Predicting the kinetics of RNA oligonucleotides using Markov state models
| Autor: | Jianbo Zhao, Frank Noé, Fabian Paul, Douglas H. Turner, Giovanni Bussi, Giovanni Pinamonti, David E. Condon |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Oligonucleotides temperature-jump 01 natural sciences Force field (chemistry) nmr Molecular dynamics molecular-dynamics simulations Computational chemistry time nuclear-magnetic-resonance amber force-fields dinucleoside monophosphates conformational properties stacking water Quantitative Biology::Biomolecules 010304 chemical physics Chemistry Temperature Computational Physics (physics.comp-ph) Markov Chains Computer Science Applications Biological Physics (physics.bio-ph) Biological system Physics - Computational Physics Kinetics Stacking FOS: Physical sciences Molecular Dynamics Simulation Article Settore FIS/03 - Fisica della Materia 03 medical and health sciences Physics - Chemical Physics 0103 physical sciences Molecule Physics - Biological Physics Physical and Theoretical Chemistry Condensed Matter - Statistical Mechanics Chemical Physics (physics.chem-ph) Statistical Mechanics (cond-mat.stat-mech) Markov chain Oligonucleotide RNA Biomolecules (q-bio.BM) 030104 developmental biology Quantitative Biology - Biomolecules FOS: Biological sciences Nucleic Acid Conformation |
| Popis: | Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time or spatial resolution. Here we use state-of-the-art computational techniques, namely atomistic molecular dynamics and Markov state models, to provide insight into the rapid dynamics of short RNA oligonucleotides, in order to elucidate the kinetics of stacking interactions. Analysis of multiple microsecond-long simulations indicates that the main relaxation modes of such molecules can consist of transitions between alternative folded states, rather than between random coils and native structures. After properly removing structures that are artificially stabilized by known inaccuracies of the current RNA AMBER force field, the kinetic properties predicted are consistent with the timescales of previously reported relaxation experiments. Accepted for publication on J. Chem. Theory Comput |
| Databáze: | OpenAIRE |
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