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Structural Insight into RNA Hairpin Folding Intermediates
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Hairpins are a ubiquitous secondary structure motif in RNA molecules. Despite their simple structure, there is some debate over whether they fold in a two-state or multi-state manner. We have studied the folding of a small tetraloop hairpin using a serial version of replica exchange molecular dynamics on a distributed computing environment. On the basis of these simulations, we have identified a number of intermediates that are consistent with experimental results. We also find that folding is not simply the reverse of high-temperature unfolding and suggest that this may be a general feature of biomolecular folding.
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Ribonucleic Acid Folding Prediction Based on Iterative Multiscale Simulation
Zhang, D., Li, Y., Zhong, Q., Wang, A., Weng, J., Gong, L., & Li, G. (2022) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c01342 · Cited by 3
Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids
Curuksu, J. D., Kannan, S., & Zacharias, M. (2015) · Springer eBooks · doi:10.1007/978-94-007-6169-8_32-2 · Cited by 1
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Topology of Reticulate Evolution
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Curuksu, J. D., Kannan, S., & Zacharias, M. (2012) · Springer eBooks · doi:10.1007/978-94-007-0711-5_32
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Curuksu, J. D., Kannan, S., & Zacharias, M. (2017) · Springer eBooks · doi:10.1007/978-3-319-27282-5_32
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Metadata
- Authors
- Bowman, G. R., Huang, X., Yao, Y., Sun, J., Carlsson, G., Guibas, L. J., & Pande, V. S.
- Affiliations
- Stanford University (US)
- Corresponding author
- Pande, Vijay S.
- ORCID
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2008-07-01
- Volume
- 130
- Issue
- 30
- Pages
- 9676-9678
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- PMC
- PMC2652247
- OpenAlex
- W2035793643
- Cited by
- 101
- References
- 27
- Citations by year
- 2026: 3 · 2025: 1 · 2023: 2 · 2022: 5 · 2021: 3 · 2020: 3 · 2019: 2 · 2018: 3 · 2017: 5 · 2016: 9 · 2015: 10 · 2014: 5 · 2013: 12 · 2012: 12
- FWCI
- 3.42
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of the American Chemical Society (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- Funders
- National Science Foundation (0619926, 0354543)
- National Institutes of Health (GM-072970, GM066275)
- Defense Advanced Research Projects Agency (HR0011, HR0011-05-1-0007)
- National Institute of General Medical Sciences (P01GM066275, GM 072970, U54GM072970)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- folding intermediates, tetraloop, two-state folding, replica exchange molecular dynamics, distributed computing, RNA secondary structure
- MeSH terms
- Algorithms, Computer Simulation, Models, Molecular, Nucleic Acid Conformation, RNA, Thermodynamics, Nuclear Magnetic Resonance, Biomolecular
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