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Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
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Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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2
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Prokaryotic Solute/Sodium Symporters: Versatile Functions and Mechanisms of a Transporter Family. Int J Mol Sci 2021; 22:ijms22041880. [PMID: 33668649 PMCID: PMC7918813 DOI: 10.3390/ijms22041880] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The solute/sodium symporter family (SSS family; TC 2.A.21; SLC5) consists of integral membrane proteins that use an existing sodium gradient to drive the uphill transport of various solutes, such as sugars, amino acids, vitamins, or ions across the membrane. This large family has representatives in all three kingdoms of life. The human sodium/iodide symporter (NIS) and the sodium/glucose transporter (SGLT1) are involved in diseases such as iodide transport defect or glucose-galactose malabsorption. Moreover, the bacterial sodium/proline symporter PutP and the sodium/sialic acid symporter SiaT play important roles in bacteria–host interactions. This review focuses on the physiological significance and structural and functional features of prokaryotic members of the SSS family. Special emphasis will be given to the roles and properties of proteins containing an SSS family domain fused to domains typically found in bacterial sensor kinases.
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3
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Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics. Biochem Soc Trans 2016; 44:905-15. [DOI: 10.1042/bst20160024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/19/2022]
Abstract
During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated.
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4
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Bracher S, Guérin K, Polyhach Y, Jeschke G, Dittmer S, Frey S, Böhm M, Jung H. Glu-311 in External Loop 4 of the Sodium/Proline Transporter PutP Is Crucial for External Gate Closure. J Biol Chem 2016; 291:4998-5008. [PMID: 26728461 DOI: 10.1074/jbc.m115.675306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 12/17/2022] Open
Abstract
The available structural information on LeuT and structurally related transporters suggests that external loop 4 (eL4) and the outer end of transmembrane domain (TM) 10' participate in the reversible occlusion of the outer pathway to the solute binding sites. Here, the functional significance of eL4 and the outer region of TM10' are explored using the sodium/proline symporter PutP as a model. Glu-311 at the tip of eL4, and various amino acids around the outer end of TM10' are identified as particularly crucial for function. Substitutions at these sites inhibit the transport cycle, and affect in part ligand binding. In addition, changes at selected sites induce a global structural alteration in the direction of an outward-open conformation. It is suggested that interactions between the tip of eL4 and the peptide backbone at the end of TM10' participate in coordinating conformational alterations underlying the alternating access mechanism of transport. Together with the structural information on LeuT-like transporters, the results further specify the idea that common design and functional principles are maintained across different transport families.
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Affiliation(s)
- Susanne Bracher
- From the Department of Biology 1, Division of Microbiology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany and
| | - Kamila Guérin
- the ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Yevhen Polyhach
- the ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Gunnar Jeschke
- the ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Sophie Dittmer
- From the Department of Biology 1, Division of Microbiology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany and
| | - Sabine Frey
- From the Department of Biology 1, Division of Microbiology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany and
| | - Maret Böhm
- From the Department of Biology 1, Division of Microbiology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany and
| | - Heinrich Jung
- From the Department of Biology 1, Division of Microbiology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany and
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5
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Solution NMR Structure Determination of Polytopic α-Helical Membrane Proteins: A Guide to Spin Label Paramagnetic Relaxation Enhancement Restraints. Methods Enzymol 2015; 557:329-48. [PMID: 25950972 DOI: 10.1016/bs.mie.2014.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solution nuclear magnetic resonance structures of polytopic α-helical membrane proteins require additional restraints beyond the traditional Nuclear Overhauser Effect (NOE) restraints. Several methods have been developed and this review focuses on paramagnetic relaxation enhancement (PRE). Important aspects of spin labeling, PRE measurements, structure calculations, and structural quality are discussed.
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6
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Raba M, Dunkel S, Hilger D, Lipiszko K, Polyhach Y, Jeschke G, Bracher S, Klare JP, Quick M, Jung H, Steinhoff HJ. Extracellular loop 4 of the proline transporter PutP controls the periplasmic entrance to ligand binding sites. Structure 2014; 22:769-80. [PMID: 24768113 DOI: 10.1016/j.str.2014.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/24/2014] [Accepted: 03/26/2014] [Indexed: 12/30/2022]
Abstract
The Na(+)/proline symporter (PutP), like several other Na(+)-coupled symporters, belongs to the so-called LeuT-fold structural family, which features ten core transmembrane domains (cTMs) connected by extra- and intracellular loops. The role of these loops has been discussed in context with the gating function in the alternating access model of secondary active transport processes. Here we report the complete spin-labeling site scan of extracellular loop 4 (eL4) in PutP that reveals the presence of two α-helical segments, eL4a and eL4b. Among the eL4 residues that are directly implicated in the functional dynamics of the transporter, Phe314 in eL4b anchors the loop by means of hydrophobic contacts to cTM1 close to the ligand binding sites. We propose that ligand-induced conformational changes at the binding sites are transmitted via the anchoring residue to eL4 and through eL4 further to adjacent cTMs, leading to closure of the extracellular gate.
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Affiliation(s)
- Michael Raba
- Division of Microbiology, Department Biology I, LMU Munich, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Sabrina Dunkel
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany
| | - Daniel Hilger
- Division of Microbiology, Department Biology I, LMU Munich, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Kamila Lipiszko
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Susanne Bracher
- Division of Microbiology, Department Biology I, LMU Munich, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany
| | - Matthias Quick
- Center for Molecular Recognition and Department of Psychiatry, Columbia University College of Physicians and Surgeons, 630 W. 168th Street, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY 10032, USA
| | - Heinrich Jung
- Division of Microbiology, Department Biology I, LMU Munich, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany.
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany.
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7
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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8
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Darrouzet E, Lindenthal S, Marcellin D, Pellequer JL, Pourcher T. The sodium/iodide symporter: state of the art of its molecular characterization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:244-53. [PMID: 23988430 DOI: 10.1016/j.bbamem.2013.08.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/05/2013] [Accepted: 08/19/2013] [Indexed: 12/30/2022]
Abstract
The sodium/iodide symporter (NIS or SLC5A5) is an intrinsic membrane protein implicated in iodide uptake into thyroid follicular cells. It plays a crucial role in iodine metabolism and thyroid regulation and its function is widely exploited in the diagnosis and treatment of benign and malignant thyroid diseases. A great effort is currently being made to develop a NIS-based gene therapy also allowing the radiotreatment of nonthyroidal tumors. NIS is also expressed in other tissues, such as salivary gland, stomach and mammary gland during lactation, where its physiological role remains unclear. The molecular identity of the thyroid iodide transporter was elucidated approximately fifteen years ago. It belongs to the superfamily of sodium/solute symporters, SSS (and to the human transporter family, SLC5), and is composed of 13 transmembrane helices and 643 amino acid residues in humans. Knowledge concerning NIS structure/function relationship has been obtained by taking advantage of the high resolution structure of one member of the SSS family, the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT), and from studies of gene mutations leading to congenital iodine transport defects (ITD). This review will summarize current knowledge regarding the molecular characterization of NIS.
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Affiliation(s)
- Elisabeth Darrouzet
- SBTN, bât 170, centre de Marcoule, BP 17171, 30207 Bagnols sur Cèze CEDEX, France; Laboratoire TIRO, Faculté de médecine, Université de Nice Sophia-Antipolis, 28 Avenue de Valombrose, 06107 Nice CEDEX, France; CAL, TIRO, F-06107 Nice, France.
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9
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Mirabella A, Yañez Villanueva RM, Delrue RM, Uzureau S, Zygmunt MS, Cloeckaert A, De Bolle X, Letesson JJ. The two-component system PrlS/PrlR of Brucella melitensis is required for persistence in mice and appears to respond to ionic strength. MICROBIOLOGY-SGM 2012; 158:2642-2651. [PMID: 22859617 DOI: 10.1099/mic.0.060863-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial adaptation to environmental conditions is essential to ensure maximal fitness in the face of several stresses. In this context, two-component systems (TCSs) represent a predominant signal transduction mechanism, allowing an appropriate response to be mounted when a stimulus is sensed. As facultative intracellular pathogens, Brucella spp. face various environmental conditions, and an adequate response is required for a successful infection process. Recently, bioinformatic analysis of Brucella genomes predicted a set of 15 bona fide TCS pairs, among which some have been previously investigated. In this report, we characterized a new TCS locus called prlS/R, for probable proline sensor-regulator. It encodes a hybrid histidine kinase (PrlS) with an unusual Na(+)/solute symporter N-terminal domain and a transcriptional regulator (belonging to the LuxR family) (PrlR). In vitro, Brucella spp. with a functional PrlR/S system form bacterial aggregates, which seems to be an adaptive response to a hypersaline environment, while a prlS/R mutant does not. We identified ionic strength as a possible signal sensed by this TCS. Finally, this work correlates the absence of a functional PrlR/S system with the lack of hypersaline-induced aggregation in particular marine Brucella spp.
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Affiliation(s)
- Aurélie Mirabella
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Rosse-Mary Yañez Villanueva
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Rose-May Delrue
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Sophie Uzureau
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Michel S Zygmunt
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France
| | - Axel Cloeckaert
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France
| | - Xavier De Bolle
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Jean-Jacques Letesson
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
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10
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Olkhova E, Raba M, Bracher S, Hilger D, Jung H. Homology model of the Na+/proline transporter PutP of Escherichia coli and its functional implications. J Mol Biol 2010; 406:59-74. [PMID: 21130773 DOI: 10.1016/j.jmb.2010.11.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 01/08/2023]
Abstract
Na(+)/solute symporters are essential membrane integrated proteins that couple the flow of Na(+) ions driven by electrochemical Na(+) gradients to the transport of solutes across biological membranes. Here, we used a combination of molecular modeling techniques and evolutionary conservation analysis to construct and validate a first model of the Na(+)/proline symporter PutP of Escherichia coli based on the crystal structure of the bacterial Na(+)/galactose symporter vSGLT. Ligand docking experiments were employed to gain information about residues involved in proline binding. The proposed model is consistent with the available experimental data and was further validated by amino acid substitutions and kinetic and protein chemical analyses. Combination of the results of molecular modeling and functional studies predicts the location and organization of the Na(+) and proline binding sites. Remarkably, as proposed computationally and discovered here experimentally, residues Y140, W244, and Y248 of transmembrane segments 4 and 7 are found to be particularly important for PutP function and suggested to participate in proline binding and/or gating.
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Affiliation(s)
- Elena Olkhova
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, D-60438 Frankfurt am Main, Germany.
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11
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Kazmier K, Alexander NS, Meiler J, McHaourab HS. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination. J Struct Biol 2010; 173:549-57. [PMID: 21074624 DOI: 10.1016/j.jsb.2010.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 10/25/2010] [Accepted: 11/04/2010] [Indexed: 11/29/2022]
Abstract
A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al. (2008)). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 54% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance.
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Affiliation(s)
- Kelli Kazmier
- Chemical and Physical Biology Program, 340 Light Hall, Vanderbilt University, Nashville, TN 37232, USA.
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12
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Raba M, Baumgartner T, Hilger D, Klempahn K, Härtel T, Jung K, Jung H. Function of transmembrane domain IX in the Na+/proline transporter PutP. J Mol Biol 2008; 382:884-93. [PMID: 18692508 DOI: 10.1016/j.jmb.2008.07.070] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 07/23/2008] [Accepted: 07/24/2008] [Indexed: 10/21/2022]
Abstract
Selected residues of transmembrane domain (TM) IX were previously shown to play key roles in ligand binding and transport in members of the Na(+)/solute symporter family. Using the Na(+)/proline transporter PutP as a model, a complete Cys scanning mutagenesis of TM IX (positions 324 to 351) was performed here to further investigate the functional significance of the domain. G328, S332, Q345, and L346 were newly identified as important for Na(+)-coupled proline uptake. Placement of Cys at one of these positions altered K(m(pro)) (S332C and L346C, 3- and 21-fold decreased, respectively; Q345C, 38-fold increased), K(0.5(Na+)) (S332C, 13-fold decreased; Q345C, 19-fold increased), and/or V(max) [G328C, S332C, Q345C, and L346C, 3-, 22-, 2-, and 8-fold decreased compared to PutP(wild type), respectively]. Membrane-permeant N-ethylmaleimide inhibited proline uptake into cells containing PutP with Cys at distinct positions in the middle (T341C) and cytoplasmic half of TM IX (C344, L347C, V348C, and S351C) and had little or no effect on all other single Cys PutP variants. The inhibition pattern was in agreement with the pattern of labeling with fluorescein-5-maleimide. In addition, Cys placed into the cytoplasmic half of TM IX (C344, L347C, V348C, and S351C) was protected from fluorescein-5-maleimide labeling by proline while Na(+) alone had no effect. Membrane-impermeant methanethiosulfonate ethyltrimethylammonium modified Cys in the middle (A337C and T341C) and periplasmic half (L331C) but not in the cytoplasmic half of TM IX in intact cells. Furthermore, Cys at the latter positions was partially protected by Na(+) but not by proline. Based on these results, a model is discussed according to which residues of TM IX participate in the formation of ligand-sensitive, hydrophilic cavities in the protein that may reconstitute part of the Na(+) and/or proline translocation pathway of PutP.
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Affiliation(s)
- Michael Raba
- LMU Munich, Department Biology I, Microbiology, Grosshaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany
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13
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Hilger D, Böhm M, Hackmann A, Jung H. Role of Ser-340 and Thr-341 in transmembrane domain IX of the Na+/proline transporter PutP of Escherichia coli in ligand binding and transport. J Biol Chem 2007; 283:4921-9. [PMID: 18156179 DOI: 10.1074/jbc.m706741200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na+/solute symporter family comprises more than 400 members of pro- and eukaryotic origin. Using the Na+/proline transporter PutP of Escherichia coli as a model, the role of two conserved residues, Ser-340 and Thr-341, is investigated to obtain insights into the mechanism of transport catalyzed by members of this family. Substitution of these amino acids alters the transport kinetics of cells and proteoliposomes containing the PutP variants significantly. In particular, the apparent affinities for Na+ and Li+ are reduced by 2 orders of magnitude or more. Also proline binding is affected, albeit to a lesser extent than ion binding. Thereby, the presence of a hydroxyl group at position 341 is essential for high affinity ligand binding. Furthermore, Cys placed at position 340 or 341 reacts with sulfhydryl reagents of different polarity, indicating accessibility from the water phase. In addition, Cys cross-linking suggests proximity of the residues to other amino acids previously shown to be crucial for ligand binding. For these reasons it is suggested that Ser-340 and Thr-341 are located in a ligand translocation pathway. Furthermore, it is proposed that the side chain of Thr-341 directly participates in Na+ binding.
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Affiliation(s)
- Daniel Hilger
- LMU Munich, Department Biology I, Microbiology and Munich Center for integrated Protein Science (CiPS), D-80638 Munich, Germany
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14
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Jung H, Pirch T, Hilger D. Secondary transport of amino acids in prokaryotes. J Membr Biol 2007; 213:119-33. [PMID: 17417701 DOI: 10.1007/s00232-006-0880-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Indexed: 01/09/2023]
Abstract
Amino acid transport is a ubiquitous phenomenon and serves a variety of functions in prokaryotes, including supply of carbon and nitrogen for catabolic and anabolic processes, pH homeostasis, osmoprotection, virulence, detoxification, signal transduction and generation of electrochemical ion gradients. Many of the participating proteins have eukaryotic relatives and are successfully used as model systems for exploration of transporter structure and function. Distribution, physiological roles, functional properties, and structure-function relationships of prokaryotic alpha-amino acid transporters are discussed.
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Affiliation(s)
- H Jung
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, D-80638, München, Germany.
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15
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Mascher T, Helmann JD, Unden G. Stimulus perception in bacterial signal-transducing histidine kinases. Microbiol Mol Biol Rev 2007; 70:910-38. [PMID: 17158704 PMCID: PMC1698512 DOI: 10.1128/mmbr.00020-06] [Citation(s) in RCA: 505] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. They consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. Histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. They can be identified and classified by virtue of their conserved cytoplasmic kinase domains. In contrast, the sensor domains are highly variable, reflecting the plethora of different signals and modes of sensing. In order to gain insight into the mechanisms of stimulus perception by bacterial histidine kinases, we here survey sensor domain architecture and topology within the bacterial membrane, functional aspects related to this topology, and sequence and phylogenetic conservation. Based on these criteria, three groups of histidine kinases can be differentiated. (i) Periplasmic-sensing histidine kinases detect their stimuli (often small solutes) through an extracellular input domain. (ii) Histidine kinases with sensing mechanisms linked to the transmembrane regions detect stimuli (usually membrane-associated stimuli, such as ionic strength, osmolarity, turgor, or functional state of the cell envelope) via their membrane-spanning segments and sometimes via additional short extracellular loops. (iii) Cytoplasmic-sensing histidine kinases (either membrane anchored or soluble) detect cellular or diffusible signals reporting the metabolic or developmental state of the cell. This review provides an overview of mechanisms of stimulus perception for members of all three groups of bacterial signal-transducing histidine kinases.
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Affiliation(s)
- Thorsten Mascher
- Department of General Microbiology, Georg-August-University, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Steinhoff HJ. Inter- and intra-molecular distances determined by EPR spectroscopy and site-directed spin labeling reveal protein-protein and protein-oligonucleotide interaction. Biol Chem 2005; 385:913-20. [PMID: 15551865 DOI: 10.1515/bc.2004.119] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recent developments including pulse and multi-frequency techniques make the combination of site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy an attractive approach for the study of protein-protein or protein-oligonucleotide interaction. Analysis of the spin label side chain mobility, its solvent accessibility, the polarity of the spin label micro-environment and distances between spin label side chains allow the modeling of protein domains or protein-protein interaction sites and their conformational changes with a spatial resolution at the level of the backbone fold. Structural changes can be detected with millisecond time resolution. Inter- and intra-molecular distances are accessible in the range from approximately 0.5 to 8 nm by the combination of continuous wave and pulse EPR methods. Recent applications include the study of transmembrane substrate transport, membrane channel gating, gene regulation and signal transfer.
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Zhou A, Wozniak A, Meyer-Lipp K, Nietschke M, Jung H, Fendler K. Charge translocation during cosubstrate binding in the Na+/proline transporter of E.coli. J Mol Biol 2004; 343:931-42. [PMID: 15476811 DOI: 10.1016/j.jmb.2004.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Revised: 09/02/2004] [Accepted: 09/02/2004] [Indexed: 10/26/2022]
Abstract
Charge translocation associated with the activity of the Na(+)/proline cotransporter PutP of Escherichia coli was analyzed for the first time. Using a rapid solution exchange technique combined with a solid-supported membrane (SSM), it was demonstrated that Na(+)and/or proline individually or together induce a displacement of charge. This was assigned to an electrogenic Na(+)and/or proline binding process at the cytoplasmic face of the enzyme with a rate constant of k>50s(-1) which preceeds the rate-limiting step. Based on the kinetic analysis of our electrical signals, the following characteristics are proposed for substrate binding in PutP. (1) Substrate binding is electrogenic not only for Na(+), but also for the uncharged cosubstrate proline. The charge displacement associated with the binding of both substrates is of comparable size and independent of the presence of the respective cosubstrate. (2) Both substrates can bind individually to the transporter. Under physiological conditions, an ordered binding mechanism prevails, while at sufficiently high concentrations, each substrate can bind in the absence of the other. (3) Both substrate binding sites interact cooperatively with each other by increasing the affinity and/or the speed of binding of the respective cosubstrate. (4) Proline binding proceeds in a two-step process: low affinity (approximately 1mM) electroneutral substrate binding followed by a nearly irreversible electrogenic conformational transition.
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Affiliation(s)
- A Zhou
- Max Planck Institut für Biophysik, Marie Curie Strasse 15, D-60439 Frankfurt/Main, Germany
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18
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Jeschke G, Wegener C, Nietschke M, Jung H, Steinhoff HJ. Interresidual distance determination by four-pulse double electron-electron resonance in an integral membrane protein: the Na+/proline transporter PutP of Escherichia coli. Biophys J 2004; 86:2551-7. [PMID: 15041691 PMCID: PMC1304102 DOI: 10.1016/s0006-3495(04)74310-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Proximity relationships within three doubly spin-labeled variants of the Na+/proline transporter PutP of Escherichia coli were studied by means of four-pulse double electron-electron resonance spectroscopy. The large value of 4.8 nm for the interspin distance determined between positions 107 in loop 4 and 223 in loop 7 strongly supports the idea of these positions being located on opposite sides of the membrane. Significant smaller values of between 1.8 and 2.5 nm were found for the average interspin distances between spin labels attached to the cytoplasmic loops 2 and 4 (position 37 and 107) and loops 2 and 6 (position 37 and 187). The large distance distribution widths visible in the pair correlation functions reveal a high flexibility of the studied loop regions. An increase of the distance between positions 37 and 187 upon Na+ binding suggests ligand-induced structural alterations of PutP. The results demonstrate that four-pulse double electron-electron resonance spectroscopy is a powerful means to investigate the structure and conformational changes of integral membrane proteins reconstituted in proteoliposomes.
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Affiliation(s)
- Gunnar Jeschke
- Max-Planck-Institut für Polymerforschung, 55128 Mainz, Germany
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Pirch T, Landmeier S, Jung H. Transmembrane domain II of the Na+/proline transporter PutP of Escherichia coli forms part of a conformationally flexible, cytoplasmic exposed aqueous cavity within the membrane. J Biol Chem 2003; 278:42942-9. [PMID: 12923181 DOI: 10.1074/jbc.m308253200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na+/proline transporter PutP of Escherichia coli is a member of a large family of Na+/substrate symporters. Previous work on PutP suggests an involvement of the region ranging from Asp-55 to Gly-58 in binding of Na+ and/or proline (Pirch, T., Quick, M., Nietschke, M., Langkamp, M., Jung, H. (2002) J. Biol. Chem. 277, 8790-8796). In this study, a complete Cys scanning mutagenesis of transmembrane domain II (TM II) of PutP was performed to further elucidate the role of the TM in the transport process. Strong defects of PutP function were observed upon substitution of Ala-48, Ala-53, Trp-59, and Gly-63 by Cys in addition to the previously characterized residues Asp-55, Ser-57, and Gly-58. However, except for Asp-55 none of these residues proved essential for function. The activity of eight mutants was sensitive to N-ethylmaleimide inhibition with the sensitive positions clustering predominantly on a hydrophilic face in the cytoplasmic half of TM II. The same face was also highly accessible to the bulky sulfhydryl reagent fluorescein 5-maleimide in randomly oriented membrane vesicles, suggesting an unrestricted accessibility of the corresponding amino acid positions via an aqueous pathway. Na+ stimulated the reactivity of Cys toward fluorescein 5-maleimide at two positions while proline inhibited reaction of the sulfhydryl group at nine positions. Taken together, the results demonstrate that TM II of PutP is of particular functional importance. It is proposed that hydrophilic residues in the cytoplasmic half of TM II participate in the formation of an aqueous cavity in the membrane that allows Na+ and/or proline binding to residues located in the middle of the TM (e.g. Asp-55 and Ser-57). In addition, the data indicate that TM II participates in Na+- and proline-induced conformational alterations.
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Affiliation(s)
- Torsten Pirch
- Universität Osnabrück, Fachbereich Biologie/Chemie, Abteilung Mikrobiologie, D-49069 Osnabrück, Germany
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Dohán O, De la Vieja A, Paroder V, Riedel C, Artani M, Reed M, Ginter CS, Carrasco N. The sodium/iodide Symporter (NIS): characterization, regulation, and medical significance. Endocr Rev 2003; 24:48-77. [PMID: 12588808 DOI: 10.1210/er.2001-0029] [Citation(s) in RCA: 534] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Na(+)/I(-) symporter (NIS) is an integral plasma membrane glycoprotein that mediates active I(-) transport into the thyroid follicular cells, the first step in thyroid hormone biosynthesis. NIS-mediated thyroidal I(-) transport from the bloodstream to the colloid is a vectorial process made possible by the selective targeting of NIS to the basolateral membrane. NIS also mediates active I(-) transport in other tissues, including salivary glands, gastric mucosa, and lactating mammary gland, in which it translocates I(-) into the milk for thyroid hormone biosynthesis by the nursing newborn. NIS provides the basis for the effective diagnostic and therapeutic management of thyroid cancer and its metastases with radioiodide. NIS research has proceeded at an astounding pace after the 1996 isolation of the rat NIS cDNA, comprising the elucidation of NIS secondary structure and topology, biogenesis and posttranslational modifications, transcriptional and posttranscriptional regulation, electrophysiological analysis, isolation of the human NIS cDNA, and determination of the human NIS genomic organization. Clinically related topics include the analysis of congenital I(-) transport defect-causing NIS mutations and the role of NIS in thyroid cancer. NIS has been transduced into various kinds of cancer cells to render them susceptible to destruction with radioiodide. Most dramatically, the discovery of endogenous NIS expression in more than 80% of human breast cancer samples has raised the possibility that radioiodide may be a valuable novel tool in breast cancer diagnosis and treatment.
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Affiliation(s)
- Orsolya Dohán
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Abstract
Members of the sodium/substrate symporter family (SSSF, TC 2.A.21) catalyze the uptake of a wide variety of solutes including sugars, proline, pantothenate, and iodide into cells of pro- and eukaryotic origin. Extensive analyses of the topology of different SSSF proteins suggest an arrangement of 13 transmembrane domains as a common topological motif. Regions involved in sodium and/or substrate binding were identified. Furthermore, protein chemical and spectroscopic studies reveal ligand-induced structural alterations which are consistent with close interactions between the sites of sodium and substrate binding, thereby supporting an ordered binding mechanism for transport.
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Affiliation(s)
- Heinrich Jung
- Universität Osnabrück, Fachbereich Biologie/Chemie, Abteilung Mikrobiologie, D-49069, Osnabrück, Germany.
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Pirch T, Quick M, Nietschke M, Langkamp M, Jung H. Sites important for Na+ and substrate binding in the Na+/proline transporter of Escherichia coli, a member of the Na+/solute symporter family. J Biol Chem 2002; 277:8790-6. [PMID: 11756453 DOI: 10.1074/jbc.m111008200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To elucidate the functional importance of transmembrane domain II in the Na(+)/proline transporter (PutP) of Escherichia coli we analyzed the effect of replacing Ser-54 through Gly-58. Substitution of Asp-55 or Met-56 dramatically reduces the apparent affinity for Na(+) and Li(+) in a cation-dependent manner. Conversely, Cys in place of Gly-58 significantly reduces only the apparent proline affinity while substitution of Ser-57 results in a dramatic reduction of the apparent proline and cation affinities. Interestingly, upon increasing the proline concentration the apparent Na(+) affinity of Ser-57 replacement mutants converges toward the wild-type value, indicating a close cooperativity between cation and substrate site(s). This notion is supported by the fact that Na(+)-stimulated site-specific fluorescence labeling of a single Cys at position 57 is completely reversed by the addition of proline. Similar results are obtained upon labeling of a Cys at position 54 or 58. Taken together, these results indicate that Asp-55 and Met-56 are located at or close to the ion-binding site while Ser-54, Ser-57, and Gly-58 may be close to the proline translocation pathway. In addition, the data prod at an involvement of the latter residues in ligand-induced conformational dynamics that are crucial for cation-coupled transport.
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Affiliation(s)
- Torsten Pirch
- Universität Osnabrück, Fachbereich Biologie/Chemie, Abteilung Mikrobiologie, Barbarastrasse 11, D-49069 Osnabrück, Germany
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Jung H. Towards the molecular mechanism of Na(+)/solute symport in prokaryotes. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1505:131-43. [PMID: 11248195 DOI: 10.1016/s0005-2728(00)00283-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Na(+)/solute symporter family (SSF, TC No. 2.A.21) contains more than 40 members of pro- and eukaryotic origin. Besides their sequence similarity, the transporters share the capability to utilize the free energy stored in electrochemical Na(+) gradients for the accumulation of solutes. As part of catabolic pathways most of the transporters are most probably involved in the acquisition of nutrients. Some transporters play a role in osmoadaptation. With a high resolution structure still missing, a combination of genetic, protein chemical and spectroscopic methods has been used to gain new insights into the structure and molecular mechanism of action of the transport proteins. The studies suggest a common 13-helix motif for all members of the SSF according to which the N-terminus is located in the periplasm and the C-terminus is directed into the cytoplasm (except for proteins containing a N- or C-terminal extension). Furthermore, an amino acid substitution analysis of the Na(+)/proline transporter (PutP) of Escherichia coli, a member of the SSF, has identified regions of particular functional importance. For example, amino acids of TM II of PutP proved to be critical for high affinity binding of Na(+) and proline. In addition, it was shown that ligand binding induces widespread conformational alterations in the transport protein. Taken together, the studies substantiate the common idea that Na(+)/solute symport is the result of a series of ligand-induced structural changes.
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Affiliation(s)
- H Jung
- Universität Osnabrück, Fachbereich Biologie/Chemie, Abteilung Mikrobiologie, D-49069, Osnabrück, Germany.
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Abstract
In humans, the kidneys filter approximately 180 g of D-glucose from plasma each day, and this is normally reabsorbed in the proximal tubules. Although the mechanism of reabsorption is well understood, Na(+)-glucose cotransport across the brush-border membrane and facilitated diffusion across the basolateral membrane, questions remain about the identity of the genes responsible for cotransport across the brush border. Genetic studies suggest that two different genes regulate Na(+)-glucose cotransport, and there is evidence from animal studies to suggest that the major bulk of sugar is reabsorbed in the convoluted proximal tubule by a low-affinity, high-capacity transporter and that the remainder is absorbed in the straight proximal tubule by a high-affinity, low-capacity transporter. There are at least three different candidates for these human renal Na(+)-glucose cotransporters. This review will focus on the structure-function relationships of these three transporters, SGLT1, SGLT2, and SGLT3.
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Affiliation(s)
- E M Wright
- Department of Physiology, University of California Los Angeles School of Medicine, Los Angeles, California 90095-1751, USA.
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Chapter 13 Molecular aspects of intestinal brush-border Na+/glucose transport. CURRENT TOPICS IN MEMBRANES 2000. [DOI: 10.1016/s1063-5823(00)50015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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