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Molecular simulation of adsorption from dilute solutions

100%

Billes W., Tscheliessnig R., Fischer J.

Acta Biochimica Polonica

2005

tom 52

nr 3

Adsorption of biomolecules on surfaces is a perennial and general challenge relevant to many fields in biotechnology. A change of the Helmholtz free energy ΔA takes place when a molecule becomes adsorbed out of a bulk solution. The purpose of our investigations is to explore routes for the calculation of ΔA by molecular simulations. ΔA can be obtained both by integration over the mean force on a molecule and via the local density. It turns out that the route via the potential of mean force prevails over the latter due to better consistency. In this work we present results for systems of 1-centre and 2-centre Lennard-Jones mixtures at a 9/3 Lennard-Jones wall.

The geometry of intercalation complex of antitumor mitoxantrone and ametantrone with DNA: Molecular dynamics simulations

75%

Mazerski J., Martelli S., Borowski E.

Acta Biochimica Polonica

1998

tom 45

nr 1

Intercalative binding of the antitumor drugs ametantrone and mitoxantrone to the dodecamer duplex d(CGCGAGCTCGCG)2 was studied by applying molecular dynamics in water with the GROMOS 87 force field. A number of reasonable binding orientations were tested by short pre-simulations. It was shown that in energetically favorable orientation the anthraquinone chromophore is perpendicular to the direction of inter-base hydrogen bonds. Helically shaped side-chains of the drugs fit to the minor groove. The best orientation obtained in pre-simulations was applied in the main simulations. Small but significant differences were found between structures of intercalation complexes of the two drugs with the dodecamer duplex, the mitoxantrone complex possessing more favorable energy. The molecular nature of interactions responsible for those differences has been discussed.

Ograniczanie wyników

2 Acta Biochimica Polonica

1 Billes W.

1 Borowski E.

1 Fischer J.

1 Martelli S.

1 Mazerski J.

1 Tscheliessnig R.

1 2005

1 1998

Wyniki wyszukiwania

Molecular simulation of adsorption from dilute solutions

The geometry of intercalation complex of antitumor mitoxantrone and ametantrone with DNA: Molecular dynamics simulations