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Kotov V, Killer M, Jungnickel KEJ, Lei J, Finocchio G, Steinke J, Bartels K, Strauss J, Dupeux F, Humm AS, Cornaciu I, Márquez JA, Pardon E, Steyaert J, Löw C. Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition. Cell Rep 2023; 42:112831. [PMID: 37467108 DOI: 10.1016/j.celrep.2023.112831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/09/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.
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Affiliation(s)
- Vadim Kotov
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Maxime Killer
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Hamburg, Germany
| | - Katharina E J Jungnickel
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jian Lei
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan 610041, People's Republic of China
| | - Giada Finocchio
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Josi Steinke
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Kim Bartels
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jan Strauss
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Florine Dupeux
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Anne-Sophie Humm
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Irina Cornaciu
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - José A Márquez
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Christian Löw
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany.
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Killer M, Finocchio G, Mertens HDT, Svergun DI, Pardon E, Steyaert J, Löw C. Cryo-EM Structure of an Atypical Proton-Coupled Peptide Transporter: Di- and Tripeptide Permease C. Front Mol Biosci 2022; 9:917725. [PMID: 35898305 PMCID: PMC9309889 DOI: 10.3389/fmolb.2022.917725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Proton-coupled Oligopeptide Transporters (POTs) of the Major Facilitator Superfamily (MFS) mediate the uptake of short di- and tripeptides in all phyla of life. POTs are thought to constitute the most promiscuous class of MFS transporters, with the potential to transport more than 8400 unique substrates. Over the past two decades, transport assays and biophysical studies have shown that various orthologues and paralogues display differences in substrate selectivity. The E. coli genome codes for four different POTs, known as Di- and tripeptide permeases A-D (DtpA-D). DtpC was shown previously to favor positively charged peptides as substrates. In this study, we describe, how we determined the structure of the 53 kDa DtpC by cryogenic electron microscopy (cryo-EM), and provide structural insights into the ligand specificity of this atypical POT. We collected and analyzed data on the transporter fused to split superfolder GFP (split sfGFP), in complex with a 52 kDa Pro-macrobody and with a 13 kDa nanobody. The latter sample was more stable, rigid and a significant fraction dimeric, allowing us to reconstruct a 3D volume of DtpC at a resolution of 2.7 Å. This work provides a molecular explanation for the selectivity of DtpC, and highlights the value of small and rigid fiducial markers such as nanobodies for structure determination of low molecular weight integral membrane proteins lacking soluble domains.
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Affiliation(s)
- Maxime Killer
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Giada Finocchio
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Haydyn D. T. Mertens
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Dmitri I. Svergun
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- *Correspondence: Christian Löw,
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Kuťák D, Poppleton E, Miao H, Šulc P, Barišić I. Unified Nanotechnology Format: One Way to Store Them All. Molecules 2021; 27:63. [PMID: 35011301 PMCID: PMC8746876 DOI: 10.3390/molecules27010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.
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Affiliation(s)
- David Kuťák
- Business Unit Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
- Visualization Laboratory, Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic
| | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA; (E.P.); (P.Š.)
| | - Haichao Miao
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA; (E.P.); (P.Š.)
| | - Ivan Barišić
- Business Unit Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
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Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
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Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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Recent advances in understanding prodrug transport through the SLC15 family of proton-coupled transporters. Biochem Soc Trans 2021; 48:337-346. [PMID: 32219385 PMCID: PMC7200629 DOI: 10.1042/bst20180302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/28/2022]
Abstract
Solute carrier (SLC) transporters play important roles in regulating the movement of small molecules and ions across cellular membranes. In mammals, they play an important role in regulating the uptake of nutrients and vitamins from the diet, and in controlling the distribution of their metabolic intermediates within the cell. Several SLC families also play an important role in drug transport and strategies are being developed to hijack SLC transporters to control and regulate drug transport within the body. Through the addition of amino acid and peptide moieties several novel antiviral and anticancer agents have been developed that hijack the proton-coupled oligopeptide transporters, PepT1 (SCL15A1) and PepT2 (SLC15A2), for improved intestinal absorption and renal retention in the body. A major goal is to understand the rationale behind these successes and expand the library of prodrug molecules that utilise SLC transporters. Recent co-crystal structures of prokaryotic homologues of the human PepT1 and PepT2 transporters have shed important new insights into the mechanism of prodrug recognition. Here, I will review recent developments in our understanding of ligand recognition and binding promiscuity within the SLC15 family, and discuss current models for prodrug recognition.
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Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies. Methods 2020; 180:111-126. [PMID: 32422249 DOI: 10.1016/j.ymeth.2020.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning helices, encompass families of proteins which are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels and transporters. Although these proteins have typically been targeted by small molecule drugs and peptides, the high specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. However, it remains the case that isolation of antibodies with desired pharmacological function(s) has proven difficult due to technical challenges in preparing membrane protein antigens suitable to support antibody drug discovery. In this review recent progress in defining strategies for generation of membrane protein antigens is outlined. We also highlight antibody isolation strategies which have generated antibodies which bind the membrane protein and modulate the protein function.
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Lloris-Garcerá P, Klinter S, Chen L, Skynner MJ, Löving R, Frauenfeld J. DirectMX - One-Step Reconstitution of Membrane Proteins From Crude Cell Membranes Into Salipro Nanoparticles. Front Bioeng Biotechnol 2020; 8:215. [PMID: 32266242 PMCID: PMC7096351 DOI: 10.3389/fbioe.2020.00215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/03/2020] [Indexed: 01/14/2023] Open
Abstract
Integral membrane proteins (IMPs) are central to many physiological processes and represent ∼60% of current drug targets. An intricate interplay with the lipid molecules in the cell membrane is known to influence the stability, structure and function of IMPs. Detergents are commonly used to solubilize and extract IMPs from cell membranes. However, due to the loss of the lipid environment, IMPs usually tend to be unstable and lose function in the continuous presence of detergent. To overcome this problem, various technologies have been developed, including protein engineering by mutagenesis to improve IMP stability, as well as methods to reconstitute IMPs into detergent-free entities, such as nanodiscs based on apolipoprotein A or its membrane scaffold protein (MSP) derivatives, amphipols, and styrene-maleic acid copolymer-lipid particles (SMALPs). Although significant progress has been made in this field, working with inherently unstable human IMP targets (e.g., GPCRs, ion channels and transporters) remains a challenging task. Here, we present a novel methodology, termed DirectMX (for direct membrane extraction), taking advantage of the saposin-lipoprotein (Salipro) nanoparticle technology to reconstitute fragile IMPs directly from human crude cell membranes. We demonstrate the applicability of the DirectMX methodology by the reconstitution of a human solute carrier transporter and a wild-type GPCR belonging to the human chemokine receptor (CKR) family. We envision that DirectMX bears the potential to enable studies of IMPs that so far remained inaccessible to other solubilization, stabilization or reconstitution methods.
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Kalienkova V, Alvadia C, Clerico Mosina V, Paulino C. Single-Particle Cryo-EM of Membrane Proteins in Lipid Nanodiscs. Methods Mol Biol 2020; 2127:245-273. [PMID: 32112327 DOI: 10.1007/978-1-0716-0373-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single-particle cryo-electron microscopy has become an indispensable technique in structural biology. In particular when studying membrane proteins, it allows the use of membrane-mimicking tools, which can be crucial for a comprehensive understanding of the structure-function relationship of the protein in its native environment. In this chapter we focus on the application of nanodiscs and use our recent studies on the TMEM16 family as an example.
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Affiliation(s)
- Valeria Kalienkova
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Carolina Alvadia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Vanessa Clerico Mosina
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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