On the Role of London Dispersion Forces in Biomolecular Structure Determination

0367999 - ÚOCHB 2012 RIV US eng J - Journal Article
Kolář, Michal - Kubař, T. - Hobza, Pavel
On the Role of London Dispersion Forces in Biomolecular Structure Determination.
Journal of Physical Chemistry B. Roč. 115, č. 24 (2011), s. 8038-8046. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT LC512; GA ČR GAP208/11/0295
Grant - others:Korea Science and Ingineering Foundation(KR) R32-2008-000-10180-0; European Scince Found(XE) CZ.1.05/2.1.00/03.0058
Institutional research plan: CEZ:AV0Z40550506
Keywords : dispersion interaction * DNA * molecular dynamics
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.696, year: 2011

A DNA dodecamer and the methyladenine...methylthymine complex in aqueous environment have been studied by means of molecular dynamics simulation, with a modified force field accounting for the hypothetical absence of London dispersion forces. While the hydrophobic effect of the solvent accounts for the sufficient stabilization of the complex, the appearance of the native biomolecular conformation is attributed to the London dispersion forces. Thus, the London dispersion seems to provide the native structure of a biomolecular complex with the largest additional stabilization, preferring it among several possible aggregated structures. The observations are affected by the construction of the modified force field, and this effect is discussed thoroughly as well as the description of nonbonded interactions with the current biomolecular force fields.
Permanent Link: http://hdl.handle.net/11104/0006696