engleski

Enhanced sampling of nucleobase assemblies in water: extracting structural motifs from simulations

The properties of systems like aggregates in solutions are controlled by interactions between the molecular units. In this work we have focused on nucleobase assemblies in water. Nucleobases and their specific base pairing is the paradigm of molecular recognition in nature. For computational prediction of the structure of molecular assemblies enhanced sampling techniques are ideally requested. In this work we explore the formation of N-mer nucleobase assemblies (N = 2 – 8) with classical potentials, combined with well- tempered metadynamics. The AMBER99 RNA force field was parameterized in order to avoid overestimation of stacking interaction. We have employed both a) a combination of 2 collective variables defined as contact numbers for pi-stacking and Watson-Crick hydrogen bonding interactions b) a newly developed descriptor based on distance and orientation of molecular pairs. Finally, on the smallest assemblies, we plan to benchmark the results with QM/MM calculations in order to validate the method.

nucleobase assemblies ; structural motifs ; molecular dynamics

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