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RNA-Specific Force Field Optimization with CMAP and Reweighting
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DOI：10.1021/acs.jcim.1c01148.png)
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摘要
En 中文
RNA plays a key role in a variety of cell activities. However, it is difficult to capture its structure dynamics by the traditional experimental methods because of the inherent limitations. Molecular dynamics simulation has become a valuable complement to the experimental methods. Previous studies have indicated that the current force fields cannot accurately reproduce the conformations and structural dynamics of RNA. Therefore, an RNA-specific force field was developed to improve the conformation sampling of RNA. The distribution of zeta/alpha dihedrals of tetranucleotides was optimized by a reweighting method, and the grid-based energy correction map (CMAP) term was first introduced into the Amber RNA force field of ff 99bsc0 chi OL3, named ff 99OL3_CMAP1. Extensive validations of tetranucleotides and tetraloops show that ff 99OL3_CMAP1 can significantly decrease the population of an incorrect structure, increase the consistency between the simulation results and experimental values for tetranucleotides, and improve the stability of tetraloops. ff 99OL3_CMAP1 can also precisely reproduce the conformation of a duplex and riboswitches. These findings confirm that the newly developed force field ff 99OL3_CMAP1 can improve the conformer sampling of RNA.
Keyword:
MOLECULAR-DYNAMICS SIMULATIONS
BIOMOLECULAR SIMULATION
NUCLEIC-ACIDS
PARAMETERS
STRATEGIES
BACKBONE
HELIX
MODEL
NMR
DNA
期刊
IF:
5.3
论文数:
9.1K
被引数:
4.0W
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引用论文
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