Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT
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Abstract
ABSTRACT Transporter proteins change their conformation to carry their substrate across the cell membrane. The conformational dynamics are vital to understanding the transport function. We have studied the oxalate transporter (OxlT), an oxalate:formate antiporter from Oxalobacter formigenes , significant in avoiding kidney stone formation. The atomic structure of OxlT has been recently solved in the outward-open and occluded states. However, the inward-open conformation is still missing, hindering a complete understanding of the transporter. Here, we performed an accelerated molecular dynamics simulation to sample the extensive conformational space of OxlT and successfully obtained the inward-open conformation where cytoplasmic substrate formate binding was preferred over oxalate binding. We also identified critical interactions for the inward- open conformation. The results were complemented by the highly accurate structure prediction by AlphaFold2. Although AlphaFold2 solely predicted OxlT in the outward-open conformation, mutation of the identified critical residues made it partly predict the inward-open conformation, identifying possible state-shifting mutations. TOC GRAPHICS
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- Authors
- Ohnuki, J., Jaunet-Lahary, T., Yamashita, A., & Okazaki, K.-I.
- Affiliations
- National Institutes of Natural Sciences (JP)
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Okayama University (JP)
- Corresponding author
- Okazaki, Kei-ichi
- Venue
- The Journal of Physical Chemistry Letters
- Publisher
- American Chemical Society (ACS)
- Published
- 2024-01-12
- Volume
- 15
- Issue
- 3
- Pages
- 725-732
- ISSN
- 1948-7185 (ISSN-L)
- OpenAlex
- W4390830169
- Cited by
- 14
- References
- 41
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 4
- FWCI
- 1.91
- Type
- journal article
- Language
- en
- Open access
- green
- dx.doi.org
- Licence
- Locations
- The Journal of Physical Chemistry Letters (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Funders
- Japan Society for the Promotion of Science (JP23K14160, JP22H02595)
- Nagase Science Technology Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- Oxalobacter formigenes, transporter conformational states, inward-open conformation, outward-open conformation, occluded state, accelerated molecular dynamics, AlphaFold2, oxalate binding, kidney stone prevention
- MeSH terms
- Formates, Oxalates, Protein Conformation, Antiporters, Membrane Transport Proteins, Molecular Dynamics Simulation
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