期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 117, 期 27, 页码 8047-8060出版社
AMER CHEMICAL SOC
DOI: 10.1021/jp400786b
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资金
- Ecole Doctorale B3MI
- French government [ANR-11-LABEX-0011-01]
Although RNAs play many cellular functions, little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities, these simulations have been limited to small RNAs and to short times. HiRe-RNA, a recently proposed high-resolution coarse-grained RNA that captures many geometric details such as base pairing and stacking, is able to fold RNA molecules to near-native structures in a short computational time. So far, it had been applied to simple hairpins, and here we present its application to duplexes of a couple dozen nucleotides and show how with replica exchange molecular dynamics (REMD) we can easily predict the correct double helix from a completely random configuration and study, the dissociation curve. To show the versatility of our model, we present an application to a double stranded DNA Molecule as well. A reconstruction algorithm allows us to obtain full atom structures from the coarse-grained model. Through atomistic molecular dynamics (MD), we can compare the dynamics starting from a representative structure of a low temperature replica from the experimental structure, and show how the two are statistic-ally identical, highlighting the validity of a coarse-grained approach for structured RNAs and DNAs.
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