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arXiv · 1911.10452

Overcharging of zinc ion in the structure of zinc finger protein is needed for DNA binding stability

Ly Hai Nguyen·Tuyen Thanh Tran·Lien Ngoc Thi Truong·Hanh Hong Mai·Toan T. Nguyen
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Abstract

The zinc finger structure where a Zn2+ ion binds to 4 cysteine or histidine amino acids in a tetrahedral structure is very common motif of nucleic acid binding proteins. The corresponding interaction model is present in 3% of the genes of human genome. As a result, zinc finger has been shown to be extremely useful in various therapeutic and research capacities, as well as in biotechnology. In stable configuration, the cysteine amino acids are deprotonated and become negatively charged. This means the Zn2+ ion is overscreened by 4 cysteine charges (overcharged). It is question of whether this overcharged configuration is also stable when such negatively charged zinc finger binds to negatively charged DNA molecule. Using all atom molecular dynamics simulation up to microsecond range of an androgen receptor protein dimer, we investigate how the deprotonated state of cysteine influences its structure, dynamics, and function in binding o DNA molecules. Our results show that the deprotonated state of cysteine residues are essential for mechanical stabilization of the functional, folded conformation. Not only this state stabilizes the protein structure, it also stabilizes the protein-DNA binding complex. The differences in structural and energetic properties of the two (sequence-identical) monomers are also investigated showing the strong influence of DNA on the structure of zinc fingers upon complexation. Our result has potential impact on better molecular understanding of one of the most common classes of zinc fingers

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Ly Hai Nguyen, Tuyen Thanh Tran, Lien Ngoc Thi Truong, Hanh Hong Mai, Toan T. Nguyen. 2020-02-22. Overcharging of zinc ion in the structure of zinc finger protein is needed for DNA binding stability. https://doi.org/10.1021/acs.biochem.9b01055

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