A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase

Article Abstract:

A QM/MM method is developed by combining ONIOM quantum chemistry and molecular dynamics and applied to a step in the deamination of cytosine to uracil in yeast cytosine deaminase (yCD). It is observed that cleavage of the Zn-O4 bond occurs through a pentacoordinated Zn transition state complex and E64 has a significant role as a proton shuttle in the deamination reaction and also aids the cleavage of the zinc-oxygen bond between the catalytic zinc and the deamination product uracil so that the product can be released.

Science & research, Research, Molecular dynamics, Zinc compounds, Report, Uracil

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A systematic investigation of hydrogen-bonding effects on the [O.sup.17], [N.sup.14], and [H.sup.2] nuclear quadrupole resonance parameters of anhydrous and monohydrated cytosine crystalline structures: A density functional theory study

Article Abstract:

A systematic computational study is carried out to investigate the [O.sup.17], [N.sup.14], and [H.sup.2] nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine has indicated the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.

Usage, Crystals, Crystal structure, Hydrogen bonding, Hydrogen bonds

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Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks

Article Abstract:

A new series of hetero-ring-expanded guanine analogs, which might serve as building blocks for potential biological applications and the development of molecular electronic devices are presented.

Deoxyribonucleic Acid, Guanine, DNA, Ionization, Properties

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