Multiscale Modeling of Wobble to Watson–Crick-Like Guanine–Uracil Tautomerization Pathways in RNA
Abstract
:1. Introduction
2. Computational Methods and Details
2.1. QM
2.2. MD
2.3. QM/MM
3. Results and Discussion
3.1. QM Profile without Microsolvation
3.2. Conformational Space Sampling Using MD Simulations
3.3. QM Profile Including Microsolvation
3.4. QM/MM Profile
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
QM/MM | Quantum Mechanics/Molecular Mechanics |
MD | Molecular Dynamics |
DFT | Density Functional Theory |
NMR | Nuclear Magnetic Resonance |
WC | Watson–Crick |
guanine•uracil | G•U |
DNA | Deoxyribonucleic Acid |
RNA | Ribonucleic Acid |
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Chandorkar, S.; Raghunathan, S.; Jaganade, T.; Priyakumar, U.D. Multiscale Modeling of Wobble to Watson–Crick-Like Guanine–Uracil Tautomerization Pathways in RNA. Int. J. Mol. Sci. 2021, 22, 5411. https://doi.org/10.3390/ijms22115411
Chandorkar S, Raghunathan S, Jaganade T, Priyakumar UD. Multiscale Modeling of Wobble to Watson–Crick-Like Guanine–Uracil Tautomerization Pathways in RNA. International Journal of Molecular Sciences. 2021; 22(11):5411. https://doi.org/10.3390/ijms22115411
Chicago/Turabian StyleChandorkar, Shreya, Shampa Raghunathan, Tanashree Jaganade, and U. Deva Priyakumar. 2021. "Multiscale Modeling of Wobble to Watson–Crick-Like Guanine–Uracil Tautomerization Pathways in RNA" International Journal of Molecular Sciences 22, no. 11: 5411. https://doi.org/10.3390/ijms22115411