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An atomistic view of the YiiP structural changes upon zinc(II) binding
Davide Sala1, Andrea Giachetti2, Antonio Rosato3
1Magnetic Resonance Center (CERM), University of Florence, Tuscany, Sesto Fiorentino, Italy.
Biochimica Et Biophysica Acta. General Subjects
|June 10, 2019
Summary
YiiP, a bacterial zinc transporter, uses a unique mechanism where one cavity becomes inaccessible during zinc(II) ion transport. This process involves protein rearrangements and a high energy barrier for ion release.
Area of Science:
- Biochemistry
- Structural Biology
- Membrane Transport
Background:
- YiiP is a bacterial zinc-for-proton antiporter in the cation diffusion facilitator family.
- It facilitates zinc(II) ion transport across the cell membrane from the cytosol to the extracellular space.
Purpose of the Study:
- To elucidate the mechanism of zinc(II) ion transport by the YiiP dimer.
- To understand how metal ions interact with the protein during translocation.
Main Methods:
- Atomistic molecular dynamics simulations of the YiiP dimer.
- Simulations were performed with zinc(II) ions in solution.
Main Results:
- Only one of the YiiP dimer's cavities was accessible from the cytosol during transport.
- Zinc(II) binding to D49 induced a transmembrane domain rearrangement, closing the accessible cavity.
- High free-energy barriers were observed for metal ion release from the transport site.
Conclusions:
- The dimer-dimer interface acts as a stable scaffold, enabling transmembrane domain rearrangements.
- These findings highlight structural features potentially relevant to other zinc transporters.
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