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Abstract:
RNA molecules play important roles in biological processes, their functions are intimately related to structural dynamics. Elastic network model (ENM) has achieved great success in predicting the large-amplitude collective behavior of proteins. However, for loosely-packed RNA structures, ENM models can not reproduce their dynamics as accurate as the densely-packed ones. In this work, the multiscale Gaussian network model (mGNM) is extended to predict dynamic properties of RNAs. All tests are performed on a non-redundant RNA structure database we constructed. In results, for B-factor reproduction, encouragingly mGNM achieves a significant improvement with the average value of Pearson correlation coefficient (PCC) between theoretical and experimental B-factors being 0.732, much higher than 0.494 and 0.321 obtained by conventional GNM and parameter-free GNM (pfGNM) models, respectively. Furtherly, mGNM attains a larger improvement in B-factor prediction for loosely-packed parts. Additionally, based on the analysis of functional movements, mGNM can properly make domain decompositions for tRNA(Asp) and xrRNA. This work can strengthen the understanding of the intrinsic dynamics of RNAs, and mGNM is expected to have a bright prospect in dynamic analyses for loosely folded biomolecules, especially RNAs.
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CHEMICAL PHYSICS
ISSN: 0301-0104
Year: 2020
Volume: 538
2 . 3 0 0
JCR@2022
ESI Discipline: CHEMISTRY;
ESI HC Threshold:139
Cited Count:
WoS CC Cited Count: 7
SCOPUS Cited Count: 7
ESI Highly Cited Papers on the List: 0 Unfold All
WanFang Cited Count:
Chinese Cited Count:
30 Days PV: 8
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