Theoretical study of mechanisms for the hydrolytic deamination of cytosine <i>via</i> steered molecular dynamic simulations

Tolosa, S.; Sansón, J.A.; Hidalgo, Antonio

doi:10.1039/c8ra07390b

Cited by 4 publications

(1 citation statement)

References 64 publications

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“…Long-range electrostatic interactions were considered by the Ewald summation (Ewald, 1921) and the Jarzynski's equality (Jarzynski, 1997) was used to calculate Gibbs energy differences between two equilibrium states. The activation and reaction energies were determined through the evolution of the process, as has been shown in several works (Tolosa et al, 2014, 2016, 2017a,b, 2018a,b; Tolosa et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

Theoretical Study of Adenine to Guanine Transition Assisted by Water and Formic Acid Using Steered Molecular Dynamic Simulations

2019

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The free energy profile of the adenine to guanine transition in the gas and aqueous phases was obtained by applying steered molecular dynamic (SMD) simulations. Three processes were considered to explain the mechanism assisted by water and formic acid molecules. The first process is hydrolytic deamination of adenine, then oxidation of the hypoxanthine previously formed, and finally, the animation from xanthine to guanine. In the gas phase these processes indicate a slow and not spontaneous conversion (Δ G g = 4.07 kcal·mol −1 , k = 5.59·10 −40 s −1 ), and a lifetime for guanine of τ = 7.75·10 +22 s. The presence of solvent makes the transition more difficult by increasing the reaction energy to 26.90 kcal·mol −1 and decreasing the speed of the process to 1.63·10 −55 s −1 . However, it decreases the energy of the deamination process to −9.63 kcal·mol −1 and the lifetime of guanine base to τ = 6.85·10 +17 s when the surrounding medium used in the transition process is aqueous. The results show that the guanine could participate in genetic mutations based on the lifetimes obtained. Transition states and intermediates structures were analyzed at the molecular dynamic level. This allows to follow the mechanism over time and to calculate thermodynamic and kinetic properties.

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Section: Methodsmentioning

confidence: 99%

Theoretical Study of Adenine to Guanine Transition Assisted by Water and Formic Acid Using Steered Molecular Dynamic Simulations

2019

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Mechanisms of the T-A to C-G transition studied by SMD simulations: Deamination vs tautomerisation

Tolosa

Sansón

Hidalgo

2020

Journal of Molecular Liquids

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A procedure to understanding the C-G to A-T transversion. SMD simulations from guanine oxidation pathways assisted by one H2O2 molecule in the C-G basis pair

Tolosa

Sansón

Hidalgo

2020

Journal of Molecular Liquids

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Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

Abstract: Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

Cited by 4 publications

References 64 publications

Theoretical Study of Adenine to Guanine Transition Assisted by Water and Formic Acid Using Steered Molecular Dynamic Simulations

Theoretical Study of Adenine to Guanine Transition Assisted by Water and Formic Acid Using Steered Molecular Dynamic Simulations

Mechanisms of the T-A to C-G transition studied by SMD simulations: Deamination vs tautomerisation

A procedure to understanding the C-G to A-T transversion. SMD simulations from guanine oxidation pathways assisted by one H2O2 molecule in the C-G basis pair

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