Programme

P.1 -- Poster, VCTP-44

Date: Tuesday, 30 July 2019

Time: 08:30 - 10:00

Computational study of the effect of protonation states of PSA protein zinc fingers on its DNA binding

Nguyen Hai Ly, Nguyen The Toan

VNU, Hanoi University of Science

In this study, we investigate the binding of the Zinc finger (ZF) structure on a short DNA molecule. Zinc finger of a protein where a Zn2+ ion binds to 4 cysteine or histidine amino acids in a tetrahedral structure is a very common motif of nucleic acid binding proteins. This structure is ubiquitous and the corresponding interaction model is present in 3% of the genes of the human genome. ZF has been shown to be extremely useful in various therapeutic and research capacities, as well as in biotechnology. A recent computational study has shown that Zn finger structure is stable if the cysteine amino acids are in deprotonated. Here, we investigate how these deprotonated states influence protein structure, dynamics, and function by studying the binding of ZF to short DNA molecules in normal and in deprotonated states using molecular dynamics simulations in sub-microsecond range. Our results show that the Zn 2+ ion and the deprotonated state of cysteine are essential for mechanical stabilization of the functional, folded conformation. Not only this state stabilizes the ZF structure, but it also stabilizes the DNA binding structure. Our result has a potential impact on the better design of zinc fingers for various biotechnological application.

Presenter: Nguyen Hai Ly