TY - JOUR

T1 - Exploring combined spin-labeling approach for structural studies of mRNA in the human ribosome

AU - Kolokolov, Mikhail

AU - Malygin, Alexey

AU - Graifer, Dmitri

AU - Meschaninova, Mariya

AU - Vorobyeva, Mariya A.

AU - Fedin, Matvey

AU - Krumkacheva, Olesya

AU - Bagryanskaya, Elena

PY - 2025/3/21

Y1 - 2025/3/21

N2 - In this study, we investigated the structural variability of mRNA in the human ribosome by comparing two spin-labeling strategies: one involving an mRNA analog bearing two spin labels attached to the ribose-phosphate backbone and the other placing labels at the nucleotide bases. The use of two strategies of spin labeling of mRNAs allowed us to study for the first time the effect of the structure and location of spin labels on the measured interspin distances in human ribosome complexes. Experiments using dipolar EPR spectroscopy, supported by molecular dynamics calculations, demonstrated that labels introduced at nucleotide bases provide a higher resolution between mRNA conformations in the ribosome mRNA channel, compared to labels introduced at the ribose-phosphate backbone. Although ribose-phosphate labeling turned out to be less informative on its own for studying mRNA conformations in the ribosome than the previously used base labeling, it can find application in other complex studies of the structure of RNAs and their complexes.

AB - In this study, we investigated the structural variability of mRNA in the human ribosome by comparing two spin-labeling strategies: one involving an mRNA analog bearing two spin labels attached to the ribose-phosphate backbone and the other placing labels at the nucleotide bases. The use of two strategies of spin labeling of mRNAs allowed us to study for the first time the effect of the structure and location of spin labels on the measured interspin distances in human ribosome complexes. Experiments using dipolar EPR spectroscopy, supported by molecular dynamics calculations, demonstrated that labels introduced at nucleotide bases provide a higher resolution between mRNA conformations in the ribosome mRNA channel, compared to labels introduced at the ribose-phosphate backbone. Although ribose-phosphate labeling turned out to be less informative on its own for studying mRNA conformations in the ribosome than the previously used base labeling, it can find application in other complex studies of the structure of RNAs and their complexes.

UR - https://www.mendeley.com/catalogue/7403aa1f-1ba8-32e7-8ac0-779071cfee2b/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-105000653418&origin=inward&txGid=edeba2fbaa5fbabae017b3a3eb29f18e

U2 - 10.1063/5.0245722

DO - 10.1063/5.0245722

M3 - Article

C2 - 40116317

VL - 162

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 11

ER -