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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
User Contributions:
Comment about this article or add new information about this topic:
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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
User Contributions:
Comment about this article or add new information about this topic:
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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
User Contributions:
Comment about this article or add new information about this topic:
- Abstracts: Molecular dynamics study of the active site of methylamine dehydrogenase
- Abstracts: Molecular simulations of physical aging in polymer membrane materials. Molecular simulation and experimental study of substituted polyacetylenes: Fractional free volume, cavity size distributions and diffusion coefficients
- Abstracts: Molecular dynamics simulations of lithium alkyl carbonates. Dynamical properties. Passive transport of [C.sub.60] fullerenes through a lipid membrane: a molecular dynamics simulation study
- Abstracts: Surface-enhanced Raman scattering studies on aggregated silver nanoplates in aqueous solution. Dendron-like growth of silver nanoparticles using a water-soluble oligopeptide
- Abstracts: Role of molecular anchor groups in molecule-to-semiconductor electron transfer. Depth profiling of charging effect of Si nanocystals embedded in Si[O.sub.2]: A study of charge diffusion among Si nanocrystals