The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA

0547591 - ÚOCHB 2023 RIV US eng J - Článek v odborném periodiku
Fukal, Jiří - Buděšínský, Miloš - Páv, Ondřej - Jurečka, P. - Zgarbová, M. - Šebera, Jakub - Sychrovský, Vladimír
The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA.
Journal of Computational Chemistry. Roč. 43, č. 2 (2022), s. 132-143. ISSN 0192-8651. E-ISSN 1096-987X
Grant CEP: GA ČR(CZ) GA19-13436S
Výzkumná infrastruktura: e-INFRA CZ - 90140
Institucionální podpora: RVO:61388963
Klíčová slova: 31P NMR shift * DNA phosphate * MD averaging
Obor OECD: Biophysics
Impakt faktor: 3, rok: 2022
Způsob publikování: Omezený přístup
https://doi.org/10.1002/jcc.26778

A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31P NMR shift (δ31P) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.
Trvalý link: http://hdl.handle.net/11104/0323804