RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
[HTML][HTML] The ONIOM method and its applications
The fields of theoretical and computational chemistry have come a long way since their
inception in the mid-20th century. Fifty years ago, only rudimentary approximations for very …
inception in the mid-20th century. Fifty years ago, only rudimentary approximations for very …
Molecular dynamics simulations of nucleic acids. From tetranucleotides to the ribosome
J Šponer, P Banáš, P Jurecka… - The journal of …, 2014 - ACS Publications
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in
MA Ditzler, M Otyepka, J Sponer… - Accounts of chemical …, 2010 - ACS Publications
Structure and dynamics are both critical to RNA's vital functions in biology. Numerous
techniques can elucidate the structural dynamics of RNA, but computational approaches …
techniques can elucidate the structural dynamics of RNA, but computational approaches …
A 1.9 Å crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
JH Chen, R Yajima, DM Chadalavada, E Chase… - Biochemistry, 2010 - ACS Publications
The hepatitis delta virus (HDV) ribozyme and HDV-like ribozymes are self-cleaving RNAs
found throughout all kingdoms of life. These RNAs fold into a double-nested pseudoknot …
found throughout all kingdoms of life. These RNAs fold into a double-nested pseudoknot …
Comparative enzymology and structural biology of RNA self-cleavage
MJ Fedor - Annual review of biophysics, 2009 - annualreviews.org
Self-cleaving hammerhead, hairpin, hepatitis delta virus, and glmS ribozymes comprise a
family of small catalytic RNA motifs that catalyze the same reversible phosphodiester …
family of small catalytic RNA motifs that catalyze the same reversible phosphodiester …
The role of L1 stalk–tRNA interaction in the ribosome elongation cycle
The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during
translocation through the ribosome. This article investigates three aspects of L1 stalk–tRNA …
translocation through the ribosome. This article investigates three aspects of L1 stalk–tRNA …
The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
J Šponer, A Mládek, JE Šponer, D Svozil… - Physical Chemistry …, 2012 - pubs.rsc.org
Knowledge of geometrical and physico-chemical properties of the sugar–phosphate
backbone substantially contributes to the comprehension of the structural dynamics, function …
backbone substantially contributes to the comprehension of the structural dynamics, function …
How to understand atomistic molecular dynamics simulations of RNA and protein–RNA complexes?
We provide a critical assessment of explicit‐solvent atomistic molecular dynamics (MD)
simulations of RNA and protein/RNA complexes, written primarily for non‐specialists with an …
simulations of RNA and protein/RNA complexes, written primarily for non‐specialists with an …
Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme
The hepatitis delta virus (HDV) ribozyme catalyzes a self-cleavage reaction using a
combination of nucleobase and metal ion catalysis. Both divalent and monovalent ions can …
combination of nucleobase and metal ion catalysis. Both divalent and monovalent ions can …