Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.

Autor:	Lopez-Redondo M; Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY., Fan S; Department of Physics, Arizona State University, Tempe, AZ., Koide A; Perlmutter Cancer Center, Department of Medicine, New York University School of Medicine, New York, NY., Koide S; Perlmutter Cancer Center, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY., Beckstein O; Department of Physics, Arizona State University, Tempe, AZ., Stokes DL; Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY.
Jazyk:	angličtina
Zdroj:	The Journal of general physiology [J Gen Physiol] 2021 Aug 02; Vol. 153 (8). Date of Electronic Publication: 2021 Jul 13.
DOI:	10.1085/jgp.202112873
Abstrakt:	YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle. (© 2021 Lopez-Redondo et al.)
Databáze:	MEDLINE
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