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

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 deterinines its DNA-binding specificity. Recently, the structutes of the dimerie LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallography, In this article, molecular dynamies (MD) simulations are employed to Study two crystal Structutes 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 cOrnponent analysis (pcA) and free energy landscape (FEL) methods, the open close conformational change of the dithetization interface was found to be important for the system stability. At the dimetization interface, the protein protein interaction has multiple influences on the cooperative DNA binding of iFy. The following analysis of DNA structural parameters further revealed that the protein protein interaction contributes varying roles according to the specific DNA binding efficiency. We propose that the protein protein interaction serves a dual function as a connector between LFY monomers; and a regulator of DNA SpeCificity. It will improve the robustness and adaptivity of the LFY-DNA tertiary structure. This Study provides sortie new insights into the understanding of the dynamics and interaction mechanism, of dimeric LFY-DBD bound to ONA at the atomic level.