Open AccessFormation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter
Author(s) -
Gaurav Sharma,
Kenneth M. Merz
Publication year - 2021
Publication title -
biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.43
H-Index - 253
eISSN - 1520-4995
pISSN - 0006-2960
DOI - 10.1021/acs.biochem.1c00415
Subject(s) - zinc , chemistry , binding site , metal , metal ions in aqueous solution , protein structure , crystallography , a site , bilayer , transporter , biophysics , membrane , biology , biochemistry , organic chemistry , gene
Zinc homeostasis in mammals is constantly and precisely maintained by sophisticated regulatory proteins. Among them, the Zrt/Irt-like protein (ZIP) regulates the influx of zinc into the cytoplasm. In this work, we have employed all-atom molecular dynamics simulations to investigate the Zn 2+ transport mechanism in prokaryotic ZIP obtained from Bordetella bronchiseptica (BbZIP) in a membrane bilayer. Additionally, the structural and dynamical transformations of BbZIP during this process have been analyzed. This study allowed us to develop a hypothesis for the zinc influx mechanism and formation of the metal-binding site. We have created a model for the outward-facing form of BbZIP (experimentally only the inward-facing form has been characterized) that has allowed us, for the first time, to observe the Zn 2+ ion entering the channel and binding to the negatively charged M2 site. It is thought that the M2 site is less favored than the M1 site, which then leads to metal ion egress; however, we have not observed the M1 site being occupied in our simulations. Furthermore, removing both Zn 2+ ions from this complex resulted in the collapse of the metal-binding site, illustrating the "structural role" of metal ions in maintaining the binding site and holding the proteins together. Finally, due to the long Cd 2+ -residue bond distances observed in the X-ray structures, we have proposed the existence of an H 3 O + ion at the M2 site that plays an important role in protein stability in the absence of the metal ion.