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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F22%3A00562866" target="_blank" >RIV/61388963:_____/22:00562866 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61989592:15310/22:73615885 RIV/68407700:21230/22:00360669

Výsledek na webu

<a href="https://doi.org/10.1021/acs.jctc.2c00733" target="_blank" >https://doi.org/10.1021/acs.jctc.2c00733</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.2c00733" target="_blank" >10.1021/acs.jctc.2c00733</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10610 - Biophysics

Projekt

<a href="/cs/project/GA19-13436S" target="_blank" >GA19-13436S: Nový vhled do struktury a dynamiky páteře nukleových kyselin užitím pokročilých DFT-MD výpočtů a 31P NMR spektroskopie</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

1549-9626

Svazek periodika

18

Číslo periodika v rámci svazku

11

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

11

Strana od-do

6989-6999

Kód UT WoS článku

000877047900001

EID výsledku v databázi Scopus

2-s2.0-85139557514