101
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Harris NJ, Booth PJ. Folding and stability of membrane transport proteins in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1055-66. [PMID: 22100867 DOI: 10.1016/j.bbamem.2011.11.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/26/2011] [Accepted: 11/03/2011] [Indexed: 10/15/2022]
Abstract
Transmembrane transporters are responsible for maintaining a correct internal cellular environment. The inherent flexibility of transporters together with their hydrophobic environment means that they are challenging to study in vitro, but recently significant progress been made. This review will focus on in vitro stability and folding studies of transmembrane alpha helical transporters, including reversible folding systems and thermal denaturation. The successful re-assembly of a small number of ATP binding cassette transporters is also described as this is a significant step forward in terms of understanding the folding and assembly of these more complex, multi-subunit proteins. The studies on transporters discussed here represent substantial advances for membrane protein studies as well as for research into protein folding. The work demonstrates that large flexible hydrophobic proteins are within reach of in vitro folding studies, thus holding promise for furthering knowledge on the structure, function and biogenesis of ubiquitous membrane transporter families. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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102
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Hu NJ, Iwata S, Cameron AD, Drew D. Crystal structure of a bacterial homologue of the bile acid sodium symporter ASBT. Nature 2011; 478:408-11. [PMID: 21976025 PMCID: PMC3198845 DOI: 10.1038/nature10450] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 08/15/2011] [Indexed: 11/09/2022]
Abstract
High cholesterol levels greatly increase the risk of cardiovascular disease. By its conversion into bile acids, about 50% of cholesterol is eliminated from the body. However bile acids released from the bile duct are constantly recycled, being reabsorbed in the intestine via the Apical Sodium dependent Bile acid Transporter (ASBT). It has been shown in animal models that plasma cholesterol levels are significantly lowered by specific inhibitors of ASBT1,2, thus ASBT is a target for hypercholesterolemia drugs. Here, we describe the crystal structure of a bacterial homologue of ASBT from Neisseria meningitidis (ASBTNM) at 2.2Å. ASBTNM contains two inverted structural repeats of five transmembrane helices. A Core domain of six helices harbours two sodium ions while the remaining helices form a Panel-like domain. Overall the architecture of the protein is remarkably similar to the sodium-proton antiporter NhaA3 despite no detectable sequence homology. A bile acid molecule is situated between the Core and Panel domains in a large hydrophobic cavity. Residues near to this cavity have been shown to affect the binding of specific inhibitors of human ASBT4. The position of the bile acid together with the molecular architecture suggests the rudiments of a possible transport mechanism.
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Affiliation(s)
- Nien-Jen Hu
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
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103
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Li J, Tajkhorshid E. A gate-free pathway for substrate release from the inward-facing state of the Na⁺-galactose transporter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:263-71. [PMID: 21978597 DOI: 10.1016/j.bbamem.2011.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/02/2011] [Accepted: 09/10/2011] [Indexed: 10/17/2022]
Abstract
Employing molecular dynamics (MD) simulations, the pathway and mechanism of substrate unbinding from the inward-facing state of the Na(+)-coupled galactose transporter, vSGLT, have been investigated. During a 200-ns equilibrium simulation, repeated spontaneous unbinding events of the substrate from its binding site have been observed. In contrast to the previously proposed gating role of a tyrosine residue (Y263), the unbinding mechanism captured in the present equilibrium simulation does not rely on the displacement and/or rotation of this side chain. Rather, the unbinding involves an initial lateral displacement of the substrate out of the binding site which allows the substrate to completely emerge from the region covered by the side chain of Y263 without any noticeable conformational changes of the latter. Starting with the snapshots taken from this equilibrium simulation with the substrate outside the binding site, steered MD (SMD) simulations were then used to probe the translocation of the substrate along the remaining of the release pathway within the protein's lumen and to characterize the nature of protein-substrate interactions involved in the process. Combining the results of the equilibrium and SMD simulations, we provide a description of the full translocation pathway for the substrate release from the binding site into the cytoplasm. Residues E68, N142, T431, and N267 facilitate the initial substrate's displacement out of the binding site, while the translocation of the substrate along the remainder of the exit pathway formed between TM6 and TM8 is facilitated by H-bond interactions between the substrate and a series of conserved, polar residues (Y138, N267, R273, S365, S368, N371, S372, and T375). The observed molecular events indicate that no gating is required for the release of the substrate from the crystallographically captured structure of the inward-facing state of SGLT, suggesting that this conformation might represent an open, rather than occluded, state of the transporter. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Jing Li
- Department of Biochemistry, College of Medicine, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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104
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Veyrier FJ, Boneca IG, Cellier MF, Taha MK. A novel metal transporter mediating manganese export (MntX) regulates the Mn to Fe intracellular ratio and Neisseria meningitidis virulence. PLoS Pathog 2011; 7:e1002261. [PMID: 21980287 PMCID: PMC3182930 DOI: 10.1371/journal.ppat.1002261] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/22/2011] [Indexed: 12/16/2022] Open
Abstract
Neisseria meningitidis (Nm) and N. gonorrhoeae (Ng) are adapted to different environments within their human host. If the basis of this difference has not yet been fully understood, previous studies (including our own data) have reported that, unlike Ng, Nm tolerates high manganese concentrations. As transition metals are essential regulators of cell growth and host pathogen interactions, we aimed to address mechanisms of Nm Mn²⁺ tolerance and its pathogenic consequences. Using bioinformatics, gene deletion and heterologous expression we identified a conserved bacterial manganese resistance factor MntX (formerly YebN). The predicted structure suggests that MntX represents a new family of transporters exporting Mn. In the Neisseria genus, this exporter is present and functional in all Nm isolates but it is mutated in a majority of Ng strains and commonly absent in nonpathogenic species. In Nm, Mn²⁺ export via MntX regulates the intracellular Mn/Fe ratio and protects against manganese toxicity that is exacerbated in low iron conditions. MntX is also important for N. meningitidis to resist killing by human serum and for survival in mice blood during septicemia. The present work thus points to new clues about Mn homeostasis, its interplay with Fe metabolism and the influence on N. meningitidis physiology and pathogenicity.
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Affiliation(s)
- Frédéric J Veyrier
- Institut Pasteur, Infection Bactériennes Invasives, Dept. Infection et Epidémiologie, Paris, France.
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105
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Bauer J, Fritsch MJ, Palmer T, Unden G. Topology and Accessibility of the Transmembrane Helices and the Sensory Site in the Bifunctional Transporter DcuB of Escherichia coli. Biochemistry 2011; 50:5925-38. [DOI: 10.1021/bi1019995] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julia Bauer
- Institute for Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55099 Mainz, Germany
| | - Max J. Fritsch
- College of Life Sciences, Division of Molecular Microbiology, University of Dundee, Scotland
| | - Tracy Palmer
- College of Life Sciences, Division of Molecular Microbiology, University of Dundee, Scotland
| | - Gottfried Unden
- Institute for Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55099 Mainz, Germany
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106
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Nolan TL, Lapinsky DJ, Talbot JN, Indarte M, Liu Y, Manepalli S, Geffert LM, Amos ME, Taylor PN, Madura JD, Surratt CK. Identification of a novel selective serotonin reuptake inhibitor by coupling monoamine transporter-based virtual screening and rational molecular hybridization. ACS Chem Neurosci 2011; 2:544-552. [PMID: 21966587 DOI: 10.1021/cn200044x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ligand virtual screening (VS) using the vestibular binding pocket of a 3-D monoamine transporter (MAT) computational model followed by in vitro pharmacology led to the identification of a human serotonin transporter (hSERT) inhibitor with modest affinity (hSERT K(i) = 284 nM). Structural comparison of this VS-elucidated compound, denoted MI-17, to known SERT ligands led to the rational design and synthesis of DJLDU-3-79, a molecular hybrid of MI-17 and dual SERT/5-HT(1A) receptor antagonist SSA-426. Relative to MI-17, DJLDU-3-79 displayed 7-fold improvement in hSERT binding affinity and a 3-fold increase in [(3)H]-serotonin uptake inhibition potency at hSERT/HEK cells. This hybrid compound displayed a hSERT:hDAT selectivity ratio of 50:1, and a hSERT:hNET (human norepinephrine transporter) ratio of >200:1. In mice, DJLDU-3-79 decreased immobility in the tail suspension test comparable to the SSRI fluvoxamine, suggesting that DJLDU-3-79 may possess antidepressant properties. This proof of concept study highlights MAT virtual screening as a powerful tool for identifying novel inhibitor chemotypes and chemical fragments for rational inhibitor design.
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Affiliation(s)
- Tammy L. Nolan
- Division of Pharmaceutical Sciences, Mylan School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
- Departments of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - David J. Lapinsky
- Division of Pharmaceutical Sciences, Mylan School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffery N. Talbot
- Department of Pharmaceutical and Biomedical Sciences, Raabe College of Pharmacy, Ohio Northern University, 525 South Main Street, Ada, Ohio 45810, United States
| | - Martín Indarte
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Yi Liu
- Division of Pharmaceutical Sciences, Mylan School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Sankar Manepalli
- Departments of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Laura M. Geffert
- Division of Pharmaceutical Sciences, Mylan School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Mary Ellen Amos
- Department of Pharmaceutical and Biomedical Sciences, Raabe College of Pharmacy, Ohio Northern University, 525 South Main Street, Ada, Ohio 45810, United States
| | - Phillip N. Taylor
- Department of Pharmaceutical and Biomedical Sciences, Raabe College of Pharmacy, Ohio Northern University, 525 South Main Street, Ada, Ohio 45810, United States
| | - Jeffry D. Madura
- Departments of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Christopher K. Surratt
- Division of Pharmaceutical Sciences, Mylan School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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107
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Abstract
Diverse mechanisms for pH sensing and cytoplasmic pH homeostasis enable most bacteria to tolerate or grow at external pH values that are outside the cytoplasmic pH range they must maintain for growth. The most extreme cases are exemplified by the extremophiles that inhabit environments with a pH of below 3 or above 11. Here, we describe how recent insights into the structure and function of key molecules and their regulators reveal novel strategies of bacterial pH homeostasis. These insights may help us to target certain pathogens more accurately and to harness the capacities of environmental bacteria more efficiently.
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Affiliation(s)
- Terry A. Krulwich
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA; Tel. 212-241-7280; Fax. 212-996-7214
| | - George Sachs
- Departments of Physiology and Medicine, David Geffen School of Medicine at UCLA, 405 Hilgard Ave., Los Angeles, California 90024, USA Tel. 310-268-3923, Fax 310-312-9478
| | - Etana Padan
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel, Tel. 972 2 6585094, Fax 972 2 658947
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108
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Newstead S, Drew D, Cameron AD, Postis VLG, Xia X, Fowler PW, Ingram JC, Carpenter EP, Sansom MSP, McPherson MJ, Baldwin SA, Iwata S. Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2. EMBO J 2011; 30:417-26. [PMID: 21131908 PMCID: PMC3025455 DOI: 10.1038/emboj.2010.309] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 11/04/2010] [Indexed: 01/24/2023] Open
Abstract
PepT1 and PepT2 are major facilitator superfamily (MFS) transporters that utilize a proton gradient to drive the uptake of di- and tri-peptides in the small intestine and kidney, respectively. They are the major routes by which we absorb dietary nitrogen and many orally administered drugs. Here, we present the crystal structure of PepT(So), a functionally similar prokaryotic homologue of the mammalian peptide transporters from Shewanella oneidensis. This structure, refined using data up to 3.6 Å resolution, reveals a ligand-bound occluded state for the MFS and provides new insights into a general transport mechanism. We have located the peptide-binding site in a central hydrophilic cavity, which occludes a bound ligand from both sides of the membrane. Residues thought to be involved in proton coupling have also been identified near the extracellular gate of the cavity. Based on these findings and associated kinetic data, we propose that PepT(So) represents a sound model system for understanding mammalian peptide transport as catalysed by PepT1 and PepT2.
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Affiliation(s)
- Simon Newstead
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College London, London, UK.
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109
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Forrest LR, Krämer R, Ziegler C. The structural basis of secondary active transport mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:167-88. [PMID: 21029721 DOI: 10.1016/j.bbabio.2010.10.014] [Citation(s) in RCA: 321] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/13/2010] [Accepted: 10/15/2010] [Indexed: 12/22/2022]
Abstract
Secondary active transporters couple the free energy of the electrochemical potential of one solute to the transmembrane movement of another. As a basic mechanistic explanation for their transport function the model of alternating access was put forward more than 40 years ago, and has been supported by numerous kinetic, biochemical and biophysical studies. According to this model, the transporter exposes its substrate binding site(s) to one side of the membrane or the other during transport catalysis, requiring a substantial conformational change of the carrier protein. In the light of recent structural data for a number of secondary transport proteins, we analyze the model of alternating access in more detail, and correlate it with specific structural and chemical properties of the transporters, such as their assignment to different functional states in the catalytic cycle of the respective transporter, the definition of substrate binding sites, the type of movement of the central part of the carrier harboring the substrate binding site, as well as the impact of symmetry on fold-specific conformational changes. Besides mediating the transmembrane movement of solutes, the mechanism of secondary carriers inherently involves a mechanistic coupling of substrate flux to the electrochemical potential of co-substrate ions or solutes. Mainly because of limitations in resolution of available transporter structures, this important aspect of secondary transport cannot yet be substantiated by structural data to the same extent as the conformational change aspect. We summarize the concepts of coupling in secondary transport and discuss them in the context of the available evidence for ion binding to specific sites and the impact of the ions on the conformational state of the carrier protein, which together lead to mechanistic models for coupling.
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Affiliation(s)
- Lucy R Forrest
- Structural Biology Department, Max Planck Institute for Biophysics, Frankfurt, Germany
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