Zinc binding of a Cys2His2-type zinc finger protein is enhanced by the interaction with DNA

Hajdu, Bálint and Hunyadi-Gulyás, Éva and Kato, Kohsuke and Kawaguchi, Atsushi and Nagata, Kyosuke and Gyurcsik, Béla (2023) Zinc binding of a Cys2His2-type zinc finger protein is enhanced by the interaction with DNA. JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 28 (3). pp. 301-315. ISSN 0949-8257

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Abstract

Zinc finger proteins specifically recognize DNA sequences and, therefore, play a crucial role in living organisms. In this study the Zn(II)-, and DNA-binding of 1MEY#, an artificial zinc finger protein consisting of three finger units was characterized by multiple methods. Fluorimetric, circular dichroism and isothermal calorimetric titrations were applied to determine the accurate stability constant of a zinc finger protein. Assuming that all three zinc finger subunits behave identically, the obtained thermodynamic data for the Zn(II) binding were ΔHbinding site =  − (23.5 − 28.0) kcal/mol (depending on the applied protonation state of the cysteines) and logβ’pH 7.4 = 12.2 ± 0.1, being similar to those of the CP1 consensus zinc finger peptide. The specific DNA binding of the protein can be characterized by logβ’pH 7.4 = 8.20 ± 0.08, which is comparable to the affinity of the natural zinc finger proteins (Sp1, WT1, TFIIIA) toward DNA. This value is ~ 1.9 logβ’ unit higher than those determined for semi- or nonspecific DNA binding. Competitive circular dichroism and electrophoretic mobility shift measurements revealed that the conditional stability constant characteristic for Zn(II) binding of 1MEY# protein increased by 3.4 orders of magnitude in the presence of its target DNA sequence.

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