A Combined ONIOM Quantum Chemical−Molecular Dynamics Study of Zinc−Uracil Bond Breaking in Yeast Cytosine Deaminase
نویسندگان
چکیده
منابع مشابه
A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase.
A QM/MM method that combines ONIOM quantum chemistry and molecular dynamics is developed and applied to a step in the deamination of cytosine to uracil in yeast cytosine deaminase (yCD). A two-layer ONIOM calculation is used for the reaction complex, with an inner part treated at a high level for the chemical reaction (bond breaking) and a middle part treated at a lower level for relevant prote...
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Yeast cytosine deaminase (yCD), a zinc metalloenzyme of significant biomedical interest, is investigated by a series of molecular dynamics simulations in its free form and complexed with its reactant (cytosine), product (uracil), several reaction intermediates, and an intermediate analogue. Quantum chemical calculations, used to construct a model for the catalytic Zn ion with its ligands (two c...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2006
ISSN: 1520-6106,1520-5207
DOI: 10.1021/jp064301s