the model: elastic interactions (represented by Hooke springs) and excluded volume interactions. Hooke springs are used to keep the connectivity between beads along the strand as well as the secondary structure in the helical regions. Also, they introduce the required degree of flexibility in the model [25] and form a kind of elastic network (see Fig. 2). For the sake of minimizing the amount of interactions but keeping the double-helical shape and the stiffness at short scale, we found it adequate [28] to connect each bead i (within every double-helical region) to:


Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA.

Benítez AA, Hernández Cifre JG, Díaz Baños FG, de la Torre JG - BMC Biophys (2015)

Double-helical model for RNA. a All the connectors supported by a given bead i (beads connected to i are labeled using i as reference). b All the connectors between first neighbors beads along each helix piece (i.e. connectors between each bead i and beads i±1). Beads appear smaller than in the real model (where they are tangent) for the sake of a better visualization of the connectors
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4666080&req=5

Fig2: Double-helical model for RNA. a All the connectors supported by a given bead i (beads connected to i are labeled using i as reference). b All the connectors between first neighbors beads along each helix piece (i.e. connectors between each bead i and beads i±1). Beads appear smaller than in the real model (where they are tangent) for the sake of a better visualization of the connectors
Mentions: Beads are the model elements where the friction and the intra-molecular interactions take place. There are two types of intra-molecular interactions in the model: elastic interactions (represented by Hooke springs) and excluded volume interactions. Hooke springs are used to keep the connectivity between beads along the strand as well as the secondary structure in the helical regions. Also, they introduce the required degree of flexibility in the model [25] and form a kind of elastic network (see Fig. 2). For the sake of minimizing the amount of interactions but keeping the double-helical shape and the stiffness at short scale, we found it adequate [28] to connect each bead i (within every double-helical region) to:

Bottom Line: The general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution.Our simulation results also compare quite well with other numerical data.An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Química Física, Universidad de Murcia, Murcia, 30100 Spain.

ABSTRACT

Background: The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. The elastic interactions are modeled by a set of Hooke springs that form a minimalist elastic network. The Brownian dynamics technique is employed to simulate the time evolution of the RNA conformations.

Results: That scheme is applied to the 5S ribosomal RNA of E. Coli and the yeast phenylalanine transfer RNA. From the Brownian trajectory, several solution properties (radius of gyration, translational diffusion coefficient, and a rotational relaxation time) are calculated. For the case of yeast phenylalanine transfer RNA, the time evolution and the probability distribution of the inter-arm angle is also computed.

Conclusions: The general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution. Our simulation results also compare quite well with other numerical data. An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics.

No MeSH data available.


Related in: MedlinePlus