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作者:

Wang, Shihao (Wang, Shihao.) | Gong, Weikang (Gong, Weikang.) | Deng, Xueqing (Deng, Xueqing.) | Liu, Yang (Liu, Yang.) | Li, Chunhua (Li, Chunhua.) (学者:李春华)

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Scopus SCIE

摘要:

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.

关键词:

Multiscale Gaussian network model (mGNM) Intramolecular interactions Divide domain B-factor RNA molecules

作者机构:

  • [ 1 ] [Wang, Shihao]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China
  • [ 2 ] [Gong, Weikang]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China
  • [ 3 ] [Deng, Xueqing]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China
  • [ 4 ] [Liu, Yang]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China
  • [ 5 ] [Li, Chunhua]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China

通讯作者信息:

  • 李春华

    [Li, Chunhua]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China

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来源 :

CHEMICAL PHYSICS

ISSN: 0301-0104

年份: 2020

卷: 538

2 . 3 0 0

JCR@2022

ESI学科: CHEMISTRY;

ESI高被引阀值:139

被引次数:

WoS核心集被引频次: 6

SCOPUS被引频次: 6

ESI高被引论文在榜: 0 展开所有

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