Skip to main content
SpringerLink
Log in

Molecular Modeling of PepT1 — Towards a Structure

  • Published:
The Journal of Membrane Biology Aims and scope Submit manuscript

Abstract

The proton-coupled uptake of di- and tri-peptides is the major route of dietary nitrogen absorption in the intestine and of reabsorption of filtered protein in the kidney. In addition, the transporters involved, PepT1 (SLC15a1) and PepT2 (SLC15a2), are responsible for the uptake and tissue distribution of a wide range of pharmaceutically important compounds, including β-lactam antibiotics, angiotensin-converting enzyme inhibitors, anti-cancer and anti-viral drugs. PepT1 and PepT2 are large proteins, with over 700 amino acids, and to date there are no reports of their crystal structures, nor of those of related proteins from lower organisms. Therefore there is virtually no information about the protein 3-D structure, although computer-based approaches have been used to both model the transmembrane domain (TM) layout and to produce a substrate binding template. These models will be discussed, and a new one proposed from homology modeling rabbit PepT1 to the recently crystallized bacterial transporters LacY and GlpT. Understanding the mechanism by which PepT1 and PepT2 bind and transport their substrates is of great interest to researchers, both in academia and in the pharmaceutical industries.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Abbreviations

GlpT, E.coli glycerol-3-phosphate:

inorganic phosphate antiporter

hPepT1:

human PepT1

LacY E.coli :

proton-coupled lactose permease

rPepT1:

rabbit PepT1

TM:

transmembrane domain

References

  • Abramson J., Smirnova I., Kasho V., Verner G., Kaback H.R., Iwata S. 2003. Structure and mechanism of the lactose permease of Escherichia coli. Science 301:610–615

    Article  PubMed  CAS  Google Scholar 

  • Abramson J., Kaback H.R., Iwata S. 2004. Structural comparison of lactose permease and the glycerol-3-phosphate antiporter: members of the major facilitator superfamily. Curr. Opin. Struc. Biol. 14:413–419

    Article  CAS  Google Scholar 

  • Bailey P.D., Boyd C.A.R., Bronk J.R., Collier I.D., Meredith D., Morgan K.M., Temple C.S. 2000. How to make drugs orally active: a substrate template for peptide transporter PepT1. Angew. Chem. Int. Ed. 39:506–508

    Article  CAS  Google Scholar 

  • Bailey P.D., Boyd C.A.R., Collier I.D., George J.P., Kellett G.L., Meredith D., Morgan K.M., Pettecrew R., Price R.A. 2006. Affinity prediction for substrates of the peptide transporter PepT1. Chem. Commun. (Camb.). 2006:323–325

    Article  Google Scholar 

  • Bates P.A., Sternberg M.J.E. 1999. Model building by comparison at CASP3: Using expert knowledge and computer automation. Proteins: Structure, Function and Genetics, 3(Suppl):47–54

    Article  Google Scholar 

  • Bates P.A., Kelley L.A., MacCallum R.M., Sternberg M.J.E. 2001. Enhancement of protein modeling by human intervention in applying the automatic programs 3DJIGSAW and 3D-PSSM. Proteins: Structure, Function and Genetics, 5(Suppl):39–46

    Article  Google Scholar 

  • Boll M., Daniel H. 1995. Target size analysis of the peptide/H(+)-symporter in kidney brush-border membranes. Biochim. Biophys. Acta. 1233:145–152

    Article  PubMed  Google Scholar 

  • Bolger M.B., Haworth I.S., Yeung A.K., Ann D., von Grafenstein H., Hamm-Alvarez S., Okamoto C.T., Kim K.J., Basu S.K., Wu S., Lee V.H. 1998. Structure, function, and molecular modeling approaches to the study of the intestinal dipeptide transporter PepT1. J. Pharm. Sci. 87:1286–1291

    Article  PubMed  CAS  Google Scholar 

  • Chang A.B., Lin R., Studley W.K., Tran C.V., Saier M.H. 2004. Phylogeny as a guide to structure and function of membrane transport proteins. Mol. Membr. Biol. 21:171–181

    Article  PubMed  CAS  Google Scholar 

  • Contreras-Moreira B., Bates P.A. 2002. Domain Fishing: a first step in protein comparative modeling. Bioinformatics 18:1141–1142

    Article  PubMed  CAS  Google Scholar 

  • Covitz K.M., Amidon G.L., Sadee W. 1998. Membrane topology of the human dipeptide transporter, hPEPT1, determined by epitope insertions. Biochemistry 37:15214–15221

    Article  PubMed  CAS  Google Scholar 

  • Daniel H. 2004. Molecular and integrative physiology of intestinal peptide transport. Annu. Rev. Physiol. 66:361–384

    Article  PubMed  CAS  Google Scholar 

  • Daniel H., Kottra G. 2004. The proton oligopeptide cotransporter family SLC15 in physiology and pharmacology. Pfluegers Arch. 447:610–618

    Article  CAS  Google Scholar 

  • Daniel H., Spanier B., Kottra G., Weitz D. 2006. From bacteria to man: archaic proton-dependent peptide transporters at work. Physiology 21:93–102

    Article  PubMed  CAS  Google Scholar 

  • Fei Y.J., Kanai Y., Nussberger S., Ganapathy V., Leibach F.H., Romero M.F., Singh S.K., Boron W.F., Hediger M.A. 1994. Expression cloning of a mammalian proton-coupled oligopeptide transporter. Nature 368:563–566

    Article  PubMed  CAS  Google Scholar 

  • Gebauer S., Knutter I., Hartrodt B., Brandsch M., Neubert K., Thondorf I. 2003. Three-dimensional quantitative structure-activity relationship analyses of peptide substrates of the mammalian H+/peptide cotransporter PEPT1. J. Med. Chem. 46:5725

    Article  PubMed  CAS  Google Scholar 

  • Huang Y., Lemieux M.J., Song J., Auer M. & Wang D.N. 2003. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301:616–620

    Article  PubMed  CAS  Google Scholar 

  • Kaback H.R., Sahin-Toth M., Weinglass A.B. 2001. The kamikaze approach to membrane transport. Nature Rev. Mol. Cell Biol. 2:610–620

    Article  CAS  Google Scholar 

  • Kaback H.R. 2005. Structure and mechanism of the lactose permease. C R Biol 328:557–567

    Article  PubMed  CAS  Google Scholar 

  • Kulkarni A.A., Haworth I.S., Lee V.H. 2003a. Transmembrane segment 5 of the dipeptide transporter hPepT1 forms a part of the substrate translocation pathway. Biochem. Biophys. Res. Commun. 306:177–185

    Article  CAS  Google Scholar 

  • Kulkarni A.A., Haworth I.S., Uchiyama T., Lee V.H. 2003b. Analysis of transmembrane segment 7 of the dipeptide transporter hPepT1 by cysteine-scanning mutagenesis. J. Biol. Chem. 278:51833–51840

    Article  CAS  Google Scholar 

  • Lee V.H., Chu C., Mahlin E.D., Basu S.K., Ann D.K., Bolger M.B., Haworth I.S., Yeung A.K., Wu S.K., Hamm-Alvarez S., Okamoto C.T. 1999. Biopharmaceutics of transmucosal peptide and protein drug administration: role of transport mechanisms with a focus on the involvement of PepT1. J. Control Release 62:129–140

    Article  PubMed  CAS  Google Scholar 

  • McGuffin L.J., Bryson K., Jones D.T. 2000. The PSIPRED protein structure prediction server. Bioinformatics. 16:404–405

    Article  PubMed  CAS  Google Scholar 

  • Meredith D., Boyd C.A.R. 1996. His57 is an essential residue for the transport of the anionic dipeptide D-Phe-L-Glu by PepT1 expressed in Xenopus laevis oocytes. J. Physiol. 497:89P–90P

    Google Scholar 

  • Meredith D., Boyd C.A.R., Bronk J.R., Bailey P.D., Morgan K.M., Collier I.D., Temple C.S. 1998. 4-aminomethylbenzoic acid is a non-translocated competitive inhibitor of the epithelial peptide transporter PepT1. J. Physiol. 512:629–634

    Article  PubMed  CAS  Google Scholar 

  • Meredith D., Boyd C.A.R. 2000. Structure and function of eukaryotic peptide transporters. Cell. Mol. Life Sci. 57:754–778

    Article  PubMed  CAS  Google Scholar 

  • Meredith, D. 2003. Site-directed mutagenesis investigations of the substrate-binding site of the rabbit proton-coupled peptide transporter PepT1 expressed in Xenopus oocytes. J. Physiol. 549P:C7

  • Meredith D. 2004. Site-directed mutation of arginine 282 to glutamate uncouples the movement of peptides and protons by the rabbit proton-peptide cotransporter PepT1. J. Biol. Chem. 279:15795–15798

    Article  PubMed  CAS  Google Scholar 

  • O’Donoghue P., Luthey-Schulten Z. 2003. Evolution of structure in aminoacyl-tRNA synthetases. Microbiol. Mol. Biol. Rev. 67:550–573

    Article  PubMed  CAS  Google Scholar 

  • Panitsas K.E., Boyd C.A.R., Meredith D. 2006. Evidence that the rabbit proton-peptide co-transporter PepT1 is a multimer when expressed in Xenopus laevis oocytes. Pfluegers Arch. 452:53–631

    Article  CAS  Google Scholar 

  • Paulsen, I.T., Skurray, R.A. 1994. The POT family of transport proteins. Trends Biochem. Sci. 19:404

    Article  PubMed  CAS  Google Scholar 

  • Pieri M., Boyd C.A.R., Meredith D. 2004. Studies on the proton coupling mechanism of the rabbit epithelial H+/peptide transporter PepT1, expressed in Xenopus oocytes. J. Physiol. 559P:C6

    Google Scholar 

  • Pieri M., Gan C., Boyd C.A.R., Meredith D. 2005. Systematic investigation of the role of the tyrosine residues in the transmembrane regions of the rabbit proton-coupled peptide transporter, PepT1. J. Physiol. 567P:PC171

    Google Scholar 

  • Pieri M., Boyd C.A.R., Bailey P.D., Meredith D. 2006. The functional role of tyrosine56 in the rabbit proton-peptide cotransporter, PepT1 expressed in Xenopus oocytes. Proc. Physiol. Soc. 2:PC18

    Google Scholar 

  • Saier M.H., Tran C.V., Barabote R.D. 2006. TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res. 34:D181–D186

    Article  PubMed  CAS  Google Scholar 

  • Terada T., Saito H., Mukai M., Inui K.I. 1996. Identification of the histidine residues involved in substrate recognition by a rat H+/peptide cotransporter, PEPT1. FEBS Lett. 394:196–200

    Article  PubMed  CAS  Google Scholar 

  • Terada & Inui T. K. 2004. Peptide transporters: structure, function, regulation and application for drug delivery. Curr. Drug. Metab. 5:85–94

    Article  PubMed  Google Scholar 

  • Ubarretxena-Belandia I., Tate C.G. 2004. New insights into the structure and oligomeric state of the bacterial multidrug transporter EmrE: an unusual asymmetric homo-dimer. FEBS Lett. 564:234–238

    Article  PubMed  CAS  Google Scholar 

  • Vig B.S., Stouch T.R., Timoszyk J.K., Quan Y., Wall D.A., Smith R.L., Faria T.N. 2006. Human PEPT1 pharmacophore distinguishes between dipeptide transport and binding. J. Med. Chem. 49:3636–3644

    Article  PubMed  CAS  Google Scholar 

  • Wang Y., Geer L.Y., Chappey C., Kans J.A., Bryant S.H. 2000. Cn3D: sequence and structure views for Entrez. Trends Biochem. Sci. 25:300–302

    Article  PubMed  CAS  Google Scholar 

  • Wilson M.C., Meredith D., Fox J.E., Manoharan C., Davies A.J., Halestrap A.P. 2005. Basigin (CD147) is the target for organomercurial inhibition of monocarboxylate transporter isoforms 1 and 4: the ancillary protein for the insensitive MCT2 is EMBIGIN (gp70). J. Biol. Chem. 280:27213–27221

    Article  PubMed  CAS  Google Scholar 

  • Yeung A.K., Basu S.K., Wu S.K., Chu C., Okamoto C.T., Hamm-Alvarez S.F., von Grafenstein H., Shen W.C., Kim K.J., Bolger M.B., Haworth I.S., Ann D.K., Lee V.H. 1998. Molecular identification of a role for tyrosine 167 in the function of the human intestinal proton- coupled dipeptide transporter (hPepT1). Biochem. Biophys. Res. Commun. 250:103–107

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgement

We thank the Wellcome Trust for their generous support, and Professor Pat Bailey, University of Manchester, for helpful discussion.

Author information

Authors and Affiliations

  1. Department of Physiology, Anatomy & Genetics, Le Gros Clark Building, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK

    D. Meredith

  2. School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK

    R.A. Price

Authors
  1. D. Meredith
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R.A. Price
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to D. Meredith.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Meredith, D., Price, R. Molecular Modeling of PepT1 — Towards a Structure. J Membrane Biol 213, 79–88 (2006). https://doi.org/10.1007/s00232-006-0876-6

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00232-006-0876-6

Keywords

Search

Navigation