Project

Back to overview

Structure and supramolecular organization of amino acid and peptide transport proteins

Applicant Fotiadis Dimitrios
Number 125150
Funding scheme Project funding (Div. I-III)
Research institution Institut für Biochemie und Molekulare Medizin Universität Bern
Institution of higher education University of Berne - BE
Main discipline Biophysics
Start/End 01.05.2009 - 31.10.2012
Approved amount 375'000.00
Show all

Keywords (10)

amino acid transport protein; crystallization; electron crystallography; membrane protein; peptide transport protein; structure; three-dimensional crystal; transmission electron microscopy; two-dimensional crystal; X-ray crystallography

Lay Summary (English)

Lead
Lay summary
Membrane proteins (MPs) reside in the cell membrane where they fulfill innumerous key functions. More than 30 percent of the eukaryotic genome accounts for MPs. Two thirds of all known drugs on the market target MPs, thus highlighting their critical importance in human health. While the unique structures of more than 15’000 soluble proteins are solved, the number of unique MP structures is only 190. Clearly, there is an urgent need for structural information on MPs in order to understand their function at the molecular level and to advance the structure-based design of therapeutic drugs. About 20 percent of the MPs are membrane transporters, which play a critical role in a variety of physiological processes and are implicated in numerous diseases. Membrane transporters represent important drug targets and can furthermore be exploited for drug delivery strategies, for example for the transport of prodrugs.Our project focuses on the high-resolution structure determination of selected amino acid and peptide transporters. Both are important for nutrient uptake, but are also involved in several human diseases such as the primary inherited aminoacidurias, cystinuria and lysinuric protein intolerance, cancer, etc. Our target transporters comprise prokaryotic, mammalian and human members. For structure determination, we overexpress, purify and crystallize selected transporters and analyze the crystals by cryo-transmission electron microscopy/electron crystallography and X-ray crystallography. The elucidation of structures from these two important classes of transport proteins, i.e. amino acid and peptide transporters, will contribute to our understanding of their function and transport mechanism. This information should also facilitate the development of novel pharmaceutical drugs using a structure-based drug design strategy.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection.
Jeckelmann Jean-Marc, Palacin Manuel, Fotiadis Dimitrios, A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection., in Journal of structural biology, 173(2), 375-81.
Expression of human heteromeric amino acid transporters in the yeast Pichia pastoris.
Costa Meritxell, Rosell Albert, Alvarez-Marimon Elena, Zorzano Antonio, Fotiadis Dimitrios, Palacín Manuel, Expression of human heteromeric amino acid transporters in the yeast Pichia pastoris., in Protein expression and purification, 87(1), 35-40.
Frog oocytes to unveil the structure and supramolecular organization of human transport proteins.
Bergeron Marc J, Boggavarapu Rajendra, Meury Marcel, Ucurum Zöhre, Caron Luc, Isenring Paul, Hediger Matthias A, Fotiadis Dimitrios, Frog oocytes to unveil the structure and supramolecular organization of human transport proteins., in PloS one, 6(7), 21901-21901.
Projection structure of DtpD (YbgH), a prokaryotic member of the peptide transporter family.
Casagrande Fabio, Harder Daniel, Schenk Andreas, Meury Marcel, Ucurum Zohre, Engel Andreas, Weitz Dietmar, Daniel Hannelore, Fotiadis Dimitrios, Projection structure of DtpD (YbgH), a prokaryotic member of the peptide transporter family., in Journal of molecular biology, 394(4), 708-17.
Structure determination of channel and transport proteins by high-resolution microscopy techniques.
Meury Marcel, Harder Daniel, Ucurum Zöhre, Boggavarapu Rajendra, Jeckelmann Jean-Marc, Fotiadis Dimitrios, Structure determination of channel and transport proteins by high-resolution microscopy techniques., in Biological chemistry, 392(1-2), 143-50.
Substrate binding tunes conformational flexibility and kinetic stability of an amino acid antiporter.
Bippes Christian A, Zeltina Antra, Casagrande Fabio, Ratera Merce, Palacin Manuel, Muller Daniel J, Fotiadis Dimitrios, Substrate binding tunes conformational flexibility and kinetic stability of an amino acid antiporter., in The Journal of biological chemistry, 284(28), 18651-63.

Collaboration

Group / person Country
Types of collaboration
Prof. Manuel Palacin / University of Barcelona Spain (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Prof. Matthias Hediger / University of Berne Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Prof. Hannelore Daniel / Technical University of Munich Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel

Associated projects

Number Title Start Funding scheme
139231 Advancement of functional genomics research at the University of Bern by extension of LC-MS platform 01.07.2012 R'EQUIP
144168 Structure and supramolecular organization of membrane transport proteins 01.11.2012 Project funding (Div. I-III)
144168 Structure and supramolecular organization of membrane transport proteins 01.11.2012 Project funding (Div. I-III)

Abstract

Membrane proteins (MPs) fulfill innumerous key functions in all living cells and account for more than 30 percent of the eukaryotic proteomes. Two thirds of all known drugs on the market target MPs, thus highlighting their critical importance in human health. While the unique structures of more than 15’000 soluble proteins are solved, the number of unique MP structures is only 171. Clearly, there is an urgent need for structural information on MPs in order to understand their function at the molecular level and to advance the structure-based design of therapeutic drugs. About 20 percent of the MPs are membrane transporters, which play a critical role in a variety of physiological processes and are implicated in numerous diseases. Membrane transporters represent important drug targets and can furthermore be exploited for drug delivery strategies, for example for the transport of prodrugs.In the present application, we propose to focus on the high-resolution structure determination of selected amino acid transporters from the amino acid/polyamine/organocation (APC) superfamily (SLC7*) and of peptide transporters from the proton dependent oligopeptide transporter (POT)/peptide transporter (PTR) families (SLC15). Target transporters comprise prokaryotic, mammalian and human members from the APC superfamily (including a heteromeric amino acid transporter (HAT)) and from the POT/PTR family. In this application, the bacterium Escherichia coli and the yeast Pichia pastoris are the expression systems of choice for MP overexpression. We propose to determine the structure of members from these transporter families using 2D and 3D crystals, and cryo-transmission electron microscopy (TEM)/electron crystallography and X-ray crystallography. Besides wild-type transporters, we will attempt to crystallize point mutants that are more stable. As an alternative to the mentioned crystallographic approaches, TEM and single particle analysis will be used to determine the low-resolution 3D structure of a HAT thus unveiling the supramolecular organization of the light (SLC7) and heavy (SLC3) HAT subunits. Low- and medium-resolution protein structure determination by TEM and single particle analysis requires small amounts of pure protein (micrograms) compared to 2D and 3D crystallization (miligrams). For this purpose, we want to establish expression of membrane transporters and their complexes in the promising Xenopus oocyte system.The elucidation of structures from these two important classes of transport proteins, i.e. amino acid and peptide transporters, will contribute to our understanding of their function and transport mechanism. This information should also facilitate the development of novel pharmaceutical drugs using a structure-based drug design strategy.* The solute carrier (SLC) gene series provided by the Human Genome Organisation (HUGO) Nomenclature Committee refer to solute carriers of higher organisms
-