Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments

Research output: Contribution to journal › Journal article › Research › peer-review

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Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments. / Bergonzo, Christina; Grishaev, Alexander; Bottaro, Sandro.

In: RNA, Vol. 28, No. 7, 2022, p. 937-946.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Bergonzo, C, Grishaev, A & Bottaro, S 2022, 'Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments', RNA, vol. 28, no. 7, pp. 937-946. https://doi.org/10.1261/rna.078888.121

APA

Bergonzo, C., Grishaev, A., & Bottaro, S. (2022). Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments. RNA, 28(7), 937-946. https://doi.org/10.1261/rna.078888.121

Vancouver

Bergonzo C, Grishaev A, Bottaro S. Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments. RNA. 2022;28(7):937-946. https://doi.org/10.1261/rna.078888.121

Author

Bergonzo, Christina ; Grishaev, Alexander ; Bottaro, Sandro. / Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments. In: RNA. 2022 ; Vol. 28, No. 7. pp. 937-946.

Bibtex

@article{4c8e52ff71e84c14820b01dd3c754034,
title = "Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments",
abstract = "We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and variations thereof. These structures are not present in the pool generated using FARFAR2. By comparing with available nuclear magnetic resonance (NMR) measurements, we show that the presence of both A-form-like and other extended conformations is necessary to quantitatively explain experimental data. To further validate our results, we measure solution X-ray scattering (SAXS) data on the RNA hexamer and find that simulations result in more compact structures than observed from these experiments. The integration of simulations with NMR via a maximum entropy approach shows that small modifications to the MD ensemble lead to an improved description of the conformational ensemble. Nevertheless, we identify persisting discrepancies in matching experimental SAXS data. ",
keywords = "integrative structural biology, molecular dynamics, NMR, SAXS",
author = "Christina Bergonzo and Alexander Grishaev and Sandro Bottaro",
note = "Publisher Copyright: {\textcopyright} 2022 Bergonzo et al.",
year = "2022",
doi = "10.1261/rna.078888.121",
language = "English",
volume = "28",
pages = "937--946",
journal = "RNA",
issn = "1355-8382",
publisher = "Cold Spring Harbor Laboratory Press",
number = "7",

}

RIS

TY - JOUR

T1 - Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments

AU - Bergonzo, Christina

AU - Grishaev, Alexander

AU - Bottaro, Sandro

N1 - Publisher Copyright: © 2022 Bergonzo et al.

PY - 2022

Y1 - 2022

N2 - We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and variations thereof. These structures are not present in the pool generated using FARFAR2. By comparing with available nuclear magnetic resonance (NMR) measurements, we show that the presence of both A-form-like and other extended conformations is necessary to quantitatively explain experimental data. To further validate our results, we measure solution X-ray scattering (SAXS) data on the RNA hexamer and find that simulations result in more compact structures than observed from these experiments. The integration of simulations with NMR via a maximum entropy approach shows that small modifications to the MD ensemble lead to an improved description of the conformational ensemble. Nevertheless, we identify persisting discrepancies in matching experimental SAXS data.

AB - We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and variations thereof. These structures are not present in the pool generated using FARFAR2. By comparing with available nuclear magnetic resonance (NMR) measurements, we show that the presence of both A-form-like and other extended conformations is necessary to quantitatively explain experimental data. To further validate our results, we measure solution X-ray scattering (SAXS) data on the RNA hexamer and find that simulations result in more compact structures than observed from these experiments. The integration of simulations with NMR via a maximum entropy approach shows that small modifications to the MD ensemble lead to an improved description of the conformational ensemble. Nevertheless, we identify persisting discrepancies in matching experimental SAXS data.

KW - integrative structural biology

KW - molecular dynamics

KW - NMR

KW - SAXS

U2 - 10.1261/rna.078888.121

DO - 10.1261/rna.078888.121

M3 - Journal article

C2 - 35483823

AN - SCOPUS:85132435873

VL - 28

SP - 937

EP - 946

JO - RNA

JF - RNA

SN - 1355-8382

IS - 7

ER -

ID: 312371345