Peptide Transporter Function & Structure
Human promiscuous peptide transporter 1 (PepT1) plays a crucual role in nutrition, transporting di- and tri-peptides from digested protein into intestinal cells.[1] It is also crucial in uptake of orally delivered drugs.[1] It is a member of the proton-coupled oligopeptide transporter (POT) family. These secondary active transporters are powered by the inward-directed electrochemical proton gradient, enabling intracellular accumulation of peptides/drugs above extracellular concentrations.[1].
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with an extracellular domain (beta sheets), and a transmembrane transporter domain (alpha helices) with a cytoplasmic amphipathic linker (green protrusion). The latter looks like the toe of a boot formed by the linker (toe) with the transmembrane domain. The function of the extracellular and cytoplasmic linker domains are not well understood, although the extracellular domain appears to be important in transport[2].
The transmembrane domain has a (enabling it to sit within the lipid bilayer membrane) which is . The cytoplamic linker "toe" has a net positive charge, enabling it to bind to the inner leaflet of the lipid bilayer, which typically has a negative charge.
Rocker-Switch Transport Mechanism
PepT1 is believed to transport using a rocker-switch mechanism, in which the outer (extracellular) face opens a pocket to bind peptides to a conserved binding site, then the outer face closes and the inner (cytoplasmic) face opens to release the peptide. However, prior to 2021, no structure was captured with an outward-facing opening, despite 47 structures in the PDB for bacterial homologs, representing 10 different bacterial POTs[1].
In 2021, Killer et al. reported human PepT1 structures in outward-open conformations (with and without bound dipeptide)[1]. This greatly furthered understanding of the transport mechanism. In December, 2024, no additional structures with outward-open conformations have been published.
(7pmx and 7pmy) of the transmembrane domain (extracellular domain hidden) illustrates the rocker-switch-like mechanism of transport. (7pmy is actually human PepT2, a different transporter with a very similar structure, and about 65% sequence identify with PepT1 in the transporter core domain.) This morph is oversimplified. Killer et al. actually captured 4 different conformations, revealing additional details of the rocker-switch mechanism. Their supplementary materials include a revealing morph movie (see also the movie explanation) that includes all 4 conformations.
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Channel Shapes and Sizes
Outward Facing
The shapes and sizes of open spaces in proteins can be visualized by filling them with pseudoatoms. in 7pmx. The channel has been filled by PACUPP with small pseudoatoms 2.0 Å in diameter[3]. (3.0 Å is the van der Waals diameter of an oxygen atom). .
Inward Facing
in 7pmy filled with 2.0 Å pseudoatoms. . This inward-facing opening is described as "partially occluded"[1]. Please recall that proteins are dynamic, and ligand movement may depend on transient openings not apparent in the static average cryo-EM structure. Structures of hemoglobin have no opening large enough to enable oxygen passage from outside to the heme iron, yet oxygen "hops on and off" very efficiently (see Section 2, View 11 in this hemoglobin tutorial).
Methods
Transmembrane Domains
- The coordinates of the extracellular domain of 7pmx, sequence 381-579, were deleted from the PDB file using a plain text editor.
- The coordinates of the extracellular domain of 7pmy, sequence 403-606, were deleted from the PDB file.
These PDB files were used for making the morph, and for PACUPP.
Morph
Morphs were generated with FATCAT, with the Proteopedia PyMOL Morpher, and with ChimeraX. The dipeptide ligand was absent in the FATCAT and Proteopedia/PyMOL morphs, but was retained in the ChimeraX morph PDB file. A ChimeraX morph between the isolated transmembrane domains, with hydrogen atoms deleted, was used for the above scenes, Image:7pmx-y-morph-chimerax-xmemb-noh.pdb.gz.
Some steps in making the morph in ChimeraX are easily done from the menus, e.g. Tools, Structure Analysis, MatchMaker for superposition. Other steps must be done from commands. The complete command file for making a morph between the full-length PDB files is 7pmx-y-morph.cxc. The transmembrane domain PDB files were simply dragged and dropped into ChimeraX, instead of loading from the wwPDB.
