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How Minor Sequence Changes Enable Mechanistic Diversity in MFS Transporters? An Atomic-Level Rationale for Symport
Tanner J Dean1, Jiangyan Feng2, Diwakar Shukla1,2,3,4,5
1Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Journal of Chemical Information and Modeling
|February 6, 2026
Summary
Minor sequence changes in bacterial membrane transporters like NarU can drastically alter their transport mechanism, switching from antiporter to potential symporter activity. This highlights how subtle adaptations reprogram transporter function.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Membrane transporters exhibit functional divergence despite sequence similarity.
- Nitrate and nitrite transport in bacteria involves MFS transporters NarK (antiporter) and NarU (mechanism unresolved).
Purpose of the Study:
- To elucidate the transport mechanism of NarU using computational simulations.
- To contrast NarU's mechanism with that of the known antiporter NarK.
Main Methods:
- Adaptive molecular dynamics simulations.
- Markov State Modeling to map conformational free-energy landscape.
- Analysis of gating pathways and key residue interactions.
Main Results:
- NarU exhibits pronounced asymmetry favoring outward-facing states.
- A novel apo-occluded intermediate, stabilized by arginine rotation and glycine substitution, was identified.
- These features reprogram NarU for coupled cotransport, unlike NarK.
Conclusions:
- Specific residue substitutions can fundamentally alter transporter mechanisms.
- NarU's unique gating energetics and intermediate stabilize symport activity.
- Sequence-dependent adaptations are key to functional divergence in related transporters.
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