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Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

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López-Tarifa P., Hervé du Penhoat M.-A., Vuilleumier R., Gaigeot M.-P., Rothlisberger U., Tavernelli I., Le Padellec A., Champeaux J.-P., Alcamí M., Moretto-Capelle P., Martín F., Politis M.-F.

Open Physics

2014

vol. 12

issue 2

97-102

We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.

The pH optimum of native uracil-DNA glycosylase of Archaeoglobus fulgidus compared to recombinant enzyme indicates adaption to cytosolic pH

88%

Knævelsrud I., Kazazic S., Birkeland N.-K., Bjelland S.

Acta Biochimica Polonica

2014

vol. 61

issue 2

393-395

Uracil-DNA glycosylase of Archaeoglobus fulgidus (Afung) in cell extracts exhibited maximal activity around pH 6.2 as compared to pH 4.8 for the purified recombinant enzyme expressed in Escherichia coli. Native Afung thus seems to be adapted to the intracellular pH of A. fulgidus, determined to be 7.0±0.1. Both recombinant and native Afung exhibited a broad temperature optimum for activity around 80°C, reflecting the A. fulgidus optimal growth temperature of 83°C. Adaption to the neutral conditions in the A. fulgidus cytoplasm might be due to covalent modifications or accessory factors, or due to a different folding when expressed in the native host.

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1 Acta Biochimica Polonica

1 Open Physics

2 2014

1 Alcamí M.

1 Birkeland N.-K.

1 Bjelland S.

1 Champeaux J.-P.

1 Gaigeot M.-P.

1 Hervé du Penhoat M.-A.

1 Kazazic S.

1 Knævelsrud I.

1 Le Padellec A.

1 López-Tarifa P.

1 Martín F.

1 Moretto-Capelle P.

1 Politis M.-F.

1 Rothlisberger U.

1 Tavernelli I.

1 Vuilleumier R.

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Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

The pH optimum of native uracil-DNA glycosylase of Archaeoglobus fulgidus compared to recombinant enzyme indicates adaption to cytosolic pH