Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs

Journal of Chemical Information and Modeling
Hua WanXu-hong Tian

Abstract

LEAFY (LFY) is a plant-specific transcription factor, with a variety of roles in different species. LFY contains a conserved DNA-binding domain (DBD) that determines its DNA-binding specificity. Recently, the structures of the dimeric LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallography. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of DNA-bound LFY protein from angiosperms and the moss Physcomitrella patens, respectively. The comparison of stabilities of the two systems is consistent with the experimental data of binding affinities. The calculation of hydrogen bonds showed that position 312 in LFY determines the difference of DNA-binding specificity. By using principal component analysis (PCA) and free energy landscape (FEL) methods, the open-close conformational change of the dimerization interface was found to be important for the system stability. At the dimerization interface, the protein-protein interaction has multiple influences on the cooperative DNA binding of LFY. The following analysis of DNA structural parameters further revealed that the protein-protein interaction contributes varying roles according to the specific DNA-binding ...Continue Reading

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Citations

Jan 4, 2017·The Journal of Physical Chemistry Letters·Qingtong ZhouHaojun Liang
Mar 21, 2017·Journal of Chemical Information and Modeling·Yuanxin TianJiajie Zhang
Apr 10, 2020·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Zhixiang WuJianping Hu

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