Simulation of complex biomolecular systems: the ribosome challenge

LV Bock, S Gabrielli, MH Kolář… - Annual Review of …, 2023 - annualreviews.org
Large biomolecular systems are at the heart of many essential cellular processes. The
dynamics and energetics of an increasing number of these systems are being studied by …

DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling

OA Krumkacheva, GY Shevelev… - Nucleic Acids …, 2019 - academic.oup.com
A DNA molecule is under continuous influence of endogenous and exogenous damaging
factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP …

Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy

AA Malygin, OA Krumkacheva, DM Graifer… - Nucleic acids …, 2019 - academic.oup.com
The features of previously unexplored labile complexes of human 40S ribosomal subunits
with RNAs, whose formation is manifested in the cross-linking of aldehyde derivatives of …

Spin‐Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block

F Kaiser, B Endeward, A Collauto… - … A European Journal, 2022 - Wiley Online Library
Abstract The nitroxide TPA (2, 2, 5, 5‐tetramethyl‐pyrrolin‐1‐oxyl‐3‐acetylene) is an
excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are …

Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study

NE Sannikova, MI Kolokolov, TA Khlynova… - Physical Chemistry …, 2023 - pubs.rsc.org
The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable
importance in medicinal chemistry and drug discovery due to their promising potential in …

Paramagnetic species in catalysis research: a unified approach towards (the role of EPR in) heterogeneous, homogeneous and enzyme catalysis

M Bracci, PC Bruzzese, A Famulari, D Fioco, A Guidetti… - 2020 - books.rsc.org
Paramagnetic (open-shell) systems, including transition metal ions, radical intermediates
and defect centres, are often involved in catalytic transformations. Despite the prevalence of …

Electron-deficient N-oxyl radicals–new reagents for selective oxidative functionalization of organic substrates

IB Krylov, AS Budnikov, ER Lopat'Eva… - Journal of Physics …, 2021 - iopscience.iop.org
N-oxyl radicals are well known as one of the richest classes of long-living free radicals. They
are widely used as redox catalysts, mediators of living polymerization, contrast reagents for …

Advanced EPR spectroscopy for investigation of biomolecular binding events

JL Wort, M Oranges, K Ackermann, BE Bode - 2020 - books.rsc.org
The emergence of systems biology in the post-genomic era has led to investigating
increasingly complex macromolecular assemblies, emphasising holistic approaches in …

[HTML][HTML] Two alternative conformations of mRNA in the human ribosome during elongation and termination of translation as revealed by EPR spectroscopy

KN Bulygin, IO Timofeev, AA Malygin… - Computational and …, 2021 - Elsevier
The conformation of mRNA in the region of the human 80S ribosome decoding site was
monitored using 11-mer mRNA analogues that bore nitroxide spin labels attached to the …

Studying Ribozymes with Electron Paramagnetic Resonance Spectroscopy

O Schiemann - Ribozymes, 2021 - Wiley Online Library
Summary Electron Paramagnetic Resonance (EPR) spectroscopy is a powerful method to
get insight into the structures and dynamics of RNA. In order to be applicable, the RNA …