Probabilistic Interpretation of NMR J-Couplings Determines BI-BII State Equilibria in DNA

0562866 - ÚOCHB 2023 RIV US eng J - Journal Article
Fukal, Jiří - Zgarbová, M. - Jurečka, P. - Šebera, Jakub - Sychrovský, Vladimír
Probabilistic Interpretation of NMR J-Couplings Determines BI-BII State Equilibria in DNA.
Journal of Chemical Theory and Computation. Roč. 18, č. 11 (2022), s. 6989-6999. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA19-13436S
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : molecular dynamics simulations * phosphorus chemical shifts * nucleic acid backbone
OECD category: Biophysics
Impact factor: 5.5, year: 2022
Method of publishing: Limited access
https://doi.org/10.1021/acs.jctc.2c00733

Interpretation of 3JP,H3′ NMR scalar spin-spin coupling constants in DNA becomes more reliable by including distinct structural states such as BI and BII, using the weighted-static or, better still, the recently implemented adiabatic-MD (Ad-MD) method. The calculation method employs an adiabatic (Ad) dependence of 3JP,H3′ coupling on NMR-assigned torsion angle, ϵ, weighted by P(ϵ) probability distribution calculated by molecular dynamics (MD). Ad-MD calculations enable cross-validation of the bsc1, OL15, and OL21 force fields and various parametrizations of the Karplus equation describing the dependence of 3JP,H3′ coupling on ϵ torsion (KE). The mean absolute deviation of Ad-MD 3JP,H3′ couplings from the experimental values in Dickerson-Drew DNA is comparable to the scatter of 3JP,H3′ couplings among four separate NMR experiments. A commonly accepted assumption of homogeneity of one kind of structure-dynamic state within DNA (BI or BII) is questionable because the principal characteristics of relevant P(ϵ) probabilities (shapes and positioning) vary with DNA sequence. The theory outlined in the present work sets limits to future reparameterization of MD force fields, as relevant to NMR data.
Permanent Link: https://hdl.handle.net/11104/0335048