1
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Ozturk TN, Coumoundouros C, Culham DE, Wood JM. Structural Determinants and Functional Significance of Dimerization for Osmosensing Transporter ProP in Escherichia coli. Biochemistry 2023; 62:118-133. [PMID: 36516499 DOI: 10.1021/acs.biochem.2c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Osmosensing transporter ProP forestalls cellular dehydration by detecting environments with high osmotic pressure and mediating the accumulation of organic osmolytes by bacterial cells. It is composed of 12 transmembrane helices with cytoplasmic N- and C-termini. In Escherichia coli, dimers form when the C-terminal domains of ProP molecules form homodimeric, antiparallel, α-helical coiled coils. No dominant negative effect was detected when inactive and active ProP molecules formed heterodimers in vivo. Purification of ProP in detergent dodecylmaltoside yielded monomers, which were functional after reconstitution in proteoliposomes. With other evidence, this suggests that ProP monomers function independently whether in the monomeric or dimeric state. Amino acid replacements that disrupted or reversed the coiled coil did not prevent in vivo dimerization of ProP detected with a bacterial two-hybrid system. Maleimide labeling detected no osmolality-dependent variation in the reactivities of cysteine residues introduced to transmembrane helix (TM) XII. In contrast, coarse-grained molecular dynamic simulations detected deformation of the lipid around TMs III and VI, on the lipid-exposed protein surface opposite to TM XII. This suggests that the dimer interface of ProP includes the surfaces of TMs III and VI, not of TM XII as previously suggested by crosslinking data. Homology modeling suggested that coiled-coil formation and dimerization via such an interface are not mutually exclusive. In previous work, alterations to the C-terminal coiled coil blocked co-localization of ProP with phospholipid cardiolipin at E. coli cell poles. Thus, dimerization may contribute to ProP targeting, adjust its lipid environment, and hence indirectly modify its osmotic stress response.
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Affiliation(s)
- Tugba N Ozturk
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis, Saint Louis, Missouri63110, United States.,Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland20814, United States
| | - Chelsea Coumoundouros
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, CanadaN1G 2 W1
| | - Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, CanadaN1G 2 W1
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, CanadaN1G 2 W1
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2
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Abstract
Membrane transporter proteins are divided into channels/pores and carriers and constitute protein families of physiological and pharmacological importance. Several presently used therapeutic compounds elucidate their effects by targeting membrane transporter proteins, including anti-arrhythmic, anesthetic, antidepressant, anxiolytic and diuretic drugs. The lack of three-dimensional structures of human transporters hampers experimental studies and drug discovery. In this chapter, the use of homology modeling for generating structural models of membrane transporter proteins is reviewed. The increasing number of atomic resolution structures available as templates, together with improvements in methods and algorithms for sequence alignments, secondary structure predictions, and model generation, in addition to the increase in computational power have increased the applicability of homology modeling for generating structural models of transporter proteins. Different pitfalls and hints for template selection, multiple-sequence alignments, generation and optimization, validation of the models, and the use of transporter homology models for structure-based virtual ligand screening are discussed.
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Affiliation(s)
- Ingebrigt Sylte
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Mari Gabrielsen
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kurt Kristiansen
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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3
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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/.
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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
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4
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Spontaneous Suppressors against Debilitating Transmembrane Mutants of CaMdr1 Disclose Novel Interdomain Communication via Signature Motifs of the Major Facilitator Superfamily. J Fungi (Basel) 2022; 8:jof8050538. [PMID: 35628792 PMCID: PMC9143388 DOI: 10.3390/jof8050538] [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: 04/19/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
The Major Facilitator Superfamily (MFS) drug:H+ antiporter CaMdr1, from Candida albicans, is responsible for the efflux of structurally diverse antifungals. MFS members share a common fold of 12−14 transmembrane helices (TMHs) forming two N- and C-domains. Each domain is arranged in a pseudo-symmetric fold of two tandems of 3-TMHs that alternatively expose the drug-binding site towards the inside or the outside of the yeast to promote drug binding and release. MFS proteins show great diversity in primary structure and few conserved signature motifs, each thought to have a common function in the superfamily, although not yet clearly established. Here, we provide new information on these motifs by having screened a library of 64 drug transport-deficient mutants and their corresponding suppressors spontaneously addressing the deficiency. We found that five strains recovered the drug-resistance capacity by expressing CaMdr1 with a secondary mutation. The pairs of debilitating/rescuing residues are distributed either in the same TMH (T127ATMH1- > G140DTMH1) or 3-TMHs repeat (F216ATMH4- > G260ATMH5), at the hinge of 3-TMHs repeats tandems (R184ATMH3- > D235HTMH4, L480ATMH10- > A435TTMH9), and finally between the N- and C-domains (G230ATMH4- > P528HTMH12). Remarkably, most of these mutants belong to the different signature motifs, highlighting a mechanistic role and interplay thought to be conserved among MFS proteins. Results also point to the specific role of TMH11 in the interplay between the N- and C-domains in the inward- to outward-open conformational transition.
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5
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Donovan E, Avila C, Klausner S, Parikh V, Fenollar-Ferrer C, Blakely RD, Sarter M. Disrupted Choline Clearance and Sustained Acetylcholine Release In Vivo by a Common Choline Transporter Coding Variant Associated with Poor Attentional Control in Humans. J Neurosci 2022; 42:3426-3444. [PMID: 35232764 PMCID: PMC9034784 DOI: 10.1523/jneurosci.1334-21.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 02/20/2022] [Accepted: 02/23/2022] [Indexed: 11/21/2022] Open
Abstract
Transport of choline via the neuronal high-affinity choline transporter (CHT; SLC5A7) is essential for cholinergic terminals to synthesize and release acetylcholine (ACh). In humans, we previously demonstrated an association between a common CHT coding substitution (rs1013940; Ile89Val) and reduced attentional control as well as attenuated frontal cortex activation. Here, we used a CRISPR/Cas9 approach to generate mice expressing the I89V substitution and assessed, in vivo, CHT-mediated choline transport, and ACh release. Relative to wild-type (WT) mice, CHT-mediated clearance of choline in male and female mice expressing one or two Val89 alleles was reduced by over 80% in cortex and over 50% in striatum. Choline clearance in CHT Val89 mice was further reduced by neuronal inactivation. Deficits in ACh release, 5 and 10 min after repeated depolarization at a low, behaviorally relevant frequency, support an attenuated reloading capacity of cholinergic neurons in mutant mice. The density of CHTs in total synaptosomal lysates and neuronal plasma-membrane-enriched fractions was not impacted by the Val89 variant, indicating a selective impact on CHT function. When challenged with a visual disruptor to reveal attentional control mechanisms, Val89 mice failed to adopt a more conservative response bias. Structural modeling revealed that Val89 may attenuate choline transport by altering conformational changes of CHT that support normal transport rates. Our findings support the view that diminished sustained cholinergic signaling capacity underlies perturbed attentional performance in individuals expressing CHT Val89. The CHT Val89 mouse serves as a valuable model to study heritable risk for cognitive disorders arising from cholinergic dysfunction.SIGNIFICANCE STATEMENT Acetylcholine (ACh) signaling depends on the functional capacity of the neuronal choline transporter (CHT). Previous research demonstrated that humans expressing the common CHT coding variant Val89 exhibit attentional vulnerabilities and attenuated fronto-cortical activation during attention. Here, we find that mice engineered to express the Val89 variant exhibit reduced CHT-mediated choline clearance and a diminished capacity to sustain ACh release. Additionally, Val89 mice lack cognitive flexibility in response to an attentional challenge. These findings provide a mechanistic and cognitive framework for interpreting the attentional phenotype associated with the human Val89 variant and establish a model that permits a more invasive interrogation of CNS effects as well as the development of therapeutic strategies for those, including Val89 carriers, with presynaptic cholinergic perturbations.
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Affiliation(s)
- Eryn Donovan
- Department of Psychology, University of Michigan, Ann Arbor, Michigan 48109
| | - Cassandra Avila
- Department of Psychology, University of Michigan, Ann Arbor, Michigan 48109
| | - Sarah Klausner
- Department of Psychology, University of Michigan, Ann Arbor, Michigan 48109
| | - Vinay Parikh
- Department of Psychology & Neuroscience Program, Temple University, Philadelphia, Pennsylvania 19122
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, Section of Human Genetics, National Institute on Deafness and Other Communication Disorders, Bethesda, Maryland 20892
| | - Randy D Blakely
- Stiles-Nicholson Brain Institute and Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458
| | - Martin Sarter
- Department of Psychology, Neuroscience Program and Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
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6
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Peña-Varas C, Kanstrup C, Vergara-Jaque A, González-Avendaño M, Crocoll C, Mirza O, Dreyer I, Nour-Eldin H, Ramírez D. Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking. Int J Mol Sci 2022; 23:ijms23031595. [PMID: 35163519 PMCID: PMC8836200 DOI: 10.3390/ijms23031595] [Citation(s) in RCA: 3] [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: 01/05/2022] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis thaliana transports these substrates in computational simulation approaches. The designed pipeline reported here includes massive docking of 4MTB and I3M in an ensemble of GTR1 conformations (in both inward and outward conformations) extracted from molecular dynamics simulations, followed by clustered and substrate–protein interactions profiling. The identified key residues were mutated, and their role in substrate transport was tested. We were able to identify key residues that integrate a major binding site of these substrates, which is critical for transport activity. In silico approaches employed here represent a breakthrough in the plant transportomics field, as the identification of key residues usually takes a long time if performed from a purely wet-lab experimental perspective. The inclusion of structural bioinformatics in the analyses of plant transporters significantly speeds up the knowledge-gaining process and optimizes valuable time and resources.
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Affiliation(s)
- Carlos Peña-Varas
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
| | - Christa Kanstrup
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Ariela Vergara-Jaque
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Mariela González-Avendaño
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Ingo Dreyer
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Hussam Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago 8900000, Chile
- Correspondence: ; Tel.: +56-(22)-3036667
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7
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Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, Gouaux E. Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature 2022; 610:796-803. [PMID: 36224384 PMCID: PMC9605866 DOI: 10.1038/s41586-022-05314-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023]
Abstract
The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid-protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.
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Affiliation(s)
- Hanbin Jeong
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA
| | - Sarah Clark
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA
| | - April Goehring
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR USA
| | - Sepehr Dehghani-Ghahnaviyeh
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Ali Rasouli
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Emad Tajkhorshid
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Eric Gouaux
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR USA
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8
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Holzhüter K, Geertsma ER. Uniport, Not Proton-Symport, in a Non-Mammalian SLC23 Transporter. J Mol Biol 2021; 434:167393. [PMID: 34896363 DOI: 10.1016/j.jmb.2021.167393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 10/25/2022]
Abstract
SLC23 family members are transporters of either nucleobases or ascorbate. While the mammalian SLC23 ascorbate transporters are sodium-coupled, the non-mammalian nucleobase transporters have been proposed, but not formally shown, to be proton-coupled symporters. This assignment is exclusively based on in vivo transport assays using protonophores. Here, by establishing the first in vitro transport assay for this protein family, we demonstrate that a representative member of the SLC23 nucleobase transporters operates as a uniporter instead. We explain these conflicting assignments by identifying a critical role of uracil phosphoribosyltransferase, the enzyme converting uracil to UMP, in driving uracil uptake in vivo. Detailed characterization of uracil phosphoribosyltransferase reveals that the sharp reduction of uracil uptake in whole cells in presence of protonophores is caused by acidification-induced enzyme inactivation. The SLC23 family therefore consists of both uniporters and symporters in line with the structurally related SLC4 and SLC26 families that have previously been demonstrated to accommodate both transport modes as well.
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Affiliation(s)
- Katharina Holzhüter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt am Main, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
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9
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Chloride-dependent conformational changes in the GlyT1 glycine transporter. Proc Natl Acad Sci U S A 2021; 118:2017431118. [PMID: 33658361 DOI: 10.1073/pnas.2017431118] [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] [Indexed: 02/06/2023] Open
Abstract
The human GlyT1 glycine transporter requires chloride for its function. However, the mechanism by which Cl- exerts its influence is unknown. To examine the role that Cl- plays in the transport cycle, we measured the effect of Cl- on both glycine binding and conformational changes. The ability of glycine to displace the high-affinity radioligand [3H]CHIBA-3007 required Na+ and was potentiated over 1,000-fold by Cl- We generated GlyT1b mutants containing reactive cysteine residues in either the extracellular or cytoplasmic permeation pathways and measured changes in the reactivity of those cysteine residues as indicators of conformational changes in response to ions and substrate. Na+ increased accessibility in the extracellular pathway and decreased it in the cytoplasmic pathway, consistent with stabilizing an outward-open conformation as observed in other members of this transporter family. In the presence of Na+, both glycine and Cl- independently shifted the conformation of GlyT1b toward an outward-closed conformation. Together, Na+, glycine, and Cl- stabilized an inward-open conformation of GlyT1b. We then examined whether Cl- acts by interacting with a conserved glutamine to allow formation of an ion pair that stabilizes the closed state of the extracellular pathway. Molecular dynamics simulations of a GlyT1 homolog indicated that this ion pair is formed more frequently as that pathway closes. Mutation of the glutamine blocked the effect of Cl-, and substituting it with glutamate or lysine resulted in outward- or inward-facing transporter conformations, respectively. These results provide an unexpected insight into the role of Cl- in this family of transporters.
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10
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Reggio A, Buonomo V, Berkane R, Bhaskara RM, Tellechea M, Peluso I, Polishchuk E, Di Lorenzo G, Cirillo C, Esposito M, Hussain A, Huebner AK, Hübner CA, Settembre C, Hummer G, Grumati P, Stolz A. Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Rep 2021; 22:e52289. [PMID: 34338405 PMCID: PMC8447607 DOI: 10.15252/embr.202052289] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/23/2022] Open
Abstract
Degradation of the endoplasmic reticulum (ER) via selective autophagy (ER‐phagy) is vital for cellular homeostasis. We identify FAM134A/RETREG2 and FAM134C/RETREG3 as ER‐phagy receptors, which predominantly exist in an inactive state under basal conditions. Upon autophagy induction and ER stress signal, they can induce significant ER fragmentation and subsequent lysosomal degradation. FAM134A, FAM134B/RETREG1, and FAM134C are essential for maintaining ER morphology in a LC3‐interacting region (LIR)‐dependent manner. Overexpression of any FAM134 paralogue has the capacity to significantly augment the general ER‐phagy flux upon starvation or ER‐stress. Global proteomic analysis of FAM134 overexpressing and knockout cell lines reveals several protein clusters that are distinctly regulated by each of the FAM134 paralogues as well as a cluster of commonly regulated ER‐resident proteins. Utilizing pro‐Collagen I, as a shared ER‐phagy substrate, we observe that FAM134A acts in a LIR‐independent manner and compensates for the loss of FAM134B and FAM134C, respectively. FAM134C instead is unable to compensate for the loss of its paralogues. Taken together, our data show that FAM134 paralogues contribute to common and unique ER‐phagy pathways.
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Affiliation(s)
- Alessio Reggio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Viviana Buonomo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Rayene Berkane
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Ramachandra M Bhaskara
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mariana Tellechea
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany.,Structural Genomics Consortium at BMLS, Goethe University, Frankfurt am Main, Germany
| | - Ivana Peluso
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Carmine Cirillo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Marianna Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Adeela Hussain
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University, Jena, Germany
| | - Antje K Huebner
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University, Jena, Germany
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University, Jena, Germany
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Institute for Biophysics, Goethe University, Frankfurt am Main, Germany
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Alexandra Stolz
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
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11
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Staritzbichler R, Sarti E, Yaklich E, Aleksandrova A, Stamm M, Khafizov K, Forrest LR. Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors. PLoS One 2021; 16:e0239881. [PMID: 33930031 PMCID: PMC8087094 DOI: 10.1371/journal.pone.0239881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/15/2021] [Indexed: 01/08/2023] Open
Abstract
The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly matched by a standard pairwise sequence alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the aligned regions either side of the newly matched positions. Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. Here we introduce position restraints, or "anchors" as a feature in our alignment tool AlignMe, providing an aid to pairwise global sequence alignment of alpha-helical membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of anchors can be used to modify alignments, while still maintaining the reproducibility and rigor of the rest of the alignment. Anchored alignments can be generated using the online version of AlignMe available at www.bioinfo.mpg.de/AlignMe/.
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Affiliation(s)
- René Staritzbichler
- ProteinFormatics Group, Institute of Biophysics and Medical Physics, University of Leipzig, Leipzig, Germany
| | - Edoardo Sarti
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - Emily Yaklich
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Antoniya Aleksandrova
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Marcus Stamm
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, Moscow, Russia
| | - Lucy R. Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
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12
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The organosulfur compound dimethylsulfoniopropionate (DMSP) is utilized as an osmoprotectant by Vibrio species. Appl Environ Microbiol 2021; 87:AEM.02235-20. [PMID: 33355097 PMCID: PMC8090876 DOI: 10.1128/aem.02235-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP), a key component of the global geochemical sulfur cycle, is a secondary metabolite produced in large quantities by marine phytoplankton and utilized as an osmoprotectant, thermoprotectant and antioxidant. Marine bacteria can use two pathways to degrade and catabolize DMSP, a demethylation pathway and a cleavage pathway that produces the climate active gas dimethylsulfide (DMS). Whether marine bacteria can also accumulate DMSP as an osmoprotectant to maintain the turgor pressure of the cell in response to changes in external osmolarity has received little attention. The marine halophile Vibrio parahaemolyticus, contains at least six osmolyte transporters, four betaine carnitine choline transport (BCCT) carriers BccT1-BccT4 and two ABC-family ProU transporters. In this study, we showed that DMSP is used as an osmoprotectant by V. parahaemolyticus and several other Vibrio species including V. cholerae and V. vulnificus Using a V. parahaemolyticus proU double mutant, we demonstrated that these ABC transporters are not required for DMSP uptake. However, a bccT null mutant lacking all four BCCTs had a growth defect compared to wild type in high salinity media supplemented with DMSP. Using mutants possessing only one functional BCCT in growth pattern assays, we identified two BCCT-family transporters, BccT1 and BccT2, which are carriers of DMSP. The only V. parahaemolyticus BccT homolog that V. cholerae and V. vulnificus possess is BccT3 and functional complementation in Escherichia coli MKH13 showed V. cholerae VcBccT3 could transport DMSP. In V. vulnificus strains, we identified and characterized an additional BCCT family transporter, which we named BccT5 that was also a carrier for DMSP.Importance DMSP is present in the marine environment, produced in large quantities by marine phytoplankton as an osmoprotectant, and is an important component of the global geochemical sulfur cycle. This algal osmolyte has not been previously investigated for its role in marine heterotrophic bacterial osmotic stress response. Vibrionaceae are marine species, many of which are halophiles exemplified by V. parahaemolyticus, a species that possesses at least six transporters for the uptake of osmolytes. Here, we demonstrated that V. parahaemolyticus and other Vibrio species can accumulate DMSP as an osmoprotectant and show that several BCCT family transporters uptake DMSP. These studies suggest that DMSP is a significant bacterial osmoprotectant, which may be important for understanding the fate of DMSP in the environment. DMSP is produced and present in coral mucus and Vibrio species form part of the microbial communities associated with them. The function of DMSP in these interactions is unclear, but could be an important driver for these associations allowing Vibrio proliferation. This work suggests that DMSP likely has an important role in heterotrophic bacteria ecology than previously appreciated.
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13
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Investigations of Dimethylglycine, Glycine Betaine, and Ectoine Uptake by a Betaine-Carnitine-Choline Transporter Family Transporter with Diverse Substrate Specificity in Vibrio Species. J Bacteriol 2020; 202:JB.00314-20. [PMID: 32817090 DOI: 10.1128/jb.00314-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/06/2020] [Indexed: 01/08/2023] Open
Abstract
Fluctuations in osmolarity are one of the most prevalent stresses to which bacteria must adapt, both hypo- and hyperosmotic conditions. Most bacteria cope with high osmolarity by accumulating compatible solutes (osmolytes) in the cytoplasm to maintain the turgor pressure of the cell. Vibrio parahaemolyticus, a halophile, utilizes at least six compatible solute transporters for the uptake of osmolytes: two ABC family ProU transporters and four betaine-carnitine-choline transporter (BCCT) family transporters. The full range of compatible solutes transported by this species has yet to be determined. Using an osmolyte phenotypic microarray plate for growth analyses, we expanded the known osmolytes used by V. parahaemolyticus to include N,N-dimethylglycine (DMG), among others. Growth pattern analysis of four triple-bccT mutants, possessing only one functional BCCT, indicated that BccT1 (VP1456), BccT2 (VP1723), and BccT3 (VP1905) transported DMG. BccT1 was unusual in that it could take up both compounds with methylated head groups (glycine betaine [GB], choline, and DMG) and cyclic compounds (ectoine and proline). Bioinformatics analysis identified the four coordinating amino acid residues for GB in the BccT1 protein. In silico modeling analysis demonstrated that GB, DMG, and ectoine docked in the same binding pocket in BccT1. Using site-directed mutagenesis, we showed that a strain with all four residues mutated resulted in the loss of uptake of GB, DMG, and ectoine. We showed that three of the four residues were essential for ectoine uptake, whereas only one of the residues was important for GB uptake. Overall, we have demonstrated that DMG is a highly effective compatible solute for Vibrio species and have elucidated the amino acid residues in BccT1 that are important for the coordination of GB, DMG, and ectoine transport.IMPORTANCE Vibrio parahaemolyticus possesses at least six osmolyte transporters, which allow the bacterium to adapt to high-salinity conditions. In this study, we identified several additional osmolytes that were utilized by V. parahaemolyticus We demonstrated that the compound DMG, which is present in the marine environment, was a highly effective osmolyte for Vibrio species. We determined that DMG is transported via BCCT family carriers, which have not been shown previously to take up this compound. BccT1 was a carrier for GB, DMG, and ectoine, and we identified the amino acid residues essential for the coordination of these compounds. The data suggest that for BccT1, GB is more easily accommodated than ectoine in the transporter binding pocket.
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14
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Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020; 9:e58026. [PMID: 32870157 PMCID: PMC7462613 DOI: 10.7554/elife.58026] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR's pivotal role in coagulation, its structure and active site remain poorly understood. In addition, VKOR variants can cause vitamin K-dependent clotting factor deficiency or alter warfarin response. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells. The large-scale functional data, along with an evolutionary coupling analysis, supports a four transmembrane domain topology, with variants in transmembrane domains exhibiting strongly deleterious effects on abundance and activity. Functionally constrained regions of the protein define the active site, and we find that, of four conserved cysteines putatively critical for function, only three are absolutely required. Finally, 25% of human VKOR missense variants show reduced abundance or activity, possibly conferring warfarin sensitivity or causing disease.
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Affiliation(s)
- Melissa A Chiasson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Nathan J Rollins
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Jason J Stephany
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Katherine A Sitko
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Marta Verby
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Song Sun
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | | | - Debora S Marks
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
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15
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Rojas G, Orellana I, Rosales-Rojas R, García-Olivares J, Comer J, Vergara-Jaque A. Structural Determinants of the Dopamine Transporter Regulation Mediated by G Proteins. J Chem Inf Model 2020; 60:3577-3586. [PMID: 32525311 DOI: 10.1021/acs.jcim.0c00236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dopamine clearance in the brain is controlled by the dopamine transporter (DAT), a protein residing in the plasma membrane, which drives reuptake of extracellular dopamine into presynaptic neurons. Studies have revealed that the βγ subunits of heterotrimeric G proteins modulate DAT function through a physical association with the C-terminal region of the transporter. Regulation of neurotransmitter transporters by Gβγ subunits is unprecedented in the literature; therefore, it is interesting to investigate the structural details of this particular protein-protein interaction. Here, we refined the crystal structure of the Drosophila melanogaster DAT (dDAT), modeling de novo the N- and C-terminal domains; subsequently, we used the full-length dDAT structure to generate a comparative model of human DAT (hDAT). Both proteins were assembled with Gβ1γ2 subunits employing protein-protein docking, and subsequent molecular dynamics simulations were run to identify the specific interactions governing the formation of the hDAT:Gβγ and dDAT:Gβγ complexes. A [L/F]R[Q/E]R sequence motif containing the residues R588 in hDAT and R587 in dDAT was found as key to bind the Gβγ subunits through electrostatic interactions with a cluster of negatively charged residues located at the top face of the Gβ subunit. Alterations of DAT function have been associated with multiple devastating neuropathological conditions; therefore, this work represents a step toward better understanding DAT regulation by signaling proteins, allowing us to predict therapeutic target regions.
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Affiliation(s)
- Genoveva Rojas
- Center for Bioinformatics and Molecular Simulation, Faculty of Engineering, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Ivana Orellana
- Center for Bioinformatics and Molecular Simulation, Faculty of Engineering, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Roberto Rosales-Rojas
- Center for Bioinformatics and Molecular Simulation, Faculty of Engineering, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Jennie García-Olivares
- Supernus Pharmaceuticals, 9715 Key West Avenue, Rockville, Maryland 20850, United States
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ariela Vergara-Jaque
- Center for Bioinformatics and Molecular Simulation, Faculty of Engineering, Universidad de Talca, 2 Norte 685, Talca, Chile.,Millennium Nucleus of Ion Channels-associated Diseases (MiNICAD), Santiago, Chile
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16
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Jang WD, Lee SM, Kim HU, Lee SY. Systematic and Comparative Evaluation of Software Programs for Template-Based Modeling of Protein Structures. Biotechnol J 2020; 15:e1900343. [PMID: 32130758 DOI: 10.1002/biot.201900343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/19/2020] [Indexed: 12/20/2022]
Abstract
Modeling protein structures is critical for understanding protein functions in various biological and biotechnological studies. Among representative protein structure modeling approaches, template-based modeling (TBM) is by far the most reliable and most widely used approach to model protein structures. However, it still remains as a challenge to select appropriate software programs for pairwise alignments and model building, two major steps of the TBM. In this paper, pairwise alignment methods for TBM are first compared with respect to the quality of structure models built using these methods. This comparative study is conducted using comprehensive datasets, which cover 6185 domain sequences from Structural Classification of Proteins extended for soluble proteins, and 259 Protein Data Bank entries (whole protein sequences) from Orientations of Proteins in Membranes database for membrane proteins. Overall, a profile-based method, especially PSI-BLAST, consistently shows high performance across the datasets and model evaluation metrics used. Next, use of two model building programs, MODELLER and SWISS-MODEL, does not seem to significantly affect the quality of protein structure models built except for the Hard group (a group of relatively less homologous proteins) of membrane proteins. The results presented in this study will be useful for more accurate implementation of TBM.
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Affiliation(s)
- Woo Dae Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Mi Lee
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,KAIST Institute for Artificial Intelligence, BioProcess Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,KAIST Institute for Artificial Intelligence, BioProcess Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
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17
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Structural and evolutionary analyses of the Plasmodium falciparum chloroquine resistance transporter. Sci Rep 2020; 10:4842. [PMID: 32179795 PMCID: PMC7076037 DOI: 10.1038/s41598-020-61181-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) confer resistance to several antimalarial drugs such as chloroquine (CQ) or piperaquine (PPQ), a partner molecule in current artemisinin-based combination therapies. As a member of the Drug/Metabolite Transporter (DMT) superfamily, the vacuolar transporter PfCRT may translocate substrate molecule(s) across the membrane of the digestive vacuole (DV), a lysosome-like organelle. However, the physiological substrate(s), the transport mechanism and the functional regions of PfCRT remain to be fully characterized. Here, we hypothesized that identification of evolutionary conserved sites in a tertiary structural context could help locate putative functional regions of PfCRT. Hence, site-specific substitution rates were estimated over Plasmodium evolution at each amino acid sites, and the PfCRT tertiary structure was predicted in both inward-facing (open-to-vacuole) and occluded states through homology modeling using DMT template structures sharing <15% sequence identity with PfCRT. We found that the vacuolar-half and membrane-spanning domain (and especially the transmembrane helix 9) of PfCRT were more conserved, supporting that its physiological substrate is expelled out of the parasite DV. In the PfCRT occluded state, some evolutionary conserved sites, including positions related to drug resistance mutations, participate in a putative binding pocket located at the core of the PfCRT membrane-spanning domain. Through structural comparison with experimentally-characterized DMT transporters, we identified several conserved PfCRT amino acid sites located in this pocket as robust candidates for mediating substrate transport. Finally, in silico mutagenesis revealed that drug resistance mutations caused drastic changes in the electrostatic potential of the transporter vacuolar entry and pocket, facilitating the escape of protonated CQ and PPQ from the parasite DV.
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18
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Fung TC, Vuong HE, Luna CD, Pronovost GN, Aleksandrova AA, Riley NG, Vavilina A, McGinn J, Rendon T, Forrest LR, Hsiao EY. Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut. Nat Microbiol 2019; 4:2064-2073. [PMID: 31477894 PMCID: PMC6879823 DOI: 10.1038/s41564-019-0540-4] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 07/15/2019] [Indexed: 01/16/2023]
Abstract
The gut microbiota regulates levels of serotonin (5-hydroxytryptamine (5-HT)) in the intestinal epithelium and lumen1-5. However, whether 5-HT plays a functional role in bacteria from the gut microbiota remains unknown. We demonstrate that elevating levels of intestinal lumenal 5-HT by oral supplementation or genetic deficiency in the host 5-HT transporter (SERT) increases the relative abundance of spore-forming members of the gut microbiota, which were previously reported to promote host 5-HT biosynthesis. Within this microbial community, we identify Turicibacter sanguinis as a gut bacterium that expresses a neurotransmitter sodium symporter-related protein with sequence and structural homology to mammalian SERT. T. sanguinis imports 5-HT through a mechanism that is inhibited by the selective 5-HT reuptake inhibitor fluoxetine. 5-HT reduces the expression of sporulation factors and membrane transporters in T. sanguinis, which is reversed by fluoxetine exposure. Treating T. sanguinis with 5-HT or fluoxetine modulates its competitive colonization in the gastrointestinal tract of antibiotic-treated mice. In addition, fluoxetine reduces the membership of T. sanguinis in the gut microbiota of conventionally colonized mice. Host association with T. sanguinis alters intestinal expression of multiple gene pathways, including those important for lipid and steroid metabolism, with corresponding reductions in host systemic triglyceride levels and inguinal adipocyte size. Together, these findings support the notion that select bacteria indigenous to the gut microbiota signal bidirectionally with the host serotonergic system to promote their fitness in the intestine.
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Affiliation(s)
- Thomas C. Fung
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA,Correspondence to: and
| | - Helen E. Vuong
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher D.G. Luna
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Geoffrey N. Pronovost
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Antoniya A. Aleksandrova
- Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noah G. Riley
- Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastasia Vavilina
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Julianne McGinn
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tomiko Rendon
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lucy R. Forrest
- Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elaine Y. Hsiao
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA,Correspondence to: and
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19
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Bresso E, Fernandez D, Amora DX, Noel P, Petitot AS, de Sa MEL, Albuquerque EVS, Danchin EGJ, Maigret B, Martins NF. A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants. Molecules 2019; 24:E3798. [PMID: 31652525 PMCID: PMC6832152 DOI: 10.3390/molecules24203798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 01/10/2023] Open
Abstract
Root-knot nematodes (RKN), from the Meloidogyne genus, have a worldwide distribution and cause severe economic damage to many life-sustaining crops. Because of their lack of specificity and danger to the environment, most chemical nematicides have been banned from use. Thus, there is a great need for new and safe compounds to control RKN. Such research involves identifying beforehand the nematode proteins essential to the invasion. Since G protein-coupled receptors GPCRs are the target of a large number of drugs, we have focused our research on the identification of putative nematode GPCRs such as those capable of controlling the movement of the parasite towards (or within) its host. A datamining procedure applied to the genome of Meloidogyne incognita allowed us to identify a GPCR, belonging to the neuropeptide GPCR family that can serve as a target to carry out a virtual screening campaign. We reconstructed a 3D model of this receptor by homology modeling and validated it through extensive molecular dynamics simulations. This model was used for large scale molecular dockings which produced a filtered limited set of putative antagonists for this GPCR. Preliminary experiments using these selected molecules allowed the identification of an active compound, namely C260-2124, from the ChemDiv provider, which can serve as a starting point for further investigations.
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Affiliation(s)
- Emmanuel Bresso
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France.
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
| | - Diana Fernandez
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
- IRD, CIRAD, Université de Montpellier, IPME, F-34398 Montpellier, France.
| | - Deisy X Amora
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
| | - Philippe Noel
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France.
| | | | | | | | - Etienne G J Danchin
- INRA, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, F-06903 Sophia-Antipolis, France.
| | - Bernard Maigret
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France.
| | - Natália F Martins
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
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20
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Tiwari V, Karpe SD, Sowdhamini R. Topology prediction of insect olfactory receptors. Curr Opin Struct Biol 2019; 55:194-203. [PMID: 31233963 DOI: 10.1016/j.sbi.2019.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
Olfactory receptors are important transmembrane proteins that enable organisms to perceive odours and react to them. Structural understanding of insect olfactory receptors is scarce. In this review, we discuss different transmembrane helix prediction methods, consensus methods, topology prediction methods which can enable topology prediction of these proteins. We discuss the current success rates by applying the algorithms on few G-protein coupled receptors of known structure and olfactory receptor sequences and outstanding challenges. Finally, we discuss the impact of topology prediction on biology and modeling of ORs.
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Affiliation(s)
- Vikas Tiwari
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Snehal D Karpe
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India.
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21
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A Structural Model of the Inactivation Gate of Voltage-Activated Potassium Channels. Biophys J 2019; 117:377-387. [PMID: 31278002 DOI: 10.1016/j.bpj.2019.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/21/2019] [Accepted: 06/07/2019] [Indexed: 11/24/2022] Open
Abstract
After opening, the Shaker voltage-gated potassium (KV) channel rapidly inactivates when one of its four N-termini enters and occludes the channel pore. Although it is known that the tip of the N-terminus reaches deep into the central cavity, the conformation adopted by this domain during inactivation and the nature of its interactions with the rest of the channel remain unclear. Here, we use molecular dynamics simulations coupled with electrophysiology experiments to reveal the atomic-scale mechanisms of inactivation. We find that the first six amino acids of the N-terminus spontaneously enter the central cavity in an extended conformation, establishing hydrophobic contacts with residues lining the pore. A second portion of the N-terminus, consisting of a long 24 amino acid α-helix, forms numerous polar contacts with residues in the intracellular entryway of the T1 domain. Double mutant cycle analysis revealed a strong relationship between predicted interatomic distances and empirically observed thermodynamic coupling, establishing a plausible model of the transition of KV channels to the inactivated state.
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22
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Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, Kudryashev M, Dikic I, Hummer G. Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nat Commun 2019; 10:2370. [PMID: 31147549 PMCID: PMC6542808 DOI: 10.1038/s41467-019-10345-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
FAM134B/RETREG1 is a selective ER-phagy receptor that regulates the size and shape of the endoplasmic reticulum. The structure of its reticulon-homology domain (RHD), an element shared with other ER-shaping proteins, and the mechanism of membrane shaping remain poorly understood. Using molecular modeling and molecular dynamics (MD) simulations, we assemble a structural model for the RHD of FAM134B. Through MD simulations of FAM134B in flat and curved membranes, we relate the dynamic RHD structure with its two wedge-shaped transmembrane helical hairpins and two amphipathic helices to FAM134B functions in membrane-curvature induction and curvature-mediated protein sorting. FAM134B clustering, as expected to occur in autophagic puncta, amplifies the membrane-shaping effects. Electron microscopy of in vitro liposome remodeling experiments support the membrane remodeling functions of the different RHD structural elements. Disruption of the RHD structure affects selective autophagy flux and leads to disease states. FAM134B/RETREG1 is a selective ER-phagy receptor that regulates the size and shape of the endoplasmic reticulum. Here authors use molecular modeling and molecular dynamics simulations to assemble a structural model for the reticulon-homology domain of FAM134B.
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Affiliation(s)
- Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Paolo Grumati
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Javier Garcia-Pardo
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology, Division for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Sissy Kalayil
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany
| | - Adriana Covarrubias-Pinto
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Wenbo Chen
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Mikhail Kudryashev
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany. .,Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany. .,Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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23
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Entry Exclusion of Conjugative Plasmids of the IncA, IncC, and Related Untyped Incompatibility Groups. J Bacteriol 2019; 201:JB.00731-18. [PMID: 30858294 DOI: 10.1128/jb.00731-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
Conjugative plasmids of incompatibility group C (IncC), formerly known as A/C2, disseminate antibiotic resistance genes globally in diverse pathogenic species of Gammaproteobacteria. Salmonella genomic island 1 (SGI1) can be mobilized by IncC plasmids and was recently shown to reshape the conjugative type IV secretion system (T4SS) encoded by these plasmids to evade entry exclusion. Entry exclusion blocks DNA translocation between cells containing identical or highly similar plasmids. Here, we report that the protein encoded by the entry exclusion gene of IncC plasmids (eexC) mediates entry exclusion in recipient cells through recognition of the IncC-encoded TraGC protein in donor cells. Phylogenetic analyses based on EexC and TraGC homologs predicted the existence of at least three different exclusion groups among IncC-related conjugative plasmids. Mating assays using Eex proteins encoded by representative IncC and IncA (former A/C1) and related untyped plasmids confirmed these predictions and showed that the IncC and IncA plasmids belong to the C exclusion group, thereby explaining their apparent incompatibility despite their compatible replicons. Representatives of the two other exclusion groups (D and E) are untyped conjugative plasmids found in Aeromonas sp. Finally, we determined through domain swapping that the carboxyl terminus of the EexC and EexE proteins controls the specificity of these exclusion groups. Together, these results unravel the role of entry exclusion in the apparent incompatibility between IncA and IncC plasmids while shedding light on the importance of the TraG subunit substitution used by SGI1 to evade entry exclusion.IMPORTANCE IncA and IncC conjugative plasmids drive antibiotic resistance dissemination among several pathogenic species of Gammaproteobacteria due to the diversity of drug resistance genes that they carry and their ability to mobilize antibiotic resistance-conferring genomic islands such as SGI1 of Salmonella enterica While historically grouped as "IncA/C," IncA and IncC replicons were recently confirmed to be compatible and to abolish each other's entry into the cell in which they reside during conjugative transfer. The significance of our study is in identifying an entry exclusion system that is shared by IncA and IncC plasmids. It impedes DNA transfer to recipient cells bearing a plasmid of either incompatibility group. The entry exclusion protein of this system is unrelated to any other known entry exclusion proteins.
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24
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Perez C, Mehdipour AR, Hummer G, Locher KP. Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation. Structure 2019; 27:669-678.e5. [PMID: 30799077 DOI: 10.1016/j.str.2019.01.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/29/2018] [Accepted: 01/25/2019] [Indexed: 12/21/2022]
Abstract
PglK is a lipid-linked oligosaccharide (LLO) flippase essential for asparagine-linked protein glycosylation in Campylobacter jejuni. Previously we have proposed a non-alternating-access LLO translocation mechanism, where postulated outward-facing states play a primary role. To investigate this unusual mechanistic proposal, we have determined a high-resolution structure of PglK that displays an outward semi-occluded state with the two nucleotide binding domains forming an asymmetric closed dimer with two bound ATPγS molecules. Based on this structure, we performed extensive molecular dynamics simulations to investigate LLO recognition and flipping. Our results suggest that PglK may employ a "substrate-hunting" mechanism to locally increase the LLO concentration and facilitate its jump into the translocation pathway, for which sugars from the LLO head group are essential. We further conclude that the release of LLO to the outside occurs before ATP hydrolysis and is followed by the closing of the periplasmic cavity of PglK.
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Affiliation(s)
- Camilo Perez
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
| | - Kaspar P Locher
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
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25
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Côrte-Real L, Karas B, Gírio P, Moreno A, Avecilla F, Marques F, Buckley BT, Cooper KR, Doherty C, Falson P, Garcia MH, Valente A. Unprecedented inhibition of P-gp activity by a novel ruthenium-cyclopentadienyl compound bearing a bipyridine-biotin ligand. Eur J Med Chem 2018; 163:853-863. [PMID: 30579125 DOI: 10.1016/j.ejmech.2018.12.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 12/14/2022]
Abstract
Two new ruthenium complexes, [Ru(η5-Cp)(PPh3)(2,2'-bipy-4,4'-R)]+ with R = -CH2OH (Ru1) or dibiotin ester (Ru2) were synthesized and fully characterized. Both compounds were tested against two types of breast cancer cells (MCF7 and MDA-MB-231), showing better cytotoxicity than cisplatin in the same experimental conditions. Since multidrug resistance (MDR) is one of the main problems in cancer chemotherapy, we have assessed the potential of these compounds to overcome resistance to treatments. Ru2 showed exceptional selectivity as P-gp inhibitor, while Ru1 is possibly a substrate. In vivo studies in zebrafish showed that Ru2 is well tolerated up to 1.17 mg/L, presenting a LC50 of 5.73 mg/L at 5 days post fertilization.
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Affiliation(s)
- Leonor Côrte-Real
- Centro de Química Estrutural, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Brittany Karas
- Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ, 08854, USA; Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ, 08854, USA
| | - Patrícia Gírio
- Centro de Química Estrutural, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal; Drug Resistance and Membrane Proteins Team, Molecular Biology and Structural Biochemistry Laboratory, UMR 5086 CNRS-UCBL1, IBCP 7 Passage du Vercors, 69 367, Lyon Cedex 07, France
| | - Alexis Moreno
- Drug Resistance and Membrane Proteins Team, Molecular Biology and Structural Biochemistry Laboratory, UMR 5086 CNRS-UCBL1, IBCP 7 Passage du Vercors, 69 367, Lyon Cedex 07, France
| | - Fernando Avecilla
- Grupo Xenomar, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071 A, Coruña, Spain
| | - Fernanda Marques
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, Km 139.7, 2695-066, Bobadela LRS, Portugal
| | - Brian T Buckley
- Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Keith R Cooper
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ, 08854, USA
| | - Cathleen Doherty
- Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Team, Molecular Biology and Structural Biochemistry Laboratory, UMR 5086 CNRS-UCBL1, IBCP 7 Passage du Vercors, 69 367, Lyon Cedex 07, France
| | - M Helena Garcia
- Centro de Química Estrutural, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Andreia Valente
- Centro de Química Estrutural, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
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26
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Schlessinger A, Welch MA, van Vlijmen H, Korzekwa K, Swaan PW, Matsson P. Molecular Modeling of Drug-Transporter Interactions-An International Transporter Consortium Perspective. Clin Pharmacol Ther 2018; 104:818-835. [PMID: 29981151 PMCID: PMC6197929 DOI: 10.1002/cpt.1174] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/30/2018] [Indexed: 12/31/2022]
Abstract
Membrane transporters play diverse roles in the pharmacokinetics and pharmacodynamics of small-molecule drugs. Understanding the mechanisms of drug-transporter interactions at the molecular level is, therefore, essential for the design of drugs with optimal therapeutic effects. This white paper examines recent progress, applications, and challenges of molecular modeling of membrane transporters, including modeling techniques that are centered on the structures of transporter ligands, and those focusing on the structures of the transporters. The goals of this article are to illustrate current best practices and future opportunities in using molecular modeling techniques to understand and predict transporter-mediated effects on drug disposition and efficacy.Membrane transporters from the solute carrier (SLC) and ATP-binding cassette (ABC) superfamilies regulate the cellular uptake, efflux, and homeostasis of many essential nutrients and significantly impact the pharmacokinetics of drugs; further, they may provide targets for novel therapeutics as well as facilitate prodrug approaches. Because of their often broad substrate selectivity they are also implicated in many undesirable and sometimes life-threatening drug-drug interactions (DDIs).5,6.
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Affiliation(s)
- Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthew A. Welch
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD
| | - Herman van Vlijmen
- Computational Chemistry, Discovery Sciences, Janssen Research & Development, Beerse, Belgium
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA
| | - Peter W. Swaan
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD
| | - Pär Matsson
- Department of Pharmacy, Uppsala University, Sweden
,Address correspondence to: Pär Matsson, Department of Pharmacy, Uppsala University, Box 580, SE-75123 Uppsala, Sweden, Phone: +46-(0)18-471 46 30, Fax: +46-(0)18-471 42 23,
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27
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Lin Y, Deepak RNVK, Zheng JZ, Fan H, Zheng L. A dual substrate-accessing mechanism of a major facilitator superfamily protein facilitates lysophospholipid flipping across the cell membrane. J Biol Chem 2018; 293:19919-19931. [PMID: 30373772 DOI: 10.1074/jbc.ra118.005548] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/23/2018] [Indexed: 11/06/2022] Open
Abstract
Lysophospholipid transporter (LplT) is a member of the major facilitator superfamily present in many Gram-negative bacteria. LplT catalyzes flipping of lysophospholipids (LPLs) across the bacterial inner membrane, playing an important role in bacterial membrane homeostasis. We previously reported that LplT promotes both uptake of exogenous LPLs and intramembranous LPL flipping across the bilayer. To gain mechanistic insight into this dual LPL-flipping activity, here we implemented a combination of computational approaches and LPL transport analyses to study LPL binding of and translocation by LplT. Our results suggest that LplT translocates LPLs through an elongated cavity exhibiting an extremely asymmetric polarity. We found that two D(E)N motifs form a head group-binding site, in which the carboxylate group of Asp-30 is important for LPL head group recognition. Substitutions of residues in the head group-binding site disrupted both LPL uptake and flipping activities. However, alteration of hydrophobic residues on the interface between the N- and C-terminal domains impaired LPL flipping specifically, resulting in LPLs accumulation in the membrane, but LPL uptake remained active. These results suggest a dual substrate-accessing mechanism, in which LplT recruits LPLs to its substrate-binding site via two routes, either from its extracellular entry or through a membrane-embedded groove between transmembrane helices, and then moves them toward the inner membrane leaflet. This LPL-flipping mechanism is likely conserved in many bacterial species, and our findings illustrate how LplT adjusts the major facilitator superfamily translocation pathway to perform its versatile lipid homeostatic functions.
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Affiliation(s)
- Yibin Lin
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston Texas 77030
| | - R N V Krishna Deepak
- the Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 138671 Singapore, and
| | - Jonathan Zixiang Zheng
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston Texas 77030
| | - Hao Fan
- the Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 138671 Singapore, and .,the Department of Biological Sciences (DBS), National University of Singapore, 117558 Singapore, and Center for Computational Biology, DUKE-NUS Medical School, 169857 Singapore
| | - Lei Zheng
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston Texas 77030,
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28
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Nikolaev D, Shtyrov AA, Panov MS, Jamal A, Chakchir OB, Kochemirovsky VA, Olivucci M, Ryazantsev MN. A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction. ACS OMEGA 2018; 3:7555-7566. [PMID: 30087916 PMCID: PMC6068592 DOI: 10.1021/acsomega.8b00721] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.
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Affiliation(s)
- Dmitrii
M. Nikolaev
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Andrey A. Shtyrov
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Maxim S. Panov
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
| | - Adeel Jamal
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Oleg B. Chakchir
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Vladimir A. Kochemirovsky
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry and Pharmacy, Università di Siena, via A. Moro 2, Siena I-53100, Italy
| | - Mikhail N. Ryazantsev
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
- Institute
of Macromolecular Compounds of the Russian Academy of Sciences, 31 Bolshoy pr., St. Petersburg 199004, Russia
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29
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Ballesteros A, Fenollar-Ferrer C, Swartz KJ. Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins. eLife 2018; 7:38433. [PMID: 30063209 PMCID: PMC6067890 DOI: 10.7554/elife.38433] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 02/03/2023] Open
Abstract
The hair cell mechanotransduction (MET) channel complex is essential for hearing, yet it's molecular identity and structure remain elusive. The transmembrane channel-like 1 (TMC1) protein localizes to the site of the MET channel, interacts with the tip-link responsible for mechanical gating, and genetic alterations in TMC1 alter MET channel properties and cause deafness, supporting the hypothesis that TMC1 forms the MET channel. We generated a model of TMC1 based on X-ray and cryo-EM structures of TMEM16 proteins, revealing the presence of a large cavity near the protein-lipid interface that also harbors the Beethoven mutation, suggesting that it could function as a permeation pathway. We also find that hair cells are permeable to 3 kDa dextrans, and that dextran permeation requires TMC1/2 proteins and functional MET channels, supporting the presence of a large permeation pathway and the hypothesis that TMC1 is a pore forming subunit of the MET channel complex.
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Affiliation(s)
- Angela Ballesteros
- Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, United States.,Laboratory of Molecular Genetics, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States.,Molecular Biology and Genetics Section, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States
| | - Kenton Jon Swartz
- Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
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30
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Last NB, Stockbridge RB, Wilson AE, Shane T, Kolmakova-Partensky L, Koide A, Koide S, Miller C. A CLC-type F -/H + antiporter in ion-swapped conformations. Nat Struct Mol Biol 2018; 25:601-606. [PMID: 29941917 PMCID: PMC6044475 DOI: 10.1038/s41594-018-0082-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/31/2018] [Indexed: 11/09/2022]
Abstract
Fluoride/proton antiporters of the CLCF family combat F- toxicity in bacteria by exporting this halide from the cytoplasm. These transporters belong to the widespread CLC superfamily but display transport properties different from those of the well-studied Cl-/H+ antiporters. Here, we report a structural and functional investigation of these F--transport proteins. Crystal structures of a CLCF homolog from Enterococcus casseliflavus are captured in two conformations with simultaneous accessibility of F- and H+ ions via separate pathways on opposite sides of the membrane. Manipulation of a key glutamate residue critical for H+ and F- transport reverses the anion selectivity of transport; replacement of the glutamate with glutamine or alanine completely inhibits F- and H+ transport while allowing for rapid uncoupled flux of Cl-. The structural and functional results lead to a 'windmill' model of CLC antiport wherein F- and H+ simultaneously move through separate ion-specific pathways that switch sidedness during the transport cycle.
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Affiliation(s)
- Nicholas B Last
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Randy B Stockbridge
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Ashley E Wilson
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Tania Shane
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | | | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York University School of Medicine, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA.
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31
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Zeppelin T, Ladefoged LK, Sinning S, Periole X, Schiøtt B. A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition. PLoS Comput Biol 2018; 14:e1005907. [PMID: 29329285 PMCID: PMC5811071 DOI: 10.1371/journal.pcbi.1005907] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/13/2018] [Accepted: 11/29/2017] [Indexed: 01/30/2023] Open
Abstract
Monoamine transporters (MATs) carry out neurotransmitter reuptake from the synaptic cleft, a key step in neurotransmission, which is targeted in the treatment of neurological disorders. Cholesterol (CHOL), a major component of the synaptic plasma membrane, has been shown to exhibit a modulatory effect on MATs. Recent crystal structures of the dopamine transporter (DAT) revealed the presence of two conserved CHOL-like molecules, suggesting a functional protein-CHOL direct interaction. Here, we present extensive atomistic molecular dynamics (MD) simulations of DAT in an outward-facing conformation. In the absence of bound CHOL, DAT undergoes structural changes reflecting early events of dopamine transport: transition to an inward-facing conformation. In contrast, in the presence of bound CHOL, these conformational changes are inhibited, seemingly by an immobilization of the intracellular interface of transmembrane helix 1a and 5 by CHOL. We also provide evidence, from coarse grain MD simulations that the CHOL sites observed in the DAT crystal structures are preserved in all human monoamine transporters (dopamine, serotonin and norepinephrine), suggesting that our findings might extend to the entire family.
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Affiliation(s)
- Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Lucy Kate Ladefoged
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
| | - Steffen Sinning
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus C, Denmark
| | - Xavier Periole
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
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32
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Abstract
![]()
Several apical iodide translocation
pathways have been proposed
for iodide efflux out of thyroid follicular cells, including a pathway
mediated by the sodium-coupled monocarboxylate transporter 1 (SMCT1),
which remains controversial. Herein, we evaluate structural and functional
similarities between SMCT1 and the well-studied sodium-iodide symporter
(NIS) that mediates the first step of iodide entry into the thyroid.
Free-energy calculations using a force field with electronic polarizability
verify the presence of a conserved iodide-binding pocket between the
TM2, TM3, and TM7 segments in hNIS, where iodide is coordinated by
Phe67, Gln72, Cys91, and Gln94. We demonstrate the mutation of residue
Gly93 of hNIS to a larger amino acid expels the side chain of a critical
tryptophan residue (Trp255) into the interior of the binding pocket,
partially occluding the iodide binding site and reducing iodide affinity,
which is consistent with previous reports associating mutation of
this residue with iodide uptake deficiency and hypothyroidism. Furthermore,
we find that the position of Trp255 in this hNIS mutant mirrors that
of Trp253 in wild-type hSMCT1, where a threonine (Thr91) occupies
the position homologous to that occupied by glycine in wild-type hNIS
(Gly93). Correspondingly, mutation of Thr91 to glycine in hSMCT1 makes
the pocket structure more like that of wild-type hNIS, increasing
its iodide affinity. These results suggest that wild-type hSMCT1 in
the inward-facing conformation may bind iodide only very weakly, which
may have implications for its ability to transport iodide.
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Affiliation(s)
- Ariela Vergara-Jaque
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca , 2 Norte 685, Talca 3460000, Chile.,Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Kansas State University , Manhattan, Kansas 66506, United States
| | - Peying Fong
- Department of Anatomy and Physiology, Kansas State University College of Veterinary Medicine , Manhattan, Kansas 66506, United States
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Kansas State University , Manhattan, Kansas 66506, United States.,Department of Anatomy and Physiology, Kansas State University College of Veterinary Medicine , Manhattan, Kansas 66506, United States
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33
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Structural basis of nucleotide sugar transport across the Golgi membrane. Nature 2017; 551:521-524. [PMID: 29143814 PMCID: PMC5701743 DOI: 10.1038/nature24464] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022]
Abstract
Glycosylation is a fundamental cellular process that in eukaryotes occurs
in the lumen of both the Golgi apparatus and endoplasmic reticulum 1. Nucleotide sugar transporters (NSTs) are
an essential component of the glyscosylation pathway, providing the diverse
range of substrates required for the glycosyltransferases 2,3. NSTs are linked
to several developmental and immune disorders in humans and in pathogenic
microbes play an important role in virulence 4–8. How NSTs recognise
and transport activated monosaccharides however is currently unclear. Here we
present the first crystal structure of an NST, the GDP-mannose transporter Vrg4,
in both the substrate free and bound states. A hitherto unobserved requirement
for short chain lipids in activating the transporter supports a model for
regulation within the highly dynamic membranes of the Golgi apparatus. Our
results provide a structural basis for understanding nucleotide sugar
recognition and provide insights into the transport and regulatory mechanism for
this family of intracellular transporters.
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34
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Rafehi M, Neumann A, Baqi Y, Malik EM, Wiese M, Namasivayam V, Müller CE. Molecular Recognition of Agonists and Antagonists by the Nucleotide-Activated G Protein-Coupled P2Y 2 Receptor. J Med Chem 2017; 60:8425-8440. [PMID: 28938069 DOI: 10.1021/acs.jmedchem.7b00854] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A homology model of the nucleotide-activated P2Y2R was created based on the X-ray structures of the P2Y1 receptor. Docking studies were performed, and receptor mutants were created to probe the identified binding interactions. Mutation of residues predicted to interact with the ribose (Arg110) and the phosphates of the nucleotide agonists (Arg265, Arg292) or that contribute indirectly to binding (Tyr288) abolished activity. The Y114F, R194A, and F261A mutations led to inactivity of diadenosine tetraphosphate and to a reduced response of UTP. Significant reduction in agonist potency was observed for all other receptor mutants (Phe111, His184, Ser193, Phe261, Tyr268, Tyr269) predicted to be involved in agonist recognition. An ionic lock between Asp185 and Arg292 that is probably involved in receptor activation interacts with the phosphate groups. The antagonist AR-C118925 and anthraquinones likely bind to the orthosteric site. The updated homology models will be useful for virtual screening and drug design.
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Affiliation(s)
- Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Alexander Neumann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Younis Baqi
- Department of Chemistry, Faculty of Science, Sultan Qaboos University , PO Box 36, Postal Code 123, Muscat, Oman
| | - Enas M Malik
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Michael Wiese
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II, University of Bonn , 53121 Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany.,PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II, University of Bonn , 53121 Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
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35
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Lara P, Öjemalm K, Reithinger J, Holgado A, Maojun Y, Hammed A, Mattle D, Kim H, Nilsson I. Refined topology model of the STT3/Stt3 protein subunit of the oligosaccharyltransferase complex. J Biol Chem 2017; 292:11349-11360. [PMID: 28512128 DOI: 10.1074/jbc.m117.779421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/10/2017] [Indexed: 01/16/2023] Open
Abstract
The oligosaccharyltransferase complex, localized in the endoplasmic reticulum (ER) of eukaryotic cells, is responsible for the N-linked glycosylation of numerous protein substrates. The membrane protein STT3 is a highly conserved part of the oligosaccharyltransferase and likely contains the active site of the complex. However, understanding the catalytic determinants of this system has been challenging, in part because of a discrepancy in the structural topology of the bacterial versus eukaryotic proteins and incomplete information about the mechanism of membrane integration. Here, we use a glycosylation mapping approach to investigate these questions. We measured the membrane integration efficiency of the mouse STT3-A and yeast Stt3p transmembrane domains (TMDs) and report a refined topology of the N-terminal half of the mouse STT3-A. Our results show that most of the STT3 TMDs are well inserted into the ER membrane on their own or in the presence of the natural flanking residues. However, for the mouse STT3-A hydrophobic domains 4 and 6 and yeast Stt3p domains 2, 3a, 3c, and 6 we measured reduced insertion efficiency into the ER membrane. Furthermore, we mapped the first half of the STT3-A protein, finding two extra hydrophobic domains between the third and the fourth TMD. This result indicates that the eukaryotic STT3 has 13 transmembrane domains, consistent with the structure of the bacterial homolog of STT3 and setting the stage for future combined efforts to interrogate this fascinating system.
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Affiliation(s)
- Patricia Lara
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Karin Öjemalm
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Johannes Reithinger
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Aurora Holgado
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - You Maojun
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Abdessalem Hammed
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Daniel Mattle
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Hyun Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - IngMarie Nilsson
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
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36
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Diskowski M, Mehdipour AR, Wunnicke D, Mills DJ, Mikusevic V, Bärland N, Hoffmann J, Morgner N, Steinhoff HJ, Hummer G, Vonck J, Hänelt I. Helical jackknives control the gates of the double-pore K + uptake system KtrAB. eLife 2017; 6. [PMID: 28504641 PMCID: PMC5449183 DOI: 10.7554/elife.24303] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/14/2017] [Indexed: 12/27/2022] Open
Abstract
Ion channel gating is essential for cellular homeostasis and is tightly controlled. In some eukaryotic and most bacterial ligand-gated K+ channels, RCK domains regulate ion fluxes. Until now, a single regulatory mechanism has been proposed for all RCK-regulated channels, involving signal transduction from the RCK domain to the gating area. Here, we present an inactive ADP-bound structure of KtrAB from Vibrio alginolyticus, determined by cryo-electron microscopy, which, combined with EPR spectroscopy and molecular dynamics simulations, uncovers a novel regulatory mechanism for ligand-induced action at a distance. Exchange of activating ATP to inactivating ADP triggers short helical segments in the K+-translocating KtrB dimer to organize into two long helices that penetrate deeply into the regulatory RCK domains, thus connecting nucleotide-binding sites and ion gates. As KtrAB and its homolog TrkAH have been implicated as bacterial pathogenicity factors, the discovery of this functionally relevant inactive conformation may advance structure-guided drug development. DOI:http://dx.doi.org/10.7554/eLife.24303.001
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Affiliation(s)
- Marina Diskowski
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Dorith Wunnicke
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | | | - Natalie Bärland
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany.,Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Jan Hoffmann
- Institute for Physical and Theoretical Chemistry, Goethe-University, Frankfurt, Germany
| | - Nina Morgner
- Institute for Physical and Theoretical Chemistry, Goethe-University, Frankfurt, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute of Biophysics, Goethe-University, Frankfurt, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
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37
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Rafehi M, Malik EM, Neumann A, Abdelrahman A, Hanck T, Namasivayam V, Müller CE, Baqi Y. Development of Potent and Selective Antagonists for the UTP-Activated P2Y 4 Receptor. J Med Chem 2017; 60:3020-3038. [PMID: 28306255 DOI: 10.1021/acs.jmedchem.7b00030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
P2Y4 is a Gq protein-coupled receptor activated by uridine-5'-triphosphate (UTP), which is widely expressed in the body, e.g., in intestine, heart, and brain. No selective P2Y4 receptor antagonist has been described so far. Therefore, we developed and optimized P2Y4 receptor antagonists based on an anthraquinone scaffold. Potency was assessed by a fluorescence-based assay measuring inhibition of UTP-induced intracellular calcium release in 1321N1 astrocytoma cells stably transfected with the human P2Y4 receptor. The most potent compound of the present series, sodium 1-amino-4-[4-(2,4-dimethylphenylthio)phenylamino]-9,10-dioxo-9,10-dihydroanthracene-2-sulfonate (PSB-16133, 61) exhibited an IC50 value of 233 nM, selectivity versus other P2Y receptor subtypes, and is thought to act as an allosteric antagonist. A receptor homology model was built and docking studies were performed to analyze ligand-receptor interactions. Compound 64 (PSB-1699, sodium 1-amino-4-[4-(3-pyridin-3-ylmethylthio)phenylamino]-9,10-dioxo-9,10-dihydroanthracene-2-sulfonate) represents the most selective P2Y4 receptor antagonist known to date. Compounds 61 and 64 are therefore anticipated to become useful tools for studying this scarcely investigated receptor.
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Affiliation(s)
- Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn , An der Immenburg 4, D-53121 Bonn, Germany
| | - Enas M Malik
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn , An der Immenburg 4, D-53121 Bonn, Germany
| | - Alexander Neumann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn , An der Immenburg 4, D-53121 Bonn, Germany
| | - Aliaa Abdelrahman
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn , An der Immenburg 4, D-53121 Bonn, Germany
| | - Theodor Hanck
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn , An der Immenburg 4, D-53121 Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn , An der Immenburg 4, D-53121 Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn , An der Immenburg 4, D-53121 Bonn, Germany
| | - Younis Baqi
- Department of Chemistry, Faculty of Science, Sultan Qaboos University , PO Box 36, Postal Code 123, Muscat, Oman
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38
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Dayan O, Nagarajan A, Shah R, Ben-Yona A, Forrest LR, Kanner BI. An Extra Amino Acid Residue in Transmembrane Domain 10 of the γ-Aminobutyric Acid (GABA) Transporter GAT-1 Is Required for Efficient Ion-coupled Transport. J Biol Chem 2017; 292:5418-5428. [PMID: 28213519 DOI: 10.1074/jbc.m117.775189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/09/2017] [Indexed: 11/06/2022] Open
Abstract
The GABA transporter GAT-1 mediates electrogenic transport of its substrate together with sodium and chloride. It is a member of the neurotransmitter:sodium:symporters, which are crucial for synaptic transmission. Compared with all other neurotransmitter:sodium:symporters, GAT-1 and other members of the GABA transporter subfamily all contain an extra amino acid residue at or near a conserved glycine in transmembrane segment 10. Therefore, we studied the functional impact of deletion and replacement mutants of Gly-457 and its two adjacent residues in GAT-1. The glycine replacement mutants were devoid of transport activity, but remarkably the deletion mutant was active, as were mutants obtained by deleting positions on either side of Gly-457. However, the inward rectification of GABA-induced transport currents by all three deletion mutants was diminished, and the charge-to-flux ratio was increased by more than 2.5-fold, both of which indicate substantial uncoupled transport. These observations suggest that the deletions render the transporters less tightly packed. Consistent with this interpretation, the inactive G457A mutant was partially rescued by removing the adjacent serine residue. Moreover, the activity of several gating mutants was also partially rescued upon deletion of Gly-457. Structural modeling showed that the stretch surrounding Gly-457 is likely to form a π-helix. Our data indicate that the "extra" residue in transmembrane domain 10 of the GABA transporter GAT-1 provides extra bulk, probably in the form of a π-helix, which is required for stringent gating and tight coupling of ion and substrate fluxes in the GABA transporter family.
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Affiliation(s)
- Oshrat Dayan
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel and
| | - Anu Nagarajan
- the Computational Structural Biology Section, NINDS, National Institutes of Health, Bethesda, Maryland 20892
| | - Raven Shah
- the Computational Structural Biology Section, NINDS, National Institutes of Health, Bethesda, Maryland 20892
| | - Assaf Ben-Yona
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel and
| | - Lucy R Forrest
- the Computational Structural Biology Section, NINDS, National Institutes of Health, Bethesda, Maryland 20892
| | - Baruch I Kanner
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel and
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39
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Venko K, Roy Choudhury A, Novič M. Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J 2017; 15:232-242. [PMID: 28228927 PMCID: PMC5312651 DOI: 10.1016/j.csbj.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/23/2022] Open
Abstract
The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix–helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.
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Affiliation(s)
- Katja Venko
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - A Roy Choudhury
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Novič
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
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40
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Nikolaev DM, Emelyanov A, Boitsov VM, Panov MS, Ryazantsev MN. A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling. F1000Res 2017; 6:33. [PMID: 28435665 PMCID: PMC5381632 DOI: 10.12688/f1000research.10541.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2017] [Indexed: 12/25/2022] Open
Abstract
It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. While it has already shown encouraging results, there is still a large room for improvement. One of possible directions is increasing the intensity of the protein's fluorescent signal. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.
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Affiliation(s)
- Dmitrii M Nikolaev
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Anton Emelyanov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Vitaly M Boitsov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Maxim S Panov
- Saint-Petersburg State University, St. Petersburg, Russian Federation
| | - Mikhail N Ryazantsev
- Saint-Petersburg State University, St. Petersburg, Russian Federation.,Saint-Petersburg Scientific Center of the Russian Academy of Sciences, St. Petersburg, Russian Federation
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41
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Yan R, Wang X, Huang L, Tian Y, Cai W. Transmembrane region prediction by using sequence-derived features and machine learning methods. RSC Adv 2017. [DOI: 10.1039/c7ra03883f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Membrane proteins are central to carrying out impressive biological functions.
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Affiliation(s)
- Renxiang Yan
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Xiaofeng Wang
- College of Mathematics and Computer Science
- Shanxi Normal University
- Linfen 041004
- China
| | - Lanqing Huang
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Yarong Tian
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Weiwen Cai
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
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42
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Emulating proton-induced conformational changes in the vesicular monoamine transporter VMAT2 by mutagenesis. Proc Natl Acad Sci U S A 2016; 113:E7390-E7398. [PMID: 27821772 DOI: 10.1073/pnas.1605162113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neurotransporters located in synaptic vesicles are essential for communication between nerve cells in a process mediated by neurotransmitters. Vesicular monoamine transporter (VMAT), a member of the largest superfamily of transporters, mediates transport of monoamines to synaptic vesicles and storage organelles in a process that involves exchange of two H+ per substrate. VMAT transport is inhibited by the competitive inhibitor reserpine, a second-line agent to treat hypertension, and by the noncompetitive inhibitor tetrabenazine, presently in use for symptomatic treatment of hyperkinetic disorders. During the transport cycle, VMAT is expected to occupy at least three different conformations: cytoplasm-facing, occluded, and lumen-facing. The lumen- to cytoplasm-facing transition, facilitated by protonation of at least one of the essential membrane-embedded carboxyls, generates a binding site for reserpine. Here we have identified residues in the cytoplasmic gate and show that mutations that disrupt the interactions in this gate also shift the equilibrium toward the cytoplasm-facing conformation, emulating the effect of protonation. These experiments provide significant insight into the role of proton translocation in the conformational dynamics of a mammalian H+-coupled antiporter, and also identify key aspects of the mode of action and binding of two potent inhibitors of VMAT2: reserpine binds the cytoplasm-facing conformation, and tetrabenazine binds the lumen-facing conformation.
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43
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Nim S, Lobato LG, Moreno A, Chaptal V, Rawal MK, Falson P, Prasad R. Atomic modelling and systematic mutagenesis identify residues in multiple drug binding sites that are essential for drug resistance in the major Candida transporter Cdr1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2858-2870. [DOI: 10.1016/j.bbamem.2016.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 01/07/2023]
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44
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Lehnert E, Mao J, Mehdipour AR, Hummer G, Abele R, Glaubitz C, Tampé R. Antigenic Peptide Recognition on the Human ABC Transporter TAP Resolved by DNP-Enhanced Solid-State NMR Spectroscopy. J Am Chem Soc 2016; 138:13967-13974. [DOI: 10.1021/jacs.6b07426] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | | | - Ahmad Reza Mehdipour
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str.
3, 60438 Frankfurt
am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str.
3, 60438 Frankfurt
am Main, Germany
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45
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Colas C, Ung PMU, Schlessinger A. SLC Transporters: Structure, Function, and Drug Discovery. MEDCHEMCOMM 2016; 7:1069-1081. [PMID: 27672436 PMCID: PMC5034948 DOI: 10.1039/c6md00005c] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The human Solute Carrier (SLC) transporters are important targets for drug development. Structure-based drug discovery for SLC transporters requires the description of their structure, dynamics, and mechanism of interaction with small molecule ligands and ions. The recent determination of atomic structures of human SLC transporters and their homologs, combined with improved computational power and prediction methods have led to an increased applicability of structure-based drug design methods for human SLC members. In this review, we provide an overview of the SLC transporters' structures and transport mechanisms. We then describe computational techniques, such as homology modeling and virtual screening that are emerging as key tools to discover chemical probes for human SLC members. We illustrate the utility of these methods by presenting case studies in which rational integration of computation and experiment was used to characterize SLC members that transport key nutrients and metabolites, including the amino acid transporters LAT-1 and ASCT2, the SLC13 family of citric acid cycle intermediate transporters, and the glucose transporter GLUT1. We conclude with a brief discussion about future directions in structure-based drug discovery for the human SLC superfamily, one of the most structurally and functionally diverse protein families in human.
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Affiliation(s)
- Claire Colas
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Peter Man-Un Ung
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Avner Schlessinger
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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46
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Kumar S, Bradley CL, Mukashyaka P, Doerrler WT. Identification of essential arginine residues ofEscherichia coliDedA/Tvp38 family membrane proteins YqjA and YghB. FEMS Microbiol Lett 2016; 363:fnw133. [DOI: 10.1093/femsle/fnw133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2016] [Indexed: 12/15/2022] Open
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Atsmon-Raz Y, Miller Y. Non-Amyloid-β Component of Human α-Synuclein Oligomers Induces Formation of New Aβ Oligomers: Insight into the Mechanisms That Link Parkinson's and Alzheimer's Diseases. ACS Chem Neurosci 2016; 7:46-55. [PMID: 26479553 DOI: 10.1021/acschemneuro.5b00204] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Parkinson's disease (PD) is characterized by the formation of Lewy bodies (LBs), of which their major component is the non-amyloid-β component (NAC) of α-synuclein (AS). Clinical studies have identified a link between PD and Alzheimer's disease (AD), but the question of why PD patients are at risk to develop various types of dementia, such as AD, is still elusive. In vivo studies have shown that Aβ can act as a seed for NAC/AS aggregation, promoting NAC/AS aggregation and thus contributing to the etiology of PD. However, the mechanisms by which NAC/AS oligomers interact with Aβ oligomers are still elusive. This work presents the interactions between NAC oligomers and Aβ oligomers at atomic resolution by applying extensive molecular dynamics simulations for an ensemble of cross-seeded NAC-Aβ(1-42) oligomers. The main conclusions of this study are as follows: first, the cross-seeded NAC-Aβ(1-42) oligomers represent polymorphic states, yet NAC oligomers prefer to interact with Aβ(1-42) oligomers to form double-layer over single-layer conformations due to electrostatic/hydrophobic interactions; second, among the single-layer conformations, the NAC oligomers induce formation of new β-strands in Aβ(1-42) oligomers, thus leading to new Aβ oligomer structures; and third, NAC oligomers stabilize the cross-β structure of Aβ oligomers, i.e., yielding compact Aβ fibril-like structures.
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Affiliation(s)
- Yoav Atsmon-Raz
- Department of Chemistry, ‡Ilse Katz Institute for Nanoscale
Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, ‡Ilse Katz Institute for Nanoscale
Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Andersen J, Ladefoged LK, Wang D, Kristensen TNB, Bang-Andersen B, Kristensen AS, Schiøtt B, Strømgaard K. Binding of the multimodal antidepressant drug vortioxetine to the human serotonin transporter. ACS Chem Neurosci 2015; 6:1892-900. [PMID: 26389667 DOI: 10.1021/acschemneuro.5b00225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Selective inhibitors of the human serotonin transporter (hSERT) have been first-line treatment against depression for several decades. Recently, vortioxetine was approved as a new therapeutic option for the treatment of depression. Vortioxetine represents a new class of antidepressant drugs with a multimodal pharmacological profile that in addition to potent inhibition of hSERT include agonistic or antagonistic effects at different serotonin receptors. We used a combination of computational, chemical, and biological methods to decipher the molecular basis for high affinity binding of vortioxetine in hSERT. X-ray crystal structures of the bacterial amino acid transporter LeuT and the Drosophila melanogaster dopamine transporter were used to build homology models of hSERT. Comparative modeling and ligand docking suggest that vortioxetine can adopt several distinct binding modes within the central binding site of hSERT. To distinguish between the identified binding modes, we determined the effect of 57 functional hSERT point mutants on vortioxetine potency and characterized seven structurally related analogs of vortioxetine in a subset of the point mutants. This allowed us to determine the orientation of vortioxetine within the central binding site and showed that only one of the proposed binding modes is functionally relevant. The findings provide important new insight about the molecular basis for high affinity recognition of vortioxetine in hSERT, which is essential for future structure-based drug discovery of novel multimodal drugs with fine-tuned selectivity across different transporter and receptor proteins in the human brain.
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Affiliation(s)
- Jacob Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lucy Kate Ladefoged
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Danyang Wang
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Trine N. Bjerre Kristensen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Benny Bang-Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Lundbeck Research Denmark, H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark
| | - Anders S. Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Computational approaches to study the effects of small genomic variations. J Mol Model 2015; 21:251. [PMID: 26350246 DOI: 10.1007/s00894-015-2794-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/23/2015] [Indexed: 10/23/2022]
Abstract
Advances in DNA sequencing technologies have led to an avalanche-like increase in the number of gene sequences deposited in public databases over the last decade as well as the detection of an enormous number of previously unseen nucleotide variants therein. Given the size and complex nature of the genome-wide sequence variation data, as well as the rate of data generation, experimental characterization of the disease association of each of these variations or their effects on protein structure/function would be costly, laborious, time-consuming, and essentially impossible. Thus, in silico methods to predict the functional effects of sequence variations are constantly being developed. In this review, we summarize the major computational approaches and tools that are aimed at the prediction of the functional effect of mutations, and describe the state-of-the-art databases that can be used to obtain information about mutation significance. We also discuss future directions in this highly competitive field.
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Atsmon-Raz Y, Miller Y. A Proposed Atomic Structure of the Self-Assembly of the Non-Amyloid-β Component of Human α-Synuclein As Derived by Computational Tools. J Phys Chem B 2015; 119:10005-15. [PMID: 26147432 DOI: 10.1021/acs.jpcb.5b03760] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
α-Synuclein (AS) fibrils are the major hallmarks of Parkinson's disease (PD). It is known that the central domain of the 140-residue AS protein, known as the non-amyloid-β component (NAC), plays a crucial role in aggregation. The secondary structure of AS fibrils (including the NAC domain) has been proposed on the basis of solid-state nuclear magnetic resonance studies, but the atomic structure of the self-assembly of NAC (or AS itself) is still elusive. This is the first study that presents a detailed three-dimensional structure of NAC at atomic resolution. The proposed self-assembled structure of NAC consists of three β-strands connected by two turn regions. Our study shows that calculated structural parameter values of the simulated fibril-like cross-β structure of NAC are in excellent agreement with the experimental values. Moreover, the diameter dimensions of the proposed fibril-like structure are also in agreement with experimental measurements. The proposed fibril-like structure of NAC may assist in future work aimed at understanding the formation of aggregates in PD and developing compounds to modulate aggregation.
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Affiliation(s)
- Yoav Atsmon-Raz
- †Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,‡Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Miller
- †Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,‡Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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