1
|
Pyrris Y, Papadaki GF, Mikros E, Diallinas G. The last two transmembrane helices in the APC-type FurE transporter act as an intramolecular chaperone essential for concentrative ER-exit. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:1-15. [PMID: 38225947 PMCID: PMC10788122 DOI: 10.15698/mic2024.01.811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 01/17/2024]
Abstract
FurE is a H+ symporter specific for the cellular uptake of uric acid, allantoin, uracil, and toxic nucleobase analogues in the fungus Aspergillus nidulans. Being member of the NCS1 protein family, FurE is structurally related to the APC-superfamily of transporters. APC-type transporters are characterised by a 5+5 inverted repeat fold made of ten transmembrane segments (TMS1-10) and function through the rocking-bundle mechanism. Most APC-type transporters possess two extra C-terminal TMS segments (TMS11-12), the function of which remains elusive. Here we present a systematic mutational analysis of TMS11-12 of FurE and show that two specific aromatic residues in TMS12, Trp473 and Tyr484, are essential for ER-exit and trafficking to the plasma membrane (PM). Molecular modeling shows that Trp473 and Tyr484 might be essential through dynamic interactions with residues in TMS2 (Leu91), TMS3 (Phe111), TMS10 (Val404, Asp406) and other aromatic residues in TMS12. Genetic analysis confirms the essential role of Phe111, Asp406 and TMS12 aromatic residues in FurE ER-exit. We further show that co-expression of FurE-Y484F or FurE-W473A with wild-type FurE leads to a dominant negative phenotype, compatible with the concept that FurE molecules oligomerize or partition in specific microdomains to achieve concentrative ER-exit and traffic to the PM. Importantly, truncated FurE versions lacking TMS11-12 are unable to reproduce a negative effect on the trafficking of co-expressed wild-type FurE. Overall, we show that TMS11-12 acts as an intramolecular chaperone for proper FurE folding, which seems to provide a structural code for FurE partitioning in ER-exit sites.
Collapse
Affiliation(s)
- Yiannis Pyrris
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15784, Greece
| | - Georgia F. Papadaki
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15784, Greece
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15771, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15784, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, 70013, Greece
| |
Collapse
|
2
|
Becker L, Hausmann J, Hartmann AM. Both chloride-binding sites are required for KCC2-mediated transport. J Biol Chem 2023; 299:105190. [PMID: 37625593 PMCID: PMC10518353 DOI: 10.1016/j.jbc.2023.105190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
The K+-Cl- cotransporter 2 (KCC2) plays an important role in inhibitory neurotransmission, and its impairment is associated with neurological and psychiatric disorders, including epilepsy, schizophrenia, and autism. Although KCCs transport K+ and Cl- in a 1:1 stoichiometry, two Cl- coordination sites were indicated via cryo-EM. In a comprehensive analysis, we analyzed the consequences of point mutations of residues coordinating Cl- in Cl1 and Cl2. Individual mutations of residues in Cl1 and Cl2 reduce or abolish KCC2WT function, indicating a crucial role of both Cl- coordination sites for KCC2 function. Structural changes in the extracellular loop 2 by inserting a 3xHA tag switches the K+ coordination site to another position. To investigate, whether the extension of the extracellular loop 2 with the 3xHA tag also affects the coordination of the two Cl- coordination sites, we carried out the analogous experiments for both Cl- coordinating sites in the KCC2HA construct. These analyses showed that most of the individual mutation of residues in Cl1 and Cl2 in the KCC2HA construct reduces or abolishes KCC2 function, indicating that the coordination of Cl- remains at the same position. However, the coupling of K+ and Cl- in Cl1 is still apparent in the KCC2HA construct, indicating a mutual dependence of both ions. In addition, the coordination residue Tyr569 in Cl2 shifted in KCC2HA. Thus, conformational changes in the extracellular domain affect K+ and Cl--binding sites. However, the effect on the Cl--binding sites is subtler.
Collapse
Affiliation(s)
- Lisa Becker
- Division of Neurogenetics, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Jens Hausmann
- Division of Anatomy, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Anna-Maria Hartmann
- Division of Neurogenetics, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Research Center for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| |
Collapse
|
3
|
Insights into the Transport Cycle of LAT1 and Interaction with the Inhibitor JPH203. Int J Mol Sci 2023; 24:ijms24044042. [PMID: 36835453 PMCID: PMC9965313 DOI: 10.3390/ijms24044042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
The large Amino Acid Transporter 1 (LAT1) is an interesting target in drug discovery since this transporter is overexpressed in several human cancers. Furthermore, due to its location in the blood-brain barrier (BBB), LAT1 is interesting for delivering pro-drugs to the brain. In this work, we focused on defining the transport cycle of LAT1 using an in silico approach. So far, studies of the interaction of LAT1 with substrates and inhibitors have not considered that the transporter must undergo at least four different conformations to complete the transport cycle. We built outward-open and inward-occluded conformations of LAT1 using an optimized homology modelling procedure. We used these 3D models and the cryo-EM structures in outward-occluded and inward-open conformations to define the substrate/protein interaction during the transport cycle. We found that the binding scores for the substrate depend on the conformation, with the occluded states as the crucial steps affecting the substrate affinity. Finally, we analyzed the interaction of JPH203, a high-affinity inhibitor of LAT1. The results indicate that conformational states must be considered for in silico analyses and early-stage drug discovery. The two built models, together with the available cryo-EM 3D structures, provide important information on the LAT1 transport cycle, which could be used to speed up the identification of potential inhibitors through in silico screening.
Collapse
|
4
|
Llanos MA, Alberca LN, Ruiz MD, Sbaraglini ML, Miranda C, Pino-Martinez A, Fraccaroli L, Carrillo C, Alba Soto CD, Gavernet L, Talevi A. A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity. J Comput Aided Mol Des 2023; 37:75-90. [PMID: 36494599 DOI: 10.1007/s10822-022-00491-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the protozoa Trypanosoma cruzi, affecting nearly 7 million people only in the Americas. Polyamines are essential compounds for parasite growth, survival, and differentiation. However, because trypanosomatids are auxotrophic for polyamines, they must be obtained from the host by specific transporters. In this investigation, an ensemble of QSAR classifiers able to identify polyamine analogs with trypanocidal activity was developed. Then, a multi-template homology model of the dimeric polyamine transporter of T. cruzi, TcPAT12, was created with Rosetta, and then refined by enhanced sampling molecular dynamics simulations. Using representative snapshots extracted from the trajectory, a docking model able to discriminate between active and inactive compounds was developed and validated. Both models were applied in a parallel virtual screening campaign to repurpose known drugs as anti-trypanosomal compounds inhibiting polyamine transport in T. cruzi. Montelukast, Quinestrol, Danazol, and Dutasteride were selected for in vitro testing, and all of them inhibited putrescine uptake in biochemical assays, confirming the predictive ability of the computational models. Furthermore, all the confirmed hits proved to inhibit epimastigote proliferation, and Quinestrol and Danazol were able to inhibit, in the low micromolar range, the viability of trypomastigotes and the intracellular growth of amastigotes.
Collapse
Affiliation(s)
- Manuel A Llanos
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - Lucas N Alberca
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - María D Ruiz
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - María L Sbaraglini
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - Cristian Miranda
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Agustina Pino-Martinez
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Laura Fraccaroli
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Carolina Carrillo
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Catalina D Alba Soto
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Luciana Gavernet
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina.
| | - Alan Talevi
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| |
Collapse
|
5
|
Zhou Y, Lewis JH, Lu Z. Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules. eLife 2023; 12:82175. [PMID: 36800214 PMCID: PMC9937647 DOI: 10.7554/elife.82175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/15/2023] [Indexed: 02/18/2023] Open
Abstract
Most membrane protein molecules undergo conformational changes as they transition from one functional state to another one. An understanding of the mechanism underlying these changes requires the ability to resolve individual conformational states, whose changes often occur on millisecond and angstrom scales. Tracking such changes and acquiring a sufficiently large amount of data remain challenging. Here, we use the amino-acid transporter AdiC as an example to demonstrate the application of a high-resolution fluorescence-polarization-microscopy method in tracking multistate conformational changes of a membrane protein. We have successfully resolved four conformations of AdiC by monitoring the emission-polarization changes of a fluorophore label and quantified their probabilities in the presence of a series of concentrations of its substrate arginine. The acquired data are sufficient for determining all equilibrium constants that fully establish the energetic relations among the four states. The KD values determined for arginine in four individual conformations are statistically comparable to the previously reported overall KD determined using isothermal titration calorimetry. This demonstrated strong resolving power of the present polarization-microscopy method will enable an acquisition of the quantitative information required for understanding the expected complex conformational mechanism underlying the transporter's function, as well as those of other membrane proteins.
Collapse
Affiliation(s)
- Yufeng Zhou
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - John H Lewis
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| |
Collapse
|
6
|
Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
Collapse
Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| |
Collapse
|
7
|
Anderson CMH, Edwards N, Watson AK, Althaus M, Thwaites DT. Reshaping the Binding Pocket of the Neurotransmitter:Solute Symporter (NSS) Family Transporter SLC6A14 (ATB 0,+) Selectively Reduces Access for Cationic Amino Acids and Derivatives. Biomolecules 2022; 12:biom12101404. [PMID: 36291613 PMCID: PMC9599917 DOI: 10.3390/biom12101404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
SLC6A14 (ATB0,+) is unique among SLC proteins in its ability to transport 18 of the 20 proteinogenic (dipolar and cationic) amino acids and naturally occurring and synthetic analogues (including anti-viral prodrugs and nitric oxide synthase (NOS) inhibitors). SLC6A14 mediates amino acid uptake in multiple cell types where increased expression is associated with pathophysiological conditions including some cancers. Here, we investigated how a key position within the core LeuT-fold structure of SLC6A14 influences substrate specificity. Homology modelling and sequence analysis identified the transmembrane domain 3 residue V128 as equivalent to a position known to influence substrate specificity in distantly related SLC36 and SLC38 amino acid transporters. SLC6A14, with and without V128 mutations, was heterologously expressed and function determined by radiotracer solute uptake and electrophysiological measurement of transporter-associated current. Substituting the amino acid residue occupying the SLC6A14 128 position modified the binding pocket environment and selectively disrupted transport of cationic (but not dipolar) amino acids and related NOS inhibitors. By understanding the molecular basis of amino acid transporter substrate specificity we can improve knowledge of how this multi-functional transporter can be targeted and how the LeuT-fold facilitates such diversity in function among the SLC6 family and other SLC amino acid transporters.
Collapse
Affiliation(s)
- Catriona M. H. Anderson
- School of Natural & Environmental Sciences, Faculty of Science, Engineering & Agriculture, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Correspondence: (C.M.H.A.); (D.T.T.)
| | - Noel Edwards
- Biosciences Institute, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew K. Watson
- Biosciences Institute, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mike Althaus
- School of Natural & Environmental Sciences, Faculty of Science, Engineering & Agriculture, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Natural Sciences & Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53359 Rheinbach, Germany
| | - David T. Thwaites
- Biosciences Institute, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Correspondence: (C.M.H.A.); (D.T.T.)
| |
Collapse
|
8
|
Conformational transition induced in the aspartate:alanine antiporter by L-Ala binding. Sci Rep 2022; 12:15871. [PMID: 36151227 PMCID: PMC9508256 DOI: 10.1038/s41598-022-19974-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
An aspartate:alanine antiporter (AspT) from the lactic acid bacterium Tetragenococcus halophilus catalyzes the electrogenic aspartate<sup>1-</sup>:alanine<sup>0</sup> exchange reaction. Our previous kinetic analyses of transport reactions mediated by AspT in reconstituted liposomes suggested that, although the substrate transport reactions are physiologically coupled, the putative binding sites of L-aspartate (-Asp) and L-alanine (-Ala) are independently located on AspT. By using the fluorescent probe Oregon Green maleimide (OGM), which reacts specifically with cysteine, we also found that the presence of L-Asp changes the conformation of AspT. In this study, we conducted an OGM labeling assay in the presence of L-Ala. The labeling efficiency of single cysteine mutants (G62C and P79C) in transmembrane helix 3 of the AspT showed novel patterns depending on the presence of L-Ala or analogs. A concentration-dependent shift of AspT from the conformation in the presence of one substrate to that specific to the substrate added subsequently (L-Ala or L-Asp) was observed. Moreover, size-exclusion-chromatography-based thermostability assays indicated that the thermal stability of AspT in the presence of L-Ala differed from that in the presence of L-Asp. From these results, we concluded that L-Ala binding yields a conformation different from the apo or L-Asp binding conformations.
Collapse
|
9
|
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: 8] [Impact Index Per Article: 4.0] [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.
Collapse
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.
| |
Collapse
|
10
|
Staritzbichler R, Yaklich E, Sarti E, Ristic N, Hildebrand PW, Forrest LR. AlignMe: an update of the web server for alignment of membrane protein sequences. Nucleic Acids Res 2022; 50:W29-W35. [PMID: 35609986 PMCID: PMC9252776 DOI: 10.1093/nar/gkac391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
The AlignMe web server is dedicated to accurately aligning sequences of membrane proteins, a particularly challenging task due to the strong evolutionary divergence and the low compositional complexity of hydrophobic membrane-spanning proteins. AlignMe can create pairwise alignments of either two primary amino acid sequences or two hydropathy profiles. The web server for AlignMe has been continuously available for >10 years, supporting 1000s of users per year. Recent improvements include anchoring, multiple submissions, and structure visualization. Anchoring is the ability to constrain a position in an alignment, which allows expert information about related residues in proteins to be incorporated into an alignment without manual modification. The original web interface to the server limited the user to one alignment per submission, hindering larger scale studies. Now, batches of alignments can be initiated with a single submission. Finally, to provide structural context for the relationship between proteins, sequence similarity can now be mapped onto one or more structures (or structural models) of the proteins being aligned, by links to MutationExplorer, a web-based visualization tool. Together with a refreshed user interface, these features further enhance an important resource in the membrane protein community. The AlignMe web server is freely available at https://www.bioinfo.mpg.de/AlignMe/.
Collapse
Affiliation(s)
- René Staritzbichler
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Emily Yaklich
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edoardo Sarti
- Algorithms, Biology, Structure Unit Inria Sophia Antipolis - Méditerranée, 06902 Valbonne, France
| | - Nikola Ristic
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter W Hildebrand
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany.,Charité -Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, 10117 Berlin, Germany
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
11
|
Peluffo RD. Cationic amino acid transporters and their modulation by nitric oxide in cardiac muscle cells. Biophys Rev 2022; 13:1071-1079. [PMID: 35059028 DOI: 10.1007/s12551-021-00870-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/22/2021] [Indexed: 01/03/2023] Open
Abstract
Cationic amino acid transporters (CATs) play a central role in the supply of the substrate L-arginine to intracellular nitric oxide synthases (NOS), the enzymes responsible for the synthesis of nitric oxide (NO). In heart, NO produced by cardiac myocytes has diverse and even opposite effects on myocardial contractility depending on the subcellular location of its production. Approximately a decade ago, using a combination of biophysical and biochemical approaches, we discovered and characterized high- and low-affinity CATs that function simultaneously in the cardiac myocyte plasma membrane. Later on, we reported a negative feedback regulation of NO on the activity of cardiac CATs. In this way, NO was found to modulate its own biosynthesis by regulating the amount of L-arginine that becomes available as NOS substrate. We have recently solved the molecular determinants for this NO regulation on the low-affinity high-capacity CAT-2A. This review highlights some biophysical and biochemical features of L-arginine transporters and their potential relation to cardiac muscle physiology and pathology.
Collapse
Affiliation(s)
- R Daniel Peluffo
- Group of Biophysical Chemistry, Department of Biological Sciences, CENUR Litoral Norte, Universidad de La República, Rivera 1350, CP: 50000 Salto, Uruguay.,Department of Pharmacology, Physiology and Neuroscience, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, Newark, NJ 07103 USA
| |
Collapse
|
12
|
Structural basis for substrate specificity of heteromeric transporters of neutral amino acids. Proc Natl Acad Sci U S A 2021; 118:2113573118. [PMID: 34848541 DOI: 10.1073/pnas.2113573118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
Despite having similar structures, each member of the heteromeric amino acid transporter (HAT) family shows exquisite preference for the exchange of certain amino acids. Substrate specificity determines the physiological function of each HAT and their role in human diseases. However, HAT transport preference for some amino acids over others is not yet fully understood. Using cryo-electron microscopy of apo human LAT2/CD98hc and a multidisciplinary approach, we elucidate key molecular determinants governing neutral amino acid specificity in HATs. A few residues in the substrate-binding pocket determine substrate preference. Here, we describe mutations that interconvert the substrate profiles of LAT2/CD98hc, LAT1/CD98hc, and Asc1/CD98hc. In addition, a region far from the substrate-binding pocket critically influences the conformation of the substrate-binding site and substrate preference. This region accumulates mutations that alter substrate specificity and cause hearing loss and cataracts. Here, we uncover molecular mechanisms governing substrate specificity within the HAT family of neutral amino acid transporters and provide the structural bases for mutations in LAT2/CD98hc that alter substrate specificity and that are associated with several pathologies.
Collapse
|
13
|
Zhuo TX, Wang Z, Song YY, Yan SW, Liu RD, Zhang X, Wang ZQ, Cui J. Characterization of a Novel Glutamine Synthetase From Trichinella spiralis and Its Participation in Larval Acid Resistance, Molting, and Development. Front Cell Dev Biol 2021; 9:729402. [PMID: 34616735 PMCID: PMC8488193 DOI: 10.3389/fcell.2021.729402] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 12/29/2022] Open
Abstract
Trichinella spiralis is a major foodborne parasite worldwide. After the encapsulated muscle larvae (ML) in meat are ingested, the ML are liberated in the stomach of the host and activated into intestinal infectious larvae (IIL), which develop into adult worm after molting four times. A novel glutamine synthetase (TsGS) was identified from T. spiralis IIL at 10 h post-infection, but its biological role in T. spiralis life cycle is not clear. The aim of this study was to investigate the biological characteristics of TsGS and its functions in larval acid resistance, molting, and development. TsGS has a glutamine synthetase (GS) catalytic domain. Complete TsGS sequence was cloned and expressed in Escherichia coli BL21. rTsGS has good immunogenicity. qPCR and Western blotting showed that TsGS was highly expressed at IIL stage, and immunofluorescence revealed that TsGS was principally localized at the cuticle and intrauterine embryos of this nematode. rTsGS has enzymatic activity of natural GS to hydrolyze the substrate (Glu, ATP, and NH4+). Silencing of TsGS gene significantly reduced the IIL survival at pH 2.5, decreased the IIL burden, and impeded larval molting and development. The results demonstrated that TsGS participates in T. spiralis larval acid resistance, molting and development, and it might be a candidate vaccine target against Trichinella molting and development.
Collapse
Affiliation(s)
- Tong Xu Zhuo
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Zhen Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Yan Yan Song
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Shu Wei Yan
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Ruo Dan Liu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Xi Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Zhong Quan Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cui
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
14
|
Papalazarou V, Maddocks ODK. Supply and demand: Cellular nutrient uptake and exchange in cancer. Mol Cell 2021; 81:3731-3748. [PMID: 34547236 DOI: 10.1016/j.molcel.2021.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/27/2021] [Accepted: 08/19/2021] [Indexed: 12/24/2022]
Abstract
Nutrient supply and demand delineate cell behavior in health and disease. Mammalian cells have developed multiple strategies to secure the necessary nutrients that fuel their metabolic needs. This is more evident upon disruption of homeostasis in conditions such as cancer, when cells display high proliferation rates in energetically challenging conditions where nutritional sources may be scarce. Here, we summarize the main routes of nutrient acquisition that fuel mammalian cells and their implications in tumorigenesis. We argue that the molecular mechanisms of nutrient acquisition not only tip the balance between nutrient supply and demand but also determine cell behavior upon nutrient limitation and energetic stress and contribute to nutrient partitioning and metabolic coordination between different cell types in inflamed or tumorigenic environments.
Collapse
Affiliation(s)
- Vasileios Papalazarou
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | - Oliver D K Maddocks
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK.
| |
Collapse
|
15
|
Ilgü H, Jeckelmann JM, Kalbermatter D, Ucurum Z, Lemmin T, Fotiadis D. High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding. BMC Biol 2021; 19:179. [PMID: 34461897 PMCID: PMC8406831 DOI: 10.1186/s12915-021-01102-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/16/2021] [Indexed: 12/04/2022] Open
Abstract
Background The L-arginine/agmatine transporter AdiC is part of the arginine-dependent extreme acid resistance system of the bacterium Escherichia coli and its pathogenic varieties such as strain E. coli O157:H7. At the present time, there is a lack of knowledge concerning the role of water molecules and networks for the structure and function of AdiC, and solute transporters in general. Results The structure of the L-arginine/agmatine transporter AdiC was determined at 1.7 Å resolution by X-ray crystallography. This high resolution allowed for the identification of numerous water molecules buried in the structure. In combination with molecular dynamics (MD) simulations, we demonstrate that water molecules play an important role for stabilizing the protein and key residues, and act as placeholders for atoms of the AdiC substrates L-arginine and agmatine. MD simulations unveiled flexibility and restrained mobility of gating residues W202 and W293, respectively. Furthermore, a water-filled cavity was identified at the dimer interface of AdiC. The two monomers formed bridging interactions through water-mediated hydrogen bonds. The accessibility and presence of water molecules in this cavity was confirmed with MD simulations. Point mutations disrupting the interfacial water network validated the importance of water molecules for dimer stabilization. Conclusions This work gives new insights into the role and importance of water molecules in the L-arginine/agmatine transporter AdiC for protein stabilization and substrate-binding site shaping and as placeholders of substrate atoms. Furthermore, and based on the observed flexibility and restrained mobility of gating residues, a mechanistic role of the gate flexibility in the transport cycle was proposed. Finally, we identified a water-filled cavity at the dimeric interface that contributes to the stability of the amino acid transporter oligomer. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01102-4.
Collapse
Affiliation(s)
- Hüseyin Ilgü
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland
| | - Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland
| | - David Kalbermatter
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland
| | - Thomas Lemmin
- DS3Lab, System Group, Department of Computer Sciences, ETH Zurich, CH-8093, Zürich, Switzerland. .,Trkola Group, Institute for Medical Virology, University of Zurich, CH-8057, Zürich, Switzerland.
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland.
| |
Collapse
|
16
|
Zhan J, Tan X, Wang X. Null mutation in sspA of Cronobacter sakazakii influences its tolerance to environmental stress. Can J Microbiol 2021; 67:902-918. [PMID: 34379995 DOI: 10.1139/cjm-2021-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cronobacter sakazakii is a known foodborne opportunistic pathogen that can affect the intestinal health of infants. Despite undergoing complex manufacturing processes and low water concentration in the finished product, infant formula has been associated with Cronobacter infections, suggesting that C. sakazakii's pathogenicity may be related to its tolerance to stress. In this study, the effect of the stringent starvation protein A (SspA), which plays an important role in E. coli cellular survival under environmental stresses, on the stress tolerance of C. sakazakii BAA894 was investigated by creating an sspA-knockout mutant. The effects of this mutation on the acid, desiccation and drug tolerance were assessed, and results showed that acid tolerance decreased, while desiccation tolerance increased in LB and decreased in M9. Moreover, the MICs of 10 antibiotics in LB medium and 8 antibiotics in M9 medium were determined and compared of the wild-type and ΔsspA. Transcriptome analysis showed that 27.21% or 37.78% of the genes in ΔsspA were significantly differentially expressed in LB or M9 media, the genes relevant to microbial metabolism in diverse environments and bacterial chemotaxis were detailed analyzed. The current study contributes towards an improved understanding of the role of SspA in C. sakazakii BAA894 stress tolerance.
Collapse
Affiliation(s)
- Jie Zhan
- Jiangnan University, 66374, State Key Laboratory of Food Science and Technology, Wuxi, China;
| | - Xin Tan
- Jiangnan University, 66374, Wuxi, China.,Jiangnan University, 66374, Wuxi, China;
| | - Xiaoyuan Wang
- Jiangnan University, 66374, Wuxi, China, 214122.,Jiangnan University, 66374, Wuxi, China, 214122.,Jiangnan University, 66374, Wuxi, China, 214122;
| |
Collapse
|
17
|
Nicolàs-Aragó A, Fort J, Palacín M, Errasti-Murugarren E. Rush Hour of LATs towards Their Transport Cycle. MEMBRANES 2021; 11:602. [PMID: 34436365 PMCID: PMC8399266 DOI: 10.3390/membranes11080602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/29/2022]
Abstract
The mammalian SLC7 family comprises the L-amino acid transporters (LATs) and the cationic amino acid transporters (CATs). The relevance of these transporters is highlighted by their involvement in several human pathologies, including inherited rare diseases and acquired diseases, such as cancer. In the last four years, several crystal or cryo-EM structures of LATs and CATs have been solved. These structures have started to fill our knowledge gap that previously was based on the structural biology of remote homologs of the amino acid-polyamine-organocation (APC) transporters. This review recovers this structural and functional information to start generating the molecular bases of the transport cycle of LATs. Special attention is given to the known transporter conformations within the transport cycle and the molecular bases for substrate interaction and translocation, including the asymmetric interaction of substrates at both sides of the plasma membrane.
Collapse
Affiliation(s)
- Adrià Nicolàs-Aragó
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (J.F.)
| | - Joana Fort
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (J.F.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Manuel Palacín
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (J.F.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Ekaitz Errasti-Murugarren
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (J.F.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
| |
Collapse
|
18
|
Kärkkäinen J, Laitinen T, Markowicz-Piasecka M, Montaser A, Lehtonen M, Rautio J, Gynther M, Poso A, Huttunen KM. Molecular characteristics supporting l-Type amino acid transporter 1 (LAT1)-mediated translocation. Bioorg Chem 2021; 112:104921. [PMID: 33933805 DOI: 10.1016/j.bioorg.2021.104921] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/21/2021] [Accepted: 02/23/2021] [Indexed: 01/02/2023]
Abstract
l-Type amino acid transporter 1 (LAT1) is an interesting protein due to its peculiar expression profile. It can be utilized not only as a carrier for improved or targeted drug delivery, e.g., into the brain but also as a target protein by which amino acid supply can be restricted, e.g., from the cancer cells. The recognition and binding processes of LAT1-ligands, such as amino acids and clinically used small molecules, including l-dopa, gabapentin, and melphalan, are today well-known. Binding to LAT1 is crucial, particularly when designing the LAT1-inhibitors. However, it will not guarantee effective translocation across the cell membrane via LAT1, which is a definite requirement for LAT1-substrates, such as drugs that elicit their pharmacological effects inside the cells. Therefore, in the present study, the accumulation of known LAT1-utilizing compounds into the selected LAT1-expressing cancer cells (MCF-7) was explored experimentally over a time period. The differences found among the transport efficiency and affinity of the studied compounds for LAT1 were subsequently explained by docking the ligands into the human LAT1 model (based on the recent cryo-electron microscopy structure). Thus, the findings of this study clarify the favorable structural requirements of the size, shape, and polarity of the ligands that support the translocation and effective transport across the cell membrane via LAT1. This knowledge can be applied in future drug design to attain improved or targeted drug delivery and hence, successful LAT1-utilizing drugs with increased therapeutic effects.
Collapse
Affiliation(s)
- Jussi Kärkkäinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; Department of Pharmacy, Kuopio University Hospital, Finland, P.O. Box 100, FI-70029, KYS, Kuopio, Finland
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Magdalena Markowicz-Piasecka
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry Drug Analysis and Radiopharmacy, Medical University of Lodz, Lodz, Poland
| | - Ahmed Montaser
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Jarkko Rautio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Mikko Gynther
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Kristiina M Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| |
Collapse
|
19
|
Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking. Comput Struct Biotechnol J 2021; 19:1713-1737. [PMID: 33897977 PMCID: PMC8050425 DOI: 10.1016/j.csbj.2021.03.013] [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: 11/01/2020] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
Plasma membrane transporters play pivotal roles in the import of nutrients, including sugars, amino acids, nucleobases, carboxylic acids, and metal ions, that surround fungal cells. The selective removal of these transporters by endocytosis is one of the most important regulatory mechanisms that ensures a rapid adaptation of cells to the changing environment (e.g., nutrient fluctuations or different stresses). At the heart of this mechanism lies a network of proteins that includes the arrestin‐related trafficking adaptors (ARTs) which link the ubiquitin ligase Rsp5 to nutrient transporters and endocytic factors. Transporter conformational changes, as well as dynamic interactions between its cytosolic termini/loops and with lipids of the plasma membrane, are also critical during the endocytic process. Here, we review the current knowledge and recent findings on the molecular mechanisms involved in nutrient transporter endocytosis, both in the budding yeast Saccharomyces cerevisiae and in some species of the filamentous fungus Aspergillus. We elaborate on the physiological importance of tightly regulated endocytosis for cellular fitness under dynamic conditions found in nature and highlight how further understanding and engineering of this process is essential to maximize titer, rate and yield (TRY)-values of engineered cell factories in industrial biotechnological processes.
Collapse
Key Words
- AAs, amino acids
- ACT, amino Acid/Choline Transporter
- AP, adaptor protein
- APC, amino acid-polyamine-organocation
- Arg, arginine
- Arrestins
- Arts, arrestin‐related trafficking adaptors
- Asp, aspartic acid
- Aspergilli
- Biotechnology
- C, carbon
- C-terminus, carboxyl-terminus
- Cell factories
- Conformational changes
- Cu, copper
- DUBs, deubiquitinating enzymes
- EMCs, eisosome membrane compartments
- ER, endoplasmic reticulum
- ESCRT, endosomal sorting complex required for transport
- Endocytic signals
- Endocytosis
- Fe, iron
- Fungi
- GAAC, general amino acid control
- Glu, glutamic acid
- H+, proton
- IF, inward-facing
- LAT, L-type Amino acid Transporter
- LID, loop Interaction Domain
- Lys, lysine
- MCCs, membrane compartments containing the arginine permease Can1
- MCCs/eisosomes
- MCPs, membrane compartments of Pma1
- MFS, major facilitator superfamily
- MVB, multi vesicular bodies
- Met, methionine
- Metabolism
- Mn, manganese
- N, nitrogen
- N-terminus, amino-terminus
- NAT, nucleobase Ascorbate Transporter
- NCS1, nucleobase/Cation Symporter 1
- NCS2, nucleobase cation symporter family 2
- NH4+, ammonium
- Nutrient transporters
- OF, outward-facing
- PEST, proline (P), glutamic acid (E), serine (S), and threonine (T)
- PM, plasma membrane
- PVE, prevacuolar endosome
- Saccharomyces cerevisiae
- Signaling pathways
- Structure-function
- TGN, trans-Golgi network
- TMSs, transmembrane segments
- TORC1, target of rapamycin complex 1
- TRY, titer, rate and yield
- Trp, tryptophan
- Tyr, tyrosine
- Ub, ubiquitin
- Ubiquitylation
- VPS, vacuolar protein sorting
- W/V, weight per volume
- YAT, yeast Amino acid Transporter
- Zn, Zinc
- fAATs, fungal AA transporters
Collapse
|
20
|
Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
Collapse
Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
| |
Collapse
|
21
|
Errasti-Murugarren E, Bartoccioni P, Palacín M. Membrane Protein Stabilization Strategies for Structural and Functional Studies. MEMBRANES 2021; 11:membranes11020155. [PMID: 33671740 PMCID: PMC7926488 DOI: 10.3390/membranes11020155] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies.
Collapse
Affiliation(s)
- Ekaitz Errasti-Murugarren
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
| | - Paola Bartoccioni
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
| | - Manuel Palacín
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
| |
Collapse
|
22
|
Errasti-Murugarren E, Palacín M. Heteromeric Amino Acid Transporters in Brain: from Physiology to Pathology. Neurochem Res 2021; 47:23-36. [PMID: 33606172 DOI: 10.1007/s11064-021-03261-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/12/2022]
Abstract
In humans, more than 50 transporters are responsible for the traffic and balance of amino acids within and between cells and tissues, and half of them have been associated with disease [1]. Covering all common amino acids, Heteromeric Amino acid Transporters (HATs) are one class of such transporters. This review first highlights structural and functional studies that solved the atomic structure of HATs and revealed molecular clues on substrate interaction. Moreover, this review focuses on HATs that have a role in the central nervous system (CNS) and that are related to neurological diseases, including: (i) LAT1/CD98hc and its role in the uptake of branched chain amino acids trough the blood brain barrier and autism. (ii) LAT2/CD98hc and its potential role in the transport of glutamine between plasma and cerebrospinal fluid. (iii) y+LAT2/CD98hc that is emerging as a key player in hepatic encephalopathy. xCT/CD98hc as a potential therapeutic target in glioblastoma, and (iv) Asc-1/CD98hc as a potential therapeutic target in pathologies with alterations in NMDA glutamate receptors.
Collapse
Affiliation(s)
- Ekaitz Errasti-Murugarren
- Institute for Research in Biomedicine. Institute of Science and Technology (BIST), 08028, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08028, Barcelona, Spain.
| | - Manuel Palacín
- Institute for Research in Biomedicine. Institute of Science and Technology (BIST), 08028, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08028, Barcelona, Spain. .,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain.
| |
Collapse
|
23
|
Identification of an Acidic Amino Acid Permease Involved in d-Aspartate Uptake in the Yeast Cryptococcus humicola. Microorganisms 2021; 9:microorganisms9010192. [PMID: 33477545 PMCID: PMC7831105 DOI: 10.3390/microorganisms9010192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 11/22/2022] Open
Abstract
d-aspartate oxidase (DDO) catalyzes the oxidative deamination of acidic d-amino acids, and its production is induced by d-Asp in several eukaryotes. The yeast Cryptococcus humicola strain UJ1 produces large amounts of DDO (ChDDO) only in the presence of d-Asp. In this study, we analyzed the relationship between d-Asp uptake by an amino acid permease (Aap) and the inducible expression of ChDDO. We identified two acidic Aap homologs, named “ChAap4 and ChAap5,” in the yeast genome sequence. ChAAP4 deletion resulted in partial growth defects on d-Asp as well as l-Asp, l-Glu, and l-Phe at pH 7, whereas ChAAP5 deletion caused partial growth defects on l-Phe and l-Lys, suggesting that ChAap4 might participate in d-Asp uptake as an acidic Aap. Interestingly, the growth of the Chaap4 strain on d- or l-Asp was completely abolished at pH 10, suggesting that ChAap4 is the only Aap responsible for d- and l-Asp uptake under high alkaline conditions. In addition, ChAAP4 deletion significantly decreased the induction of DDO activity and ChDDO transcription in the presence of d-Asp. This study revealed that d-Asp uptake by ChAap4 might be involved in the induction of ChDDO expression by d-Asp.
Collapse
|
24
|
Focht D, Neumann C, Lyons J, Eguskiza Bilbao A, Blunck R, Malinauskaite L, Schwarz IO, Javitch JA, Quick M, Nissen P. A non-helical region in transmembrane helix 6 of hydrophobic amino acid transporter MhsT mediates substrate recognition. EMBO J 2021; 40:e105164. [PMID: 33155685 PMCID: PMC7780149 DOI: 10.15252/embj.2020105164] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/23/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022] Open
Abstract
MhsT of Bacillus halodurans is a transporter of hydrophobic amino acids and a homologue of the eukaryotic SLC6 family of Na+ -dependent symporters for amino acids, neurotransmitters, osmolytes, or creatine. The broad range of transported amino acids by MhsT prompted the investigation of the substrate recognition mechanism. Here, we report six new substrate-bound structures of MhsT, which, in conjunction with functional studies, reveal how the flexibility of a Gly-Met-Gly (GMG) motif in the unwound region of transmembrane segment 6 (TM6) is central for the recognition of substrates of different size by tailoring the binding site shape and volume. MhsT mutants, harboring substitutions within the unwound GMG loop and substrate binding pocket that mimick the binding sites of eukaryotic SLC6A18/B0AT3 and SLC6A19/B0AT1 transporters of neutral amino acids, exhibited impaired transport of aromatic amino acids that require a large binding site volume. Conservation of a general (G/A/C)ΦG motif among eukaryotic members of SLC6 family suggests a role for this loop in a common mechanism for substrate recognition and translocation by SLC6 transporters of broad substrate specificity.
Collapse
Affiliation(s)
- Dorota Focht
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Caroline Neumann
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Joseph Lyons
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Ander Eguskiza Bilbao
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Rickard Blunck
- Department of PhysicsUniversité de MontréalMontréalQCCanada
| | - Lina Malinauskaite
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
- MRC Laboratory of Molecular BiologyCambridgeUK
| | - Ilona O Schwarz
- Department of PsychiatryColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
| | - Jonathan A Javitch
- Department of PsychiatryColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Center for Molecular RecognitionColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Department of PharmacologyColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNYUSA
| | - Matthias Quick
- Department of PsychiatryColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Center for Molecular RecognitionColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNYUSA
| | - Poul Nissen
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| |
Collapse
|
25
|
Hartmann AM, Fu L, Ziegler C, Winklhofer M, Nothwang HG. Structural changes in the extracellular loop 2 of the murine KCC2 potassium chloride cotransporter modulate ion transport. J Biol Chem 2021; 296:100793. [PMID: 34019872 PMCID: PMC8191313 DOI: 10.1016/j.jbc.2021.100793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 01/22/2023] Open
Abstract
K+-Cl- cotransporters (KCCs) play important roles in physiological processes such as inhibitory neurotransmission and cell-volume regulation. KCCs exhibit significant variations in K+ affinities, yet recent atomic structures demonstrated that K+- and Cl--binding sites are highly conserved, raising the question of whether additional structural elements may contribute to ion coordination. The termini and the large extracellular domain (ECD) of KCCs exhibit only low sequence identity and were already discussed as modulators of transport activity. Here, we used the extracellular loop 2 (EL2) that links transmembrane helices (TMs) 3 and 4, as a mechanism to modulate ECD folding. We compared consequences of point mutations in the K+-binding site on the function of WT KCC2 and in a KCC2 variant, in which EL2 was structurally altered by insertion of a IFYPYDVPDYAGYPYDVPDYAGSYPYDVPDYAAHAAA (3xHA) tag (36 amino acids). In WT KCC2, individual mutations of five residues in the K+-binding site resulted in a 2- to 3-fold decreased transport rate. However, the same mutations in the KCC2 variant with EL2 structurally altered by insertion of a 3xHA tag had no effect on transport activity. Homology models of mouse KCC2 with the 3xHA tag inserted into EL2 using ab initio prediction were generated. The models suggest subtle conformational changes occur in the ECD upon EL2 modification. These data suggest that a conformational change in the ECD, for example, by interaction with EL2, might be an elegant way to modulate the K+ affinity of the different isoforms in the KCC subfamily.
Collapse
Affiliation(s)
- Anna-Maria Hartmann
- Division of Neurogenetics, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Research Center for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - Lifei Fu
- Biophysics II, Biophysics II-Structural Biology, Faculty of Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Christine Ziegler
- Biophysics II, Biophysics II-Structural Biology, Faculty of Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Michael Winklhofer
- Institute for Biology and Environmental Sciences IBU, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Hans Gerd Nothwang
- Division of Neurogenetics, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Research Center for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Center of Excellence Hearing4all, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| |
Collapse
|
26
|
Zheng R, da Rosa G, Dans PD, Peluffo RD. Molecular Determinants for Nitric Oxide Regulation of the Murine Cationic Amino Acid Transporter CAT-2A. Biochemistry 2020; 59:4225-4237. [PMID: 33135877 DOI: 10.1021/acs.biochem.0c00729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cationic amino acid transporters (CATs) supply cells with essential and semiessential dibasic amino acids. Among them, l-arginine is the substrate for nitric oxide synthases (NOS) to produce nitric oxide (NO), a key signaling molecule and second messenger. In cardiac preparations, we showed that NO acutely and directly modulates transport activity by noncompetitively inhibiting these CATs. We hypothesize that this NO regulation occurs through modification of cysteine residues in CAT proteins. Homology modeling and a computational chemistry approach identified Cys347 as one of two putative targets for NO binding, of 15 Cys residues present in the low-affinity mouse CAT-2A (mCAT-2A). To test this prediction, mammalian cell lines overexpressing mCAT-2A were used for site-directed mutagenesis and uptake studies. When Cys347 was replaced with alanine (Cys347Ala), mCAT-2A became insensitive to inhibition by NO donors. In addition, the transport capacity of this variant decreased by >50% compared to that of the control, without affecting membrane expression levels or apparent affinities for the transported amino acids. Interestingly, replacing Cys347 with serine (Cys347Ser) restored uptake levels to those of the control while retaining NO insensitivity. Other Cys residues, when replaced with Ala, still produced a NO-sensitive CAT-2A. In cells co-expressing NOS and mCAT-2A, exposure to extracellular l-arginine inhibited the uptake activity of control mCAT-2A, via NO production, but not that of the Cys347Ser variant. Thus, the -SH moiety of Cys347 is largely responsible for mCAT-2A inhibition by NO. Because of the endogenous NO effect, this modulation is likely to be physiologically relevant and a potential intervention point for therapeutics.
Collapse
Affiliation(s)
- Ruifang Zheng
- Department of Pharmacology, Physiology and Neuroscience, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, Newark, New Jersey 07103, United States
| | - Gabriela da Rosa
- Laboratory of Molecular Microbiology, DEPBIO, School of Sciences-School of Chemistry, Universidad de la República, 11400 Montevideo, Uruguay.,Functional Genomics Laboratory, Institut Pasteur of Montevideo, Mataojo 2020, CP, 11400 Montevideo, Uruguay.,Group of Biophysical Chemistry, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Rivera 1350, CP, 50000 Salto, Uruguay
| | - Pablo D Dans
- Functional Genomics Laboratory, Institut Pasteur of Montevideo, Mataojo 2020, CP, 11400 Montevideo, Uruguay.,Group of Biophysical Chemistry, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Rivera 1350, CP, 50000 Salto, Uruguay
| | - R Daniel Peluffo
- Department of Pharmacology, Physiology and Neuroscience, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, Newark, New Jersey 07103, United States.,Group of Biophysical Chemistry, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Rivera 1350, CP, 50000 Salto, Uruguay
| |
Collapse
|
27
|
Nehser M, Dark J, Schweitzer D, Campbell M, Zwicker J, Hitt DM, Little H, Diaz-Correa A, Holley DC, Patel SA, Thompson CM, Bridges RJ. System X c- Antiporter Inhibitors: Azo-Linked Amino-Naphthyl-Sulfonate Analogues of Sulfasalazine. Neurochem Res 2020; 45:1375-1386. [PMID: 31754956 PMCID: PMC10688270 DOI: 10.1007/s11064-019-02901-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 01/18/2023]
Abstract
The cystine/glutamate antiporter system Xc- (SXc-) mediates the exchange of intracellular L-glutamate (L-Glu) with extracellular L-cystine (L-Cys2). Both the import of L-Cys2 and the export of L-Glu take on added significance in CNS cells, especially astrocytes. When the relative activity of SXc- overwhelms the regulatory capacity of the EAATs, the efflux of L-Glu through the antiporter can be significant enough to trigger excitotoxic pathology, as is thought to occur in glioblastoma. This has prompted considerable interest in the pharmacological specificity of SXc- and the development of inhibitors. The present study explores a series of analogues that are structurally related to sulfasalazine, a widely employed inhibitor of SXc-. We identify a number of novel aryl-substituted amino-naphthylsulfonate analogues that inhibit SXc- more potently than sulfasalazine. Interestingly, the inhibitors switch from a competitive to noncompetitive mechanism with increased length and lipophilic substitutions, a structure-activity relationship that was previously observed with aryl-substituted isoxazole. These results suggest that the two classes of inhibitors may interact with some of the same domains on the antiporter protein and that the substrate and inhibitor binding sites may be in close proximity to one another. Molecular modeling is used to explore this possibility.
Collapse
Affiliation(s)
- M Nehser
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - J Dark
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - D Schweitzer
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - M Campbell
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - J Zwicker
- Deciphera Pharmaceuticals, Lawrence, KA, 66044, USA
| | - D M Hitt
- Chemistry Department, Carroll College, Helena, MT, 56925, USA
| | - H Little
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - A Diaz-Correa
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - D C Holley
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - S A Patel
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - C M Thompson
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA
| | - R J Bridges
- Department of Biomedical and Pharmaceutical Science, Center for Structural and Functional Neuroscience, Skaggs School of Pharmacy, University of Montana, Missoula, MT, 59812, USA.
| |
Collapse
|
28
|
van 't Klooster JS, Cheng TY, Sikkema HR, Jeucken A, Moody B, Poolman B. Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins. eLife 2020; 9:57003. [PMID: 32301705 PMCID: PMC7182430 DOI: 10.7554/elife.57003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Yeast tolerates a low pH and high solvent concentrations. The permeability of the plasma membrane (PM) for small molecules is low and lateral diffusion of proteins is slow. These findings suggest a high degree of lipid order, which raises the question of how membrane proteins function in such an environment. The yeast PM is segregated into the Micro-Compartment-of-Can1 (MCC) and Pma1 (MCP), which have different lipid compositions. We extracted proteins from these microdomains via stoichiometric capture of lipids and proteins in styrene-maleic-acid-lipid-particles (SMALPs). We purified SMALP-lipid-protein complexes by chromatography and quantitatively analyzed periprotein lipids located within the diameter defined by one SMALP. Phospholipid and sterol concentrations are similar for MCC and MCP, but sphingolipids are enriched in MCP. Ergosterol is depleted from this periprotein lipidome, whereas phosphatidylserine is enriched relative to the bulk of the plasma membrane. Direct detection of PM lipids in the 'periprotein space' supports the conclusion that proteins function in the presence of a locally disordered lipid state.
Collapse
Affiliation(s)
- Joury S van 't Klooster
- Department of Biochemistry, University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, Netherlands
| | - Tan-Yun Cheng
- Division of Rheumatology, Inflammation and Immunity Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Hendrik R Sikkema
- Department of Biochemistry, University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, Netherlands
| | - Aike Jeucken
- Department of Biochemistry, University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, Netherlands
| | - Branch Moody
- Division of Rheumatology, Inflammation and Immunity Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Bert Poolman
- Department of Biochemistry, University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, Netherlands
| |
Collapse
|
29
|
Groeneweg S, van Geest FS, Peeters RP, Heuer H, Visser WE. Thyroid Hormone Transporters. Endocr Rev 2020; 41:5637505. [PMID: 31754699 DOI: 10.1210/endrev/bnz008] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023]
Abstract
Thyroid hormone transporters at the plasma membrane govern intracellular bioavailability of thyroid hormone. Monocarboxylate transporter (MCT) 8 and MCT10, organic anion transporting polypeptide (OATP) 1C1, and SLC17A4 are currently known as transporters displaying the highest specificity toward thyroid hormones. Structure-function studies using homology modeling and mutational screens have led to better understanding of the molecular basis of thyroid hormone transport. Mutations in MCT8 and in OATP1C1 have been associated with clinical disorders. Different animal models have provided insight into the functional role of thyroid hormone transporters, in particular MCT8. Different treatment strategies for MCT8 deficiency have been explored, of which thyroid hormone analogue therapy is currently applied in patients. Future studies may reveal the identity of as-yet-undiscovered thyroid hormone transporters. Complementary studies employing animal and human models will provide further insight into the role of transporters in health and disease. (Endocrine Reviews 41: 1 - 55, 2020).
Collapse
Affiliation(s)
- Stefan Groeneweg
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ferdy S van Geest
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Heike Heuer
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - W Edward Visser
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| |
Collapse
|
30
|
Asc-1 Transporter (SLC7A10): Homology Models And Molecular Dynamics Insights Into The First Steps Of The Transport Mechanism. Sci Rep 2020; 10:3731. [PMID: 32111919 PMCID: PMC7048771 DOI: 10.1038/s41598-020-60617-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/14/2020] [Indexed: 12/02/2022] Open
Abstract
The alanine-serine-cysteine transporter Asc-1 regulates the synaptic availability of d-serine and glycine (the two co-agonists of the NMDA receptor) and is regarded as an important drug target. To shuttle the substrate from the extracellular space to the cytoplasm, this transporter undergoes multiple distinct conformational states. In this work, homology modeling, substrate docking and molecular dynamics simulations were carried out to learn more about the transition between the “outward-open” and “outward-open occluded” states. We identified a transition state involving the highly-conserved unwound TM6 region in which the Phe243 flips close to the d-serine substrate without major movements of TM6. This feature and those of other key residues are proposed to control the binding site and substrate translocation. Competitive inhibitors ACPP, LuAE00527 and SMLC were docked and their binding modes at the substrate binding site corroborated the key role played by Phe243 of TM6. For ACPP and LuAE00527, strong hydrophobic interactions with this residue hinder its mobility and prevent the uptake and the efflux of substrates. As for SMLC, the weaker interactions maintain the flexibility of Phe243 and the efflux process. Overall, we propose a molecular basis for the inhibition of substrate translocation of the Asc-1 transporter that should be valuable for rational drug design.
Collapse
|
31
|
Abstract
We review the mechanisms responsible for amino acid homeostasis in Saccharomyces cerevisiae and other fungi. Amino acid homeostasis is essential for cell growth and survival. Hence, the de novo synthesis reactions, metabolic conversions, and transport of amino acids are tightly regulated. Regulation varies from nitrogen pool sensing to control by individual amino acids and takes place at the gene (transcription), protein (posttranslational modification and allostery), and vesicle (trafficking and endocytosis) levels. The pools of amino acids are controlled via import, export, and compartmentalization. In yeast, the majority of the amino acid transporters belong to the APC (amino acid-polyamine-organocation) superfamily, and the proteins couple the uphill transport of amino acids to the electrochemical proton gradient. Although high-resolution structures of yeast amino acid transporters are not available, homology models have been successfully exploited to determine and engineer the catalytic and regulatory functions of the proteins. This has led to a further understanding of the underlying mechanisms of amino acid sensing and subsequent downregulation of transport. Advances in optical microscopy have revealed a new level of regulation of yeast amino acid transporters, which involves membrane domain partitioning. The significance and the interrelationships of the latest discoveries on amino acid homeostasis are put in context.
Collapse
|
32
|
Effect of oxidative stress on cystine transportation by xC‾ antiporter. Arch Biochem Biophys 2019; 674:108114. [PMID: 31557465 DOI: 10.1016/j.abb.2019.108114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/19/2019] [Accepted: 09/22/2019] [Indexed: 12/15/2022]
Abstract
We performed computer simulations to investigate the effect of oxidation on the extracellular cystine (CYC) uptake by the xC- antiporter. The latter is important for killing of cancer cells. Specifically, applying molecular dynamics (MD) simulations we studied the transport of CYC across xCT, i.e., the light subunit of the xC- antiporter, in charge of bidirectional transport of CYC and glutamate. We considered the outward facing (OF) configuration of xCT, and to study the effect of oxidation, we modified the Cys327 residue, located in the vicinity of the extracellular milieu, to cysteic acid (CYO327). Our computational results showed that oxidation of Cys327 results in a free energy barrier for CYC translocation, thereby blocking the access of CYC to the substrate binding site of the OF system. The formation of the energy barrier was found to be due to the conformational changes in the channel. Analysis of the MD trajectories revealed that the reorganization of the side chains of the Tyr244 and CYO327 residues play a critical role in the OF channel blocking. Indeed, the calculated distance between Tyr244 and either Cys327 or CYO327 showed a narrowing of the channel after oxidation. The obtained free energy barrier for CYC translocation was found to be 33.9kJmol-1, indicating that oxidation of Cys327, by e.g., cold atmospheric plasma, is more effective in inhibiting the xC- antiporter than in the mutation of this amino acid to Ala (yielding a barrier of 32.4kJmol-1). The inhibition of the xC- antiporter may lead to Cys starvation in some cancer cells, eventually resulting in cancer cell death.
Collapse
|
33
|
Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
|
34
|
Abstract
Cell nutrition, detoxification, signalling, homeostasis and response to drugs, processes related to cell growth, differentiation and survival are all mediated by plasma membrane (PM) proteins called transporters. Despite their distinct fine structures, mechanism of function, energetic requirements, kinetics and substrate specificities, all transporters are characterized by a main hydrophobic body embedded in the PM as a series of tightly packed, often intertwined, α-helices that traverse the lipid bilayer in a zigzag mode, connected with intracellular or extracellular loops and hydrophilic N- and C-termini. Whereas longstanding genetic, biochemical and biophysical evidence suggests that specific transmembrane segments, and also their connecting loops, are responsible for substrate recognition and transport dynamics, emerging evidence also reveals the functional importance of transporter N- and C-termini, in respect to transport catalysis, substrate specificity, subcellular expression, stability and signalling. This review highlights selected prototypic examples of transporters in which their termini play important roles in their functioning.
Collapse
Affiliation(s)
- Emmanuel Mikros
- Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, 15771 Athens, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| |
Collapse
|
35
|
Krammer EM, Prévost M. Function and Regulation of Acid Resistance Antiporters. J Membr Biol 2019; 252:465-481. [DOI: 10.1007/s00232-019-00073-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/08/2019] [Indexed: 01/07/2023]
|
36
|
Patel D, Kharkar PS, Gandhi NS, Kaur E, Dutt S, Nandave M. Novel analogs of sulfasalazine as system x c - antiporter inhibitors: Insights from the molecular modeling studies. Drug Dev Res 2019; 80:758-777. [PMID: 31199023 DOI: 10.1002/ddr.21557] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 04/16/2019] [Accepted: 05/27/2019] [Indexed: 02/05/2023]
Abstract
System xc - (Sxc - ), a cystine-glutamate antiporter, is established as an interesting target for the treatment of several pathologies including epileptic seizures, glioma, neurodegenerative diseases, and multiple sclerosis. Erastin, sorafenib, and sulfasalazine (SSZ) are a few of the established inhibitors of Sxc - . However, its pharmacological inhibition with novel and potent agents is still very much required due to potential issues, for example, potency, bioavailability, and blood-brain barrier (BBB) permeability, with the current lead molecules such as SSZ. Therefore, in this study, we report the synthesis and structure-activity relationships (SAR) of SSZ derivatives along with molecular docking and dynamics simulations using the developed homology model of xCT chain of Sxc - antiporter. The generated homology model attempted to address the limitations of previously reported comparative protein models, thereby increasing the confidence in the computational modeling studies. The main objective of the present study was to derive a suitable lead structure from SSZ eliminating its potential issues for the treatment of glioblastoma multiforme (GBM), a deadly and malignant grade IV astrocytoma. The designed compounds with favorable Sxc - inhibitory activity following in vitro Sxc - inhibition studies, showed moderately potent cytotoxicity in patient-derived human glioblastoma cells, thereby generating potential interest in these compounds. The xCT-ligand model can be further optimized in search of potent lead molecules for novel drug discovery and development studies.
Collapse
Affiliation(s)
- Dhavalkumar Patel
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS (Deemed to be University), Vile Parle (West), Mumbai, Maharashtra, India
| | - Prashant S Kharkar
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS (Deemed to be University), Vile Parle (West), Mumbai, Maharashtra, India
| | - Neha S Gandhi
- School of Mathematical Sciences and Institute for Health and Biomedical Innovation, Queensland University of Technology, Gardens Point Campus, Brisbane, Queensland, Australia
| | - Ekjot Kaur
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Mukesh Nandave
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS (Deemed to be University), Vile Parle (West), Mumbai, Maharashtra, India.,Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| |
Collapse
|
37
|
Knöpfel EB, Vilches C, Camargo SMR, Errasti-Murugarren E, Stäubli A, Mayayo C, Munier FL, Miroshnikova N, Poncet N, Junza A, Bhattacharya SS, Prat E, Berry V, Berger W, Heon E, Moore AT, Yanes Ó, Nunes V, Palacín M, Verrey F, Kloeckener-Gruissem B. Dysfunctional LAT2 Amino Acid Transporter Is Associated With Cataract in Mouse and Humans. Front Physiol 2019; 10:688. [PMID: 31231240 PMCID: PMC6558864 DOI: 10.3389/fphys.2019.00688] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/16/2019] [Indexed: 11/13/2022] Open
Abstract
Cataract, the loss of ocular lens transparency, accounts for ∼50% of worldwide blindness and has been associated with water and solute transport dysfunction across lens cellular barriers. We show that neutral amino acid antiporter LAT2 (Slc7a8) and uniporter TAT1 (Slc16a10) are expressed on mouse ciliary epithelium and LAT2 also in lens epithelium. Correspondingly, deletion of LAT2 induced a dramatic decrease in lens essential amino acid levels that was modulated by TAT1 defect. Interestingly, the absence of LAT2 led to increased incidence of cataract in mice, in particular in older females, and a synergistic effect was observed with simultaneous lack of TAT1. Screening SLC7A8 in patients diagnosed with congenital or age-related cataract yielded one homozygous single nucleotide deletion segregating in a family with congenital cataract. Expressed in HeLa cells, this LAT2 mutation did not support amino acid uptake. Heterozygous LAT2 variants were also found in patients with cataract some of which showed a reduced transport function when expressed in HeLa cells. Whether heterozygous LAT2 variants may contribute to the pathology of cataract needs to be further investigated. Overall, our results suggest that defects of amino acid transporter LAT2 are implicated in cataract formation, a situation that may be aggravated by TAT1 defects.
Collapse
Affiliation(s)
- Emilia Boiadjieva Knöpfel
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
- Swiss National Centre of Competence in Research Kidney.CH, University of Zurich, Zurich, Switzerland
| | - Clara Vilches
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory – IDIBELL, Barcelona, Spain
- U730 and U731, Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - Simone M. R. Camargo
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Ekaitz Errasti-Murugarren
- U730 and U731, Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrina Stäubli
- Institute of Medical Molecular Genetics, University of Zurich, Zurich, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Clara Mayayo
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory – IDIBELL, Barcelona, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francis L. Munier
- Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | | | - Nadège Poncet
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Alexandra Junza
- Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain
| | - Shomi S. Bhattacharya
- Andalusian Molecular Biology and Regenerative Medicine Centre – CABIMER, Seville, Spain
- UCL Institute of Ophthalmology, London, United Kingdom
| | - Esther Prat
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory – IDIBELL, Barcelona, Spain
- U730 and U731, Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
- Genetics Section, Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Vanita Berry
- Andalusian Molecular Biology and Regenerative Medicine Centre – CABIMER, Seville, Spain
| | - Wolfgang Berger
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
- Institute of Medical Molecular Genetics, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich – ZNZ, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anthony T. Moore
- Andalusian Molecular Biology and Regenerative Medicine Centre – CABIMER, Seville, Spain
- Moorfields Eye Hospital, London, United Kingdom
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Óscar Yanes
- Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain
| | - Virginia Nunes
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory – IDIBELL, Barcelona, Spain
- U730 and U731, Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
- Genetics Section, Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Manuel Palacín
- U730 and U731, Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Francois Verrey
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
- Swiss National Centre of Competence in Research Kidney.CH, University of Zurich, Zurich, Switzerland
| | - Barbara Kloeckener-Gruissem
- Institute of Medical Molecular Genetics, University of Zurich, Zurich, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
38
|
Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc. Nat Struct Mol Biol 2019; 26:510-517. [DOI: 10.1038/s41594-019-0237-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/26/2019] [Indexed: 02/07/2023]
|
39
|
L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction. Nat Commun 2019; 10:1807. [PMID: 31000719 PMCID: PMC6472337 DOI: 10.1038/s41467-019-09837-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/02/2019] [Indexed: 11/26/2022] Open
Abstract
L-amino acid transporters (LATs) play key roles in human physiology and are implicated in several human pathologies. LATs are asymmetric amino acid exchangers where the low apparent affinity cytoplasmic side controls the exchange of substrates with high apparent affinity on the extracellular side. Here, we report the crystal structures of an LAT, the bacterial alanine-serine-cysteine exchanger (BasC), in a non-occluded inward-facing conformation in both apo and substrate-bound states. We crystallized BasC in complex with a nanobody, which blocks the transporter from the intracellular side, thus unveiling the sidedness of the substrate interaction of BasC. Two conserved residues in human LATs, Tyr 236 and Lys 154, are located in equivalent positions to the Na1 and Na2 sites of sodium-dependent APC superfamily transporters. Functional studies and molecular dynamics (MD) calculations reveal that these residues are key for the asymmetric substrate interaction of BasC and in the homologous human transporter Asc-1. L-Amino acid Transporters (LATs) are asymmetric amino acid exchangers. Here the authors determine the crystal structure of a prokaryotic LAT, the alanine-serine-cysteine exchanger (BasC) and identify key residues for asymmetric substrate interaction in both BasC and the homologous human transporter Asc-1 through functional studies.
Collapse
|
40
|
Transport of cystine across xC− antiporter. Arch Biochem Biophys 2019; 664:117-126. [DOI: 10.1016/j.abb.2019.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 01/17/2023]
|
41
|
Bartoccioni P, Fort J, Zorzano A, Errasti-Murugarren E, Palacín M. Functional characterization of the alanine-serine-cysteine exchanger of Carnobacterium sp AT7. J Gen Physiol 2019; 151:505-517. [PMID: 30696726 PMCID: PMC6445583 DOI: 10.1085/jgp.201812195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/16/2018] [Accepted: 01/03/2019] [Indexed: 01/18/2023] Open
Abstract
Proteins of the L-type amino acid transporter (LAT) subfamily take up amino acids from the environment for use in the cell. Bartoccioni et al. show that the bacterial amino acid exchanger BasC is functionally similar to the human LAT Asc1, making BasC a useful model for this class of transporters. Many key cell processes require prior cell uptake of amino acids from the environment, which is facilitated by cell membrane amino acid transporters such as those of the L-type amino acid transporter (LAT) subfamily. Alterations in LAT subfamily amino acid transport are associated with several human diseases, including cancer, aminoacidurias, and neurodegenerative conditions. Therefore, from the perspective of human health, there is considerable interest in obtaining structural information about these transporter proteins. We recently solved the crystal structure of the first LAT transporter, the bacterial alanine-serine-cysteine exchanger of Carnobacterium sp AT7 (BasC). Here, we provide a complete functional characterization of detergent-purified, liposome-reconstituted BasC transporter to allow the extension of the structural insights into mechanistic understanding. BasC is a sodium- and proton-independent small neutral amino acid exchanger whose substrate and inhibitor selectivity are almost identical to those previously described for the human LAT subfamily member Asc-1. Additionally, we show that, like its human counterparts, this transporter has apparent affinity asymmetry for the intra- and extracellular substrate binding sites—a key feature in the physiological role played by these proteins. BasC is an excellent paradigm of human LAT transporters and will contribute to our understanding of the molecular mechanisms underlying substrate recognition and translocation at both sides of the plasma membrane.
Collapse
Affiliation(s)
- Paola Bartoccioni
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - Joana Fort
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Antonio Zorzano
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain
| | - Ekaitz Errasti-Murugarren
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Palacín
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain .,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
| |
Collapse
|
42
|
Abstract
Transport of solutes across biological membranes is essential for cellular life. This process is mediated by membrane transport proteins which move nutrients, waste products, certain drugs and ions into and out of cells. Secondary active transporters couple the transport of substrates against their concentration gradients with the transport of other solutes down their concentration gradients. The alternating access model of membrane transporters and the coupling mechanism of secondary active transporters are introduced in this book chapter. Structural studies have identified typical protein folds for transporters that we exemplify by the major facilitator superfamily (MFS) and LeuT folds. Finally, substrate binding and substrate translocation of the transporters LacY of the MFS and AdiC of the amino acid-polyamine-organocation (APC) superfamily are described.
Collapse
Affiliation(s)
- Patrick D Bosshart
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Dimitrios Fotiadis
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
| |
Collapse
|
43
|
Molecular mechanism of substrate selectivity of the arginine-agmatine Antiporter AdiC. Sci Rep 2018; 8:15607. [PMID: 30353119 PMCID: PMC6199258 DOI: 10.1038/s41598-018-33963-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/08/2018] [Indexed: 12/02/2022] Open
Abstract
The arginine-agmatine antiporter (AdiC) is a component of an acid resistance system developed by enteric bacteria to resist gastric acidity. In order to avoid neutral proton antiport, the monovalent form of arginine, about as abundant as its divalent form under acidic conditions, should be selectively bound by AdiC for transport into the cytosol. In this study, we shed light on the mechanism through which AdiC distinguishes Arg+ from Arg2+ of arginine by investigating the binding of both forms in addition to that of divalent agmatine, using a combination of molecular dynamics simulations with molecular and quantum mechanics calculations. We show that AdiC indeed preferentially binds Arg+. The weaker binding of divalent compounds results mostly from their greater tendency to remain hydrated than Arg+. Our data suggests that the binding of Arg+ promotes the deprotonation of Glu208, a gating residue, which in turn reinforces its interactions with AdiC, leading to longer residence times of Arg+ in the binding site. Although the total electric charge of the ligand appears to be the determinant factor in the discrimination process, two local interactions formed with Trp293, another gating residue of the binding site, also contribute to the selection mechanism: a cation-π interaction with the guanidinium group of Arg+ and an anion-π interaction involving Glu208.
Collapse
|
44
|
Kandasamy P, Gyimesi G, Kanai Y, Hediger MA. Amino acid transporters revisited: New views in health and disease. Trends Biochem Sci 2018; 43:752-789. [PMID: 30177408 DOI: 10.1016/j.tibs.2018.05.003] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 02/09/2023]
Abstract
Amino acid transporters (AATs) are membrane-bound transport proteins that mediate transfer of amino acids into and out of cells or cellular organelles. AATs have diverse functional roles ranging from neurotransmission to acid-base balance, intracellular energy metabolism, and anabolic and catabolic reactions. In cancer cells and diabetes, dysregulation of AATs leads to metabolic reprogramming, which changes intracellular amino acid levels, contributing to the pathogenesis of cancer, obesity and diabetes. Indeed, the neutral amino acid transporters (NATs) SLC7A5/LAT1 and SLC1A5/ASCT2 are likely involved in several human malignancies. However, a clinical therapy that directly targets AATs has not yet been developed. The purpose of this review is to highlight the structural and functional diversity of AATs, their diverse physiological roles in different tissues and organs, their wide-ranging implications in human diseases and the emerging strategies and tools that will be necessary to target AATs therapeutically.
Collapse
Affiliation(s)
- Palanivel Kandasamy
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, CH-3012 Bern, Switzerland
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, CH-3012 Bern, Switzerland
| | - Yoshikatsu Kanai
- Division of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, CH-3012 Bern, Switzerland.
| |
Collapse
|
45
|
Palazzolo L, Parravicini C, Laurenzi T, Guerrini U, Indiveri C, Gianazza E, Eberini I. In silico Description of LAT1 Transport Mechanism at an Atomistic Level. Front Chem 2018; 6:350. [PMID: 30197880 PMCID: PMC6117385 DOI: 10.3389/fchem.2018.00350] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/25/2018] [Indexed: 11/24/2022] Open
Abstract
The molecular mechanism of transport mediated by LAT1, a sodium-independent antiporter of large neutral amino acids, was investigated through in silico procedures, specifically making reference to two transported substrates, tyrosine (Tyr) and leucine methyl ester (LME), and to 3,5-diiodo-L-tyrosine (DIT), a well-known LAT1 inhibitor. Two models of the transporter were built by comparative modeling, with LAT1 either in an outward-facing (OF) or in an inward-facing (IF) conformation, based, respectively, on the crystal structure of AdiC and of GadC. As frequently classic Molecular Dynamics (MD) fails to monitor large-scale conformational transitions within a reasonable simulated time, the OF structure was equilibrated for 150 ns then processed through targeted MD (tMD). During this procedure, an elastic force pulled the OF structure to the IF structure and induced, at the same time, substrates/inhibitor to move through the transport channel. This elastic force was modulated by a spring constant (k) value; by decreasing its value from 100 to 70, it was possible to comparatively account for the propensity for transport of the three tested molecules. In line with our expectations, during the tMD simulations, Tyr and LME behaved as substrates, moving down the transport channel, or most of it, for all k values. On the contrary, DIT behaved as an inhibitor, being (almost) transported across the channel only at the highest k value (100). During their transit through the channel, Tyr and LME interacted with specific amino acids (first with Phe252 then with Thr345, Arg348, Tyr259, and Phe262); this suggests that a primary as well as a putative secondary gate may contribute to the transport of substrates. Quite on the opposite, DIT appeared to establish only transient interactions with side chains lining the external part of the transport channel. Our tMD simulations could thus efficiently discriminate between two transported substrates and one inhibitor, and therefore can be proposed as a benchmark for developing novel LAT1 inhibitors of pharmacological interest.
Collapse
Affiliation(s)
- Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Cesare Indiveri
- Dipartimento di Biologia, Ecologia e Scienze della Terra, University of Calabria, Cosenza, Italy
| | - Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
46
|
Scalise M, Galluccio M, Console L, Pochini L, Indiveri C. The Human SLC7A5 (LAT1): The Intriguing Histidine/Large Neutral Amino Acid Transporter and Its Relevance to Human Health. Front Chem 2018; 6:243. [PMID: 29988369 PMCID: PMC6023973 DOI: 10.3389/fchem.2018.00243] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
SLC7A5, known as LAT1, belongs to the APC superfamily and forms a heterodimeric amino acid transporter interacting with the glycoprotein CD98 (SLC3A2) through a conserved disulfide. The complex is responsible for uptake of essential amino acids in crucial body districts such as placenta and blood brain barrier. LAT1/CD98 heterodimer has been studied over the years to unravel the transport mechanism and the role of each subunit. Studies conducted in intact cells demonstrated that LAT1/CD98 mediates a Na+ and pH independent antiport of amino acids. Some novel insights into the function of LAT1 derived from studies conducted in proteoliposomes reconstituted with the recombinant human LAT1. Using this experimental tool, it has been demonstrated that the preferred substrate is histidine and that CD98 is not required for transport being, plausibly, involved in routing LAT1 to the plasma membrane. Since a 3D structure of LAT1 is not available, homology models have been built on the basis of the AdiC transporter from E.coli. Crucial residues for substrate recognition and gating have been identified using a combined approach of bioinformatics and site-directed mutagenesis coupled to functional assays. Over the years, the interest around LAT1 increased because this transporter is involved in important human diseases such as neurological disorders and cancer. Therefore, LAT1 became an important pharmacological target together with other nutrient membrane transporters. Moving from knowledge on structure/function relationships, two cysteine residues, lying on the substrate binding site, have been exploited for designing thiol reacting covalent inhibitors. Some lead compounds have been characterized whose efficacy has been tested in a cancer cell line.
Collapse
Affiliation(s)
- Mariafrancesca Scalise
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Rende, Italy
| | - Michele Galluccio
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Rende, Italy
| | - Lara Console
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Rende, Italy
| | - Lorena Pochini
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Rende, Italy
| | - Cesare Indiveri
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Rende, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Bari, Italy
| |
Collapse
|
47
|
Gournas C, Athanasopoulos A, Sophianopoulou V. On the Evolution of Specificity in Members of the Yeast Amino Acid Transporter Family as Parts of Specific Metabolic Pathways. Int J Mol Sci 2018; 19:E1398. [PMID: 29738448 PMCID: PMC5983819 DOI: 10.3390/ijms19051398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/04/2018] [Accepted: 05/05/2018] [Indexed: 12/11/2022] Open
Abstract
In the recent years, molecular modeling and substrate docking, coupled with biochemical and genetic analyses have identified the substrate-binding residues of several amino acid transporters of the yeast amino acid transporter (YAT) family. These consist of (a) residues conserved across YATs that interact with the invariable part of amino acid substrates and (b) variable residues that interact with the side chain of the amino acid substrate and thus define specificity. Secondary structure sequence alignments showed that the positions of these residues are conserved across YATs and could thus be used to predict the specificity of YATs. Here, we discuss the potential of combining molecular modeling and structural alignments with intra-species phylogenetic comparisons of transporters, in order to predict the function of uncharacterized members of the family. We additionally define some orphan branches which include transporters with potentially novel, and to be characterized specificities. In addition, we discuss the particular case of the highly specific l-proline transporter, PrnB, of Aspergillus nidulans, whose gene is part of a cluster of genes required for the utilization of proline as a carbon and/or nitrogen source. This clustering correlates with transcriptional regulation of these genes, potentially leading to the efficient coordination of the uptake of externally provided l-Pro via PrnB and its enzymatic degradation in the cell.
Collapse
Affiliation(s)
- Christos Gournas
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications (IBE), National Centre for Scientific Research "Demokritos" (NCSRD), Patr. Grigoriou E & 27 Neapoleos St., 15341 Agia Paraskevi, Greece.
| | - Alexandros Athanasopoulos
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications (IBE), National Centre for Scientific Research "Demokritos" (NCSRD), Patr. Grigoriou E & 27 Neapoleos St., 15341 Agia Paraskevi, Greece.
| | - Vicky Sophianopoulou
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications (IBE), National Centre for Scientific Research "Demokritos" (NCSRD), Patr. Grigoriou E & 27 Neapoleos St., 15341 Agia Paraskevi, Greece.
| |
Collapse
|
48
|
Singh N, Ecker GF. Insights into the Structure, Function, and Ligand Discovery of the Large Neutral Amino Acid Transporter 1, LAT1. Int J Mol Sci 2018; 19:E1278. [PMID: 29695141 PMCID: PMC5983779 DOI: 10.3390/ijms19051278] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022] Open
Abstract
The large neutral amino acid transporter 1 (LAT1, or SLC7A5) is a sodium- and pH-independent transporter, which supplies essential amino acids (e.g., leucine, phenylalanine) to cells. It plays an important role at the Blood⁻Brain Barrier (BBB) where it facilitates the transport of thyroid hormones, pharmaceuticals (e.g., l-DOPA, gabapentin), and metabolites into the brain. Moreover, its expression is highly upregulated in various types of human cancer that are characterized by an intense demand for amino acids for growth and proliferation. Therefore, LAT1 is believed to be an important drug target for cancer treatment. With the crystallization of the arginine/agmatine antiporter (AdiC) from Escherichia Coli, numerous homology models of LAT1 have been built to elucidate the substrate binding site, ligand⁻transporter interaction, and structure⁻function relationship. The use of these models in combination with molecular docking and experimental testing has identified novel chemotypes of ligands of LAT1. Here, we highlight the structure, function, transport mechanism, and homology modeling of LAT1. Additionally, results from structure⁻function studies performed on LAT1 are addressed, which have enhanced our knowledge of the mechanism of substrate binding and translocation. This is followed by a discussion on ligand- and structure-based approaches, with an emphasis on elucidating the molecular basis of LAT1 inhibition. Finally, we provide an exhaustive summary of different LAT1 inhibitors that have been identified so far, including the recently discovered irreversible covalent inhibitors.
Collapse
Affiliation(s)
- Natesh Singh
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090 Wien, Austria.
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090 Wien, Austria.
| |
Collapse
|
49
|
Ilgü H, Jeckelmann JM, Colas C, Ucurum Z, Schlessinger A, Fotiadis D. Effects of Mutations and Ligands on the Thermostability of the l-Arginine/Agmatine Antiporter AdiC and Deduced Insights into Ligand-Binding of Human l-Type Amino Acid Transporters. Int J Mol Sci 2018; 19:ijms19030918. [PMID: 29558430 PMCID: PMC5877779 DOI: 10.3390/ijms19030918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Abstract
The l-arginine/agmatine transporter AdiC is a prokaryotic member of the SLC7 family, which enables pathogenic enterobacteria to survive the extremely acidic gastric environment. Wild-type AdiC from Escherichia coli, as well as its previously reported point mutants N22A and S26A, were overexpressed homologously and purified to homogeneity. A size-exclusion chromatography-based thermostability assay was used to determine the melting temperatures (Tms) of the purified AdiC variants in the absence and presence of the selected ligands l-arginine (Arg), agmatine, l-arginine methyl ester, and l-arginine amide. The resulting Tms indicated stabilization of AdiC variants upon ligand binding, in which Tms and ligand binding affinities correlated positively. Considering results from this and previous studies, we revisited the role of AdiC residue S26 in Arg binding and proposed interactions of the α-carboxylate group of Arg exclusively with amide groups of the AdiC backbone. In the context of substrate binding in the human SLC7 family member l-type amino acid transporter-1 (LAT1; SLC7A5), an analogous role of S66 in LAT1 to S26 in AdiC is discussed based on homology modeling and amino acid sequence analysis. Finally, we propose a binding mechanism for l-amino acid substrates to LATs from the SLC7 family.
Collapse
Affiliation(s)
- Hüseyin Ilgü
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012 Bern, Switzerland.
| | - Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012 Bern, Switzerland.
| | - Claire Colas
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012 Bern, Switzerland.
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012 Bern, Switzerland.
| |
Collapse
|
50
|
Bianchi F, Syga Ł, Moiset G, Spakman D, Schavemaker PE, Punter CM, Seinen AB, van Oijen AM, Robinson A, Poolman B. Steric exclusion and protein conformation determine the localization of plasma membrane transporters. Nat Commun 2018; 9:501. [PMID: 29402931 PMCID: PMC5799302 DOI: 10.1038/s41467-018-02864-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 01/04/2018] [Indexed: 11/09/2022] Open
Abstract
The plasma membrane (PM) of Saccharomyces cerevisiae contains membrane compartments, MCC/eisosomes and MCPs, named after the protein residents Can1 and Pma1, respectively. Using high-resolution fluorescence microscopy techniques we show that Can1 and the homologous transporter Lyp1 are able to diffuse into the MCC/eisosomes, where a limited number of proteins are conditionally trapped at the (outer) edge of the compartment. Upon addition of substrate, the immobilized proteins diffuse away from the MCC/eisosomes, presumably after taking a different conformation in the substrate-bound state. Our data indicate that the mobile fraction of all integral plasma membrane proteins tested shows extremely slow Brownian diffusion through most of the PM. We also show that proteins with large cytoplasmic domains, such as Pma1 and synthetic chimera of Can1 and Lyp1, are excluded from the MCC/eisosomes. We hypothesize that the distinct localization patterns found for these integral membrane proteins in S. cerevisiae arises from a combination of slow lateral diffusion, steric exclusion, and conditional trapping in membrane compartments.
Collapse
Affiliation(s)
- Frans Bianchi
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands
| | - Łukasz Syga
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands
| | - Gemma Moiset
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Dian Spakman
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands
| | - Paul E Schavemaker
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands
| | - Christiaan M Punter
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Anne-Bart Seinen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Andrew Robinson
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Bert Poolman
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands. .,Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG, Groningen, The Netherlands.
| |
Collapse
|