Effects of Mg2+ on the binding of the CREB/CRE complex: Full-atom molecular dynamics simulations

doi:10.1088/1674-1056/28/7/078701

Abstract

Metal ions play critical roles in the interaction between deoxyribonucleic acid (DNA) and protein. The experimental research has demonstrated that the Mg²⁺ ion can affect the binding between transcription factor and DNA. In our work, by full-atom molecular dynamic simulation, the effects of the Mg²⁺ ion on the cyclic adenosine monophosphate (cAMP) response element binding protein (CREB)/cAMP response elements (CRE) complex are investigated. It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg²⁺ ion is added. Hence, an obvious change in the structure of the DNA is observed. Then the DNA base groove and base pair parameters are analyzed. We find that, due to the introduction of the Mg²⁺ ion, the DNA base major groove becomes narrower. A potential mechanism for this observation is proposed. It is confirmed that the Mg²⁺ ion can enhance the stability of the DNA-protein complex.

Keywords: cAMP response element binding protein (CREB) molecular dynamics (MD) simulation hydrogen bond Mg²⁺ ion

Received: 27 March 2019
Revised: 09 April 2019
Accepted manuscript online:

PACS:	87.14.-g	(Biomolecules: types)
	87.15.ap	(Molecular dynamics simulation)
	87.15.kj	(Protein-polynucleotide interactions)

Fund:

Project supported by the National Natural Science Foundation of China (Grant Nos. 11705064, 11675060, and 91730301), the Fundamental Research Funds for the Central Universities, China (Grant Nos. 2662016QD005 and 26622018JC017), and the Huazhong Agricultural University Scientific and Technological Self-Innovation Foundation Program, China (Grant No. 2015RC021).

Corresponding Authors: Haiyou Deng, Ming Yi
E-mail: hydeng@mail.hzau.edu.cn;yiming@mail.hzau.edu.cn

Cite this article:

Song Mao(毛松), Shuai Wang(王帅), Haiyou Deng(邓海游), Ming Yi(易鸣) Effects of Mg²⁺ on the binding of the CREB/CRE complex: Full-atom molecular dynamics simulations 2019 Chin. Phys. B 28 078701

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Effects of Mg2+ on the binding of the CREB/CRE complex: Full-atom molecular dynamics simulations

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Effects of Mg²⁺ on the binding of the CREB/CRE complex: Full-atom molecular dynamics simulations