A molecular dynamics analysis of the GCC-box binding domain in ethylene-responsive element binding factors.
Ethylene-responsive element (ERE) binding factors is responsible for a consensus nucleotide sequence AGCCGCC (GCC-box) binding in many important process of plant growing through gene regulation and mediating signal transduction pathways in response to environmental stress. The GCC-box binding domain (GBD) as a novel fold for DNA recognition has been analyzed by means of molecular dynamics. The simulations show that the complex of GBD-DNA trajectories show similar fluctuations in the atomic positions as uncomplexed, particularly at three beta strands involving DNA binding. The calculations of entropy also affirm that GBD flexibility is basically similar for two ligation states. Further, the two complexation states present similar patterns of concerted motions, indicating that the bound DNA cannot alter GBD flexibility. It is inferred that the flexibility of GBD molecule is independent of its ligation state. So in the protein-DNA recognition, the GBD cannot be easily induced while DNA shows better flexibility. Comparison between simulations of unligated GBD and the complexed GBD (in isolation or DNA-bound) reveals intrinsic flexibilities in some certain parts of the molecule play a key role in DNA recognition. In addition, MD simulation identifies that water molecule may mediate interaction between GBD and DNA.
Zhao
Xi
X
State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, PR China.
Huang
Xu-ri
XR
Sun
Chia-chung
CC
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D004268:DNA-Binding Proteins; D010940:Plant Proteins; C093680:ethylene-responsive element binding protein