255: Lipids, Ions and the AE1 Elevator

Chen T et al., Nature Communications - Cryo-EM structures, uptake assays, and molecular dynamics show that PIP2 lipids bind at the AE1 dimer interface and inhibit the OF⇌IF conformational transition while substrate binding lowers the transition barrier. Key terms: AE1, PIP2, bicarbonate transport, cryo-EM, molecular dynamics.

Study Highlights:
Three high-resolution cryo-EM states were solved: two inward-facing (IF1, IF2) and one outward-facing (OF). Proteoliposome uptake assays show that depleting or masking PIP2 increases HCO3– and I– transport. MD simulations identify recurring anion binding in the lumen with R730 as a key coordinating residue and estimate tighter HCO3– binding than Cl–. Enhanced-sampling free energy profiles reveal that HCO3– binding lowers the OF⇌IF barrier by ~3 kcal/mol while removing PIP2 lowers it by ~2 kcal/mol. Mechanistically, HCO3– stabilizes a transition-state conformation by promoting R730 contact with the scaffold domain.

Conclusion:
PIP2 stabilizes AE1 in a conformation that raises the transport transition barrier and inhibits activity, whereas substrate binding promotes the transition and facilitates transport.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1)

First author:
Chen T

Journal:
Nature Communications

DOI:
10.1038/s41467-025-66786-6

Reference:
Chen T, Vallese F, Gil-Iturbe E, Kim K, Calì T, Quick M, Clarke OB, Tajkhorshid E. Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1). Nature Communications. 2025. https://doi.org/10.1038/s41467-025-66786-6

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/pipt2-inhibits-ae1

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-10.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript sections describing AE1 elevator mechanism (TD/SD), R730 and ion binding, bicarbonate vs chloride affinity, PIP2 as a regulatory brake, energy landscape via BEUS/SMwST, cross-linking to trap IF, and the three-state (OF, IF1, IF2) structural context, plus functional uptake assays.
- transcript topics: AE1 elevator mechanism (TD/SD architecture); R730 and luminal anion binding sites; Bicarbonate vs chloride binding affinities (Kd values); PIP2 binding site at the dimer interface and K743 salt bridge; PIP2 as molecular brake and its removal increasing activity; Energy landscape and conformational transitions (BEUS/SMwST)

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- PIP2 binds at the AE1 dimer interface and inhibits the OF⇌IF conformational transition.
- Substrate binding (HCO3−) lowers the transition barrier by ~3 kcal/mol.
- PIP2 binding raises the transition barrier by ~2 kcal/mol; removal lowers it.
- R730 is a key coordinating residue for bicarbonate and chloride binding in AE1 lumen.
- HCO3− binding affinity is higher than Cl− in both OF and IF states (Kd values reported).
- AE1 operates via an elevator mechanism with TD translating/rotating relative to SD.

QC result: Pass.