The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31 P NMR shift in DNA
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
34729803
DOI
10.1002/jcc.26778
Knihovny.cz E-zdroje
- Klíčová slova
- 31P NMR shift, DNA phosphate, MD averaging,
- MeSH
- DNA chemie MeSH
- fosfor MeSH
- konformace nukleové kyseliny MeSH
- nukleární magnetická rezonance biomolekulární * MeSH
- simulace molekulární dynamiky * MeSH
- teorie funkcionálu hustoty MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA MeSH
- fosfor MeSH
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 31 P 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 31 P 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.
Faculty of Mathematics and Physics Charles University Prague Czech Republic
Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague Czech Republic
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