RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
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 …

Why nature really chose phosphate

SCL Kamerlin, PK Sharma, RB Prasad… - Quarterly reviews of …, 2013 - cambridge.org
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and
maintaining the integrity of the genetic material. On the surface, it would appear to be a …

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

JJP Stewart - Journal of molecular modeling, 2013 - Springer
Modern semiempirical methods are of sufficient accuracy when used in the modeling of
molecules of the same type as used as reference data in the parameterization. Outside that …

Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation …

SCL Kamerlin, M Haranczyk… - The journal of physical …, 2009 - ACS Publications
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used
to provide a general scheme for chemical reactions in proteins. However, such approaches …

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

M Klähn, E Rosta, A Warshel - Journal of the American Chemical …, 2006 - ACS Publications
The nature of the hydrolysis of phosphate monoester dianions in solutions and in proteins is
a problem of significant current interest. The present work explores this problem by …

Emergence of the first catalytic oligonucleotides in a formamide‐based origin scenario

JE Šponer, J Šponer, O Nováková… - … A European Journal, 2016 - Wiley Online Library
Abstract 50 years after the historical Miller–Urey experiment, the formamide‐based scenario
is perhaps the most powerful concurrent hypothesis for the origin of life on our planet …

Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms

K Nam, Q Cui, J Gao, DM York - Journal of Chemical Theory and …, 2007 - ACS Publications
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …

New insights on the interaction of phenanthroline based ligands and metal complexes and polyoxometalates with duplex DNA and G-quadruplexes

Á Sánchez-González, NAG Bandeira… - Molecules, 2021 - mdpi.com
This work provides new insights from our team regarding advances in targeting canonical
and non-canonical nucleic acid structures. This modality of medical treatment is used as a …

[HTML][HTML] Phosphodiester models for cleavage of nucleic acids

S Mikkola, T Lönnberg… - Beilstein journal of organic …, 2018 - beilstein-journals.org
Nucleic acids that store and transfer biological information are polymeric diesters of
phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases …

Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight

H Lönnberg - Organic & biomolecular chemistry, 2011 - pubs.rsc.org
RNA molecules participate in many fundamental cellular processes either as a carrier of
genetic information or as a catalyst, and hence, RNA has received increasing interest both …