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

Autori
Ostojic, Tea ; Gunde, Miha ; Grisanti, Luca

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
PSI-K 2022 abstracts book / - , 2022, 95-95

Skup
Psi-k 2022 conference

Mjesto i datum
Lausanne, Švicarska, 22.08.2022. - 25.08.2022

Vrsta sudjelovanja
Poster

Vrsta recenzije
Nije recenziran

Ključne riječi
nucleobase assemblies ; structural motifs ; molecular dynamics

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Kemija

POVEZANOST RADA