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M Aida

Publications and source records attributed to M Aida.

89 records · Page 5Linked to original sources
PubMedDate not supplied

Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling.

Structural data of protein-DNA complex show redundancy and flexibility in base-amino acid interactions. To understand the origin of the specificity in protein-DNA recognition, we calculated the interaction free energy, enthalpy, entropy, and minimum energy maps for AT-Asn, GC-Asn, AT-Ser, and GC-Ser by means of a set of ab initio force field with extensive conformational sampling. We found that the most preferable interactions in these pairs are stabilized by hydrogen bonding, and are mainly enthalpy driven. However, minima in the free energy maps are not necessarily the same as those in the minimum energy map or enthalpy maps, due to the entropic effect. The effect of entropy is particularly important in the case of GC-Asn. Experimentally observed structures of base-amino acid interactions are within preferable regions in the calculated free energy maps, where there are many different interaction configurations with similar energy. The full geometry optimization procedure using ab initio molecular orbital method was applied to get the optimal interaction geometries for AT-Asn, GC-Asn, AT-Ser, and GC-Ser. We found that there are various base-amino acid combinations with similar interaction energies. These results suggest that the redundancy and conformational flexibility in the base-amino acid interactions play an important role in the protein-DNA recognition.

Adenine↗
PubMedDate not supplied

Free radical chemistry of cigarette smoke and its implication in human cancer.

Multiple components in cigarette smoke were analyzed for their ability to form active oxygen species using a spin trapping agent, 5, 5-dimethyl-1-pyrroline-N-oxide. The main source of O2 and H2O2 was ascribed to polyphenols in a particulate phase, whereas a synergistic effect was also observed between these polyphenols and nicotine. The vapor phase contained a factor which produced OH from H2O2 which was identified as carbonyl sulfide. Nitric oxide in the vapor phase did not show such reactivity. The formation of an active oxygen species in cigarette smoke could provide an important clue to elucidate the mechanism of tobacco carcinogenesis, since they show genotoxic effects to induce DNA strand breaks as well as epigenetic effects to act as cell proliferation signals.

Humans↗