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Studying interactions by molecular dynamics simulations at high concentration.

Fogolari F, Corazza A, Toppo S, Tosatto SC, Viglino P, Ursini F, Esposito G - J. Biomed. Biotechnol. (2012)

Bottom Line: In recent works, simulations using high concentration of interacting molecules have been performed.In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation.The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Udine, Italy. federico.fogolari@uniud.it

ABSTRACT
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

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Average of 〈cos⁡(θ)〉 versus time with standard deviations as bars, where 〈cos⁡(θ)〉 is the average cosine of the angle between two vectors rigidly anchored on the diffusing molecule at time 0 and at time t. Averaging is performed over 27 molecules. Data are from the simulation reported in [10].
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fig2: Average of 〈cos⁡(θ)〉 versus time with standard deviations as bars, where 〈cos⁡(θ)〉 is the average cosine of the angle between two vectors rigidly anchored on the diffusing molecule at time 0 and at time t. Averaging is performed over 27 molecules. Data are from the simulation reported in [10].

Mentions: The analysis of the rotational diffusional constants is provided by Figure 2. The value of 〈cos⁡(θ)〉 is computed as (1/3)tr⁡(R) where R is the matrix that describes the rotation of the molecule with respect to its orientation at the start of the simulation, and tr⁡ denotes the Trace operation, as discussed in Section 2. The average 〈cos⁡(θ)〉 is further averaged over all 27 molecules, thus providing also standard deviation. The plot of 〈〈cos⁡(θ)〉〉 is reported in Figure 2. The time constant (9.6 ns) obtained fitting the decay with an exponential is larger than expected (8.7 ns), but still consistent with the size of the protein.


Studying interactions by molecular dynamics simulations at high concentration.

Fogolari F, Corazza A, Toppo S, Tosatto SC, Viglino P, Ursini F, Esposito G - J. Biomed. Biotechnol. (2012)

Average of 〈cos⁡(θ)〉 versus time with standard deviations as bars, where 〈cos⁡(θ)〉 is the average cosine of the angle between two vectors rigidly anchored on the diffusing molecule at time 0 and at time t. Averaging is performed over 27 molecules. Data are from the simulation reported in [10].
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3303702&req=5

fig2: Average of 〈cos⁡(θ)〉 versus time with standard deviations as bars, where 〈cos⁡(θ)〉 is the average cosine of the angle between two vectors rigidly anchored on the diffusing molecule at time 0 and at time t. Averaging is performed over 27 molecules. Data are from the simulation reported in [10].
Mentions: The analysis of the rotational diffusional constants is provided by Figure 2. The value of 〈cos⁡(θ)〉 is computed as (1/3)tr⁡(R) where R is the matrix that describes the rotation of the molecule with respect to its orientation at the start of the simulation, and tr⁡ denotes the Trace operation, as discussed in Section 2. The average 〈cos⁡(θ)〉 is further averaged over all 27 molecules, thus providing also standard deviation. The plot of 〈〈cos⁡(θ)〉〉 is reported in Figure 2. The time constant (9.6 ns) obtained fitting the decay with an exponential is larger than expected (8.7 ns), but still consistent with the size of the protein.

Bottom Line: In recent works, simulations using high concentration of interacting molecules have been performed.In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation.The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Udine, Italy. federico.fogolari@uniud.it

ABSTRACT
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

Show MeSH