Issue 61, 2018, Issue in Progress

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. Two pathways were considered to explain the mechanism of this process, where the water molecule attacks the C–N bond to give an intermediate (an amino–hydroxy–oxo structure in the A-path, and a hydroxy–oxo in the B-path) as the determinant step of reaction. Stationary structures along both energy profiles were analyzed at molecular dynamics level, obtaining states with higher free energies than those from electronic calculations in the gas phase and in solution described as a continuous medium. From the results obtained, the more complex A-pathway, with five steps, was kinetically the most favorable (with an endergonic reaction energy of 7.41 kcal mol−1, a high barrier of 67.53 kcal mol−1, and a small velocity constant k2 = 1.80 × 10−37 s−1), concluding that the uracil base can participate in a spontaneous genetic mutation since the uracil–ammonia complex has a long lifetime of 6.10 × 1027 s. This process turns out exergonic and faster when carried out in gas phase simulation or electronic calculation with a continuous medium, due to the disappearance of explicit water molecules that can compete with the assistant molecule.

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

Supplementary files

Article information

Article type
Paper
Submitted
04 Sep 2018
Accepted
04 Oct 2018
First published
11 Oct 2018
This article is Open Access
Creative Commons BY-NC license

RSC Adv., 2018,8, 34867-34876

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

S. Tolosa, J. A. Sansón and A. Hidalgo, RSC Adv., 2018, 8, 34867 DOI: 10.1039/C8RA07390B

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. You can use material from this article in other publications, without requesting further permission from the RSC, provided that the correct acknowledgement is given and it is not used for commercial purposes.

To request permission to reproduce material from this article in a commercial publication, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party commercial publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements