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Cited by 12Drug Transport and Resistance MechanismsProtein Structure and DynamicsAmino Acid Enzymes and Metabolism

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The mechanism of mammalian proton-coupled peptide transporters

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Lichtinger, Simon M, Parker, Joanne L, Newstead, Simon, Biggin, Philip C·2024·eLife
DOI 10.7554/elife.96507PMC PMC11265797

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Abstract

Proton-coupled oligopeptide transporters (POTs) are of great pharmaceutical interest owing to their promiscuous substrate binding site that has been linked to improved oral bioavailability of several classes of drugs. Members of the POT family are conserved across all phylogenetic kingdoms and function by coupling peptide uptake to the proton electrochemical gradient. Cryo-EM structures and alphafold models have recently provided new insights into different conformational states of two mammalian POTs, SLC15A1, and SLC15A2. Nevertheless, these studies leave open important questions regarding the mechanism of proton and substrate coupling, while simultaneously providing a unique opportunity to investigate these processes using molecular dynamics (MD) simulations. Here, we employ extensive unbiased and enhanced-sampling MD to map out the full SLC15A2 conformational cycle and its thermodynamic driving forces. By computing conformational free energy landscapes in different protonation states and in the absence or presence of peptide substrate, we identify a likely sequence of intermediate protonation steps that drive inward-directed alternating access. These simulations identify key differences in the extracellular gate between mammalian and bacterial POTs, which we validate experimentally in cell-based transport assays. Our results from constant-PH MD and absolute binding free energy (ABFE) calculations also establish a mechanistic link between proton binding and peptide recognition, revealing key details underpining secondary active transport in POTs. This study provides a vital step forward in understanding proton-coupled peptide and drug transport in mammals and pave the way to integrate knowledge of solute carrier structural biology with enhanced drug design to target tissue and organ bioavailability.

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Metadata

Authors
Lichtinger, S. M., Parker, J. L., Newstead, S., & Biggin, P. C.
Affiliations
University of Oxford (GB)
Corresponding author
Biggin, Philip C
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2024-07-23
Volume
13
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.96507
PMC
PMC11265797
OpenAlex
W4394841620
Cited by
12
References
1
Citations by year
2026: 7 · 2025: 3 · 2024: 2
FWCI
2.04
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Wellcome Trust (218514/Z/19/Z)
  • Engineering and Physical Sciences Research Council (EP/X035603/1)
Topics
  • Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Amino Acid Enzymes and Metabolism
Keywords
proton-coupled oligopeptide transporters, SLC15A2, PepT1, transport mechanisms, alternating access mechanism, protonation states, conformational free energy landscape, peptide recognition, secondary active transport, oral bioavailability, drug transport, enhanced sampling molecular dynamics
MeSH terms
Animals, Biological Transport, Humans, Mammals, Protein Conformation, Protons, Thermodynamics, Membrane Transport Proteins, Molecular Dynamics Simulation

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