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

Maria Lopez-Redondo, Shujie Fan, Akiko Koide, Shohei Koide, Oliver Beckstein, David L. Stokes

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article numbere202112873
JournalJournal of General Physiology
Volume153
Issue number8
DOIs
StatePublished - Aug 2 2021
Externally publishedYes

Keywords

  • Biophysics
  • Membrane transport
  • Protein structure and dynamics

ASJC Scopus subject areas

  • Physiology

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