1
|
Tayebi N, Leon‐Ricardo B, McCall K, Mehinovic E, Engelstad K, Huynh V, Turner TN, Weisenberg J, Thio LL, Hruz P, Williams RSB, De Vivo DC, Petit V, Haller G, Gurnett CA. Quantitative determination of SLC2A1 variant functional effects in GLUT1 deficiency syndrome. Ann Clin Transl Neurol 2023; 10:787-801. [PMID: 37000947 PMCID: PMC10187726 DOI: 10.1002/acn3.51767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 04/03/2023] Open
Abstract
OBJECTIVE The goal of this study is to demonstrate the utility of a growth assay to quantify the functional impact of single nucleotide variants (SNVs) in SLC2A1, the gene responsible for Glut1DS. METHODS The functional impact of 40 SNVs in SLC2A1 was quantitatively determined in HAP1 cells in which SLC2A1 is required for growth. Donor libraries were introduced into the endogenous SLC2A1 gene in HAP1-Lig4KO cells using CRISPR/Cas9. Cell populations were harvested and sequenced to quantify the effect of variants on growth and generate a functional score. Quantitative functional scores were compared to 3-OMG uptake, SLC2A1 cell surface expression, CADD score, and clinical data, including CSF/blood glucose ratio. RESULTS Nonsense variants (N = 3) were reduced in cell culture over time resulting in negative scores (mean score: -1.15 ± 0.17), whereas synonymous variants (N = 10) were not depleted (mean score: 0.25 ± 0.12) (P < 2e-16). Missense variants (N = 27) yielded a range of functional scores including slightly negative scores, supporting a partial function and intermediate phenotype. Several variants with normal results on either cell surface expression (p.N34S and p.W65R) or 3-OMG uptake (p.W65R) had negative functional scores. There is a moderate but significant correlation between our functional scores and CADD scores. INTERPRETATION Cell growth is useful to quantitatively determine the functional effects of SLC2A1 variants. Nonsense variants were reliably distinguished from benign variants in this in vitro functional assay. For facilitating early diagnosis and therapeutic intervention, future work is needed to determine the functional effect of every possible variant in SLC2A1.
Collapse
Affiliation(s)
- Naeimeh Tayebi
- Department of NeurologyWashington University in St LouisSt LouisMissouriUSA
| | - Brian Leon‐Ricardo
- Department of NeurologyWashington University in St LouisSt LouisMissouriUSA
| | - Kevin McCall
- Department of NeurologyWashington University in St LouisSt LouisMissouriUSA
| | - Elvisa Mehinovic
- Department of GeneticsWashington University in St LouisSt LouisMissouriUSA
| | - Kristin Engelstad
- Department of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Vincent Huynh
- Department of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Tychele N. Turner
- Department of GeneticsWashington University in St LouisSt LouisMissouriUSA
| | - Judy Weisenberg
- Department of NeurologyWashington University in St LouisSt LouisMissouriUSA
| | - Liu L. Thio
- Department of NeurologyWashington University in St LouisSt LouisMissouriUSA
| | - Paul Hruz
- Department of PediatricsWashington University in St LouisSt LouisMissouriUSA
| | - Robin S. B. Williams
- Centre for Biomedical Sciences, Department of Biological SciencesRoyal Holloway University of LondonEghamUK
| | - Darryl C. De Vivo
- Department of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | | | - Gabe Haller
- Department of NeurologyWashington University in St LouisSt LouisMissouriUSA
- Department of GeneticsWashington University in St LouisSt LouisMissouriUSA
- Department of Neurological SurgeryWashington University in St LouisSt LouisMissouriUSA
| | | |
Collapse
|
2
|
Naftalin RJ. A critique of the alternating access transporter model of uniport glucose transport. BIOPHYSICS REPORTS 2018; 4:287-299. [PMID: 30596138 PMCID: PMC6276071 DOI: 10.1007/s41048-018-0076-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Richard J Naftalin
- Physiology and Vascular Biology Group, King's College London Medical School, Waterloo Campus, London, SE1 9HN UK
| |
Collapse
|
3
|
Kinetic Basis of Cis- and Trans-Allostery in GLUT1-Mediated Sugar Transport. J Membr Biol 2017; 251:131-152. [PMID: 29209831 DOI: 10.1007/s00232-017-0006-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/15/2017] [Indexed: 01/12/2023]
Abstract
A growing body of evidence demonstrates that GLUT1-mediated erythrocyte sugar transport is more complex than widely assumed and that contemporary interpretations of emergent GLUT1 structural data are incompatible with the available transport and biochemical data. This study examines the kinetic basis of one such incompatibility-transport allostery-and in doing so suggests how the results of studies examining GLUT1 structure and function may be reconciled. Three types of allostery are observed in GLUT1-mediated, human erythrocyte sugar transport: (1) exofacial cis-allostery in which low concentrations of extracellular inhibitors stimulate sugar uptake while high concentrations inhibit transport; (2) endofacial cis-allostery in which low concentrations of intracellular inhibitors enhance cytochalasin B binding to GLUT1 while high concentrations inhibit binding, and (3) trans-allostery in which low concentrations of ligands acting at one cell surface stimulate ligand binding at or sugar transport from the other surface while high concentrations inhibit these processes. We consider several kinetic models to account for these phenomena. Our results show that an inhibitor can only stimulate then inhibit sugar uptake if (1) the transporter binds two or more molecules of inhibitor; (2) high-affinity binding to the first site stimulates transport, and (3) low-affinity binding to the second site inhibits transport. Reviewing the available structural, transport, and ligand binding data, we propose that exofacial cis-allostery results from cross-talk between multiple, co-existent ligand interaction sites present in the exofacial cavity of each GLUT1 protein, whereas trans-allostery and endofacial cis-allostery require ligand-induced subunit-subunit interactions.
Collapse
|
4
|
Iglesias-Fernandez J, Quinn PJ, Naftalin RJ, Domene C. Membrane Phase-Dependent Occlusion of Intramolecular GLUT1 Cavities Demonstrated by Simulations. Biophys J 2017; 112:1176-1184. [PMID: 28355545 DOI: 10.1016/j.bpj.2017.01.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 12/27/2022] Open
Abstract
Experimental evidence has shown a close correlation between the composition and physical state of the membrane bilayer and glucose transport activity via the glucose transporter GLUT1. Cooling alters the membrane lipids from the fluid to gel phase, and also causes a large decrease in the net glucose transport rate. The goal of this study is to investigate how the physical phase of the membrane alters glucose transporter structural dynamics using molecular-dynamics simulations. Simulations from an initial fluid to gel phase reduce the size of the cavities and tunnels traversing the protein and connecting the external regions of the transporter and the central binding site. These effects can be ascribed solely to membrane structural changes since in silico cooling of the membrane alone, while maintaining the higher protein temperature, shows protein structural and dynamic changes very similar to those observed with uniform cooling. These results demonstrate that the protein structure is sensitive to the membrane phase, and have implications for how transmembrane protein structures respond to their physical environment.
Collapse
Affiliation(s)
| | - Peter J Quinn
- Department of Biochemistry, School of Medicine, King's College London, London, United Kingdom
| | - Richard J Naftalin
- Department of Physiology, School of Medicine, King's College London, London, United Kingdom; BHF Centre of Research Excellence, School of Medicine, King's College London, London, United Kingdom
| | - Carmen Domene
- Department of Chemistry, School of Medicine, King's College London, London, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
5
|
Ojelabi OA, Lloyd KP, Simon AH, De Zutter JK, Carruthers A. WZB117 (2-Fluoro-6-(m-hydroxybenzoyloxy) Phenyl m-Hydroxybenzoate) Inhibits GLUT1-mediated Sugar Transport by Binding Reversibly at the Exofacial Sugar Binding Site. J Biol Chem 2016; 291:26762-26772. [PMID: 27836974 DOI: 10.1074/jbc.m116.759175] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/10/2016] [Indexed: 01/26/2023] Open
Abstract
WZB117 (2-fluoro-6-(m-hydroxybenzoyloxy) phenyl m-hydroxybenzoate) inhibits passive sugar transport in human erythrocytes and cancer cell lines and, by limiting glycolysis, inhibits tumor growth in mice. This study explores how WZB117 inhibits the erythrocyte sugar transporter glucose transport protein 1 (GLUT1) and examines the transporter isoform specificity of inhibition. WZB117 reversibly and competitively inhibits erythrocyte 3-O-methylglucose (3MG) uptake with Ki(app) = 6 μm but is a noncompetitive inhibitor of sugar exit. Cytochalasin B (CB) is a reversible, noncompetitive inhibitor of 3MG uptake with Ki(app) = 0.3 μm but is a competitive inhibitor of sugar exit indicating that WZB117 and CB bind at exofacial and endofacial sugar binding sites, respectively. WZB117 inhibition of GLUTs expressed in HEK293 cells follows the order of potency: insulin-regulated GLUT4 ≫ GLUT1 ≈ neuronal GLUT3. This may explain WZB117-induced murine lipodystrophy. Molecular docking suggests the following. 1) The WZB117 binding envelopes of exofacial GLUT1 and GLUT4 conformers differ significantly. 2) GLUT1 and GLUT4 exofacial conformers present multiple, adjacent glucose binding sites that overlap with WZB117 binding envelopes. 3) The GLUT1 exofacial conformer lacks a CB binding site. 4) The inward GLUT1 conformer presents overlapping endofacial WZB117, d-glucose, and CB binding envelopes. Interrogating the GLUT1 mechanism using WZB117 reveals that subsaturating WZB117 and CB stimulate erythrocyte 3MG uptake. Extracellular WZB117 does not affect CB binding to GLUT1, but intracellular WZB117 inhibits CB binding. These findings are incompatible with the alternating conformer carrier for glucose transport but are consistent with either a multisubunit, allosteric transporter, or a transporter in which each subunit presents multiple, interacting ligand binding sites.
Collapse
Affiliation(s)
- Ogooluwa A Ojelabi
- From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Kenneth P Lloyd
- From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Andrew H Simon
- From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Julie K De Zutter
- From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Anthony Carruthers
- From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| |
Collapse
|
6
|
Fu X, Zhang G, Liu R, Wei J, Zhang-Negrerie D, Jian X, Gao Q. Mechanistic Study of Human Glucose Transport Mediated by GLUT1. J Chem Inf Model 2016; 56:517-26. [PMID: 26821218 DOI: 10.1021/acs.jcim.5b00597] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The glucose transporter 1 (GLUT1) belongs to the major facilitator superfamily (MFS) and is responsible for the constant uptake of glucose. However, the molecular mechanism of sugar transport remains obscure. In this study, homology modeling and molecular dynamics (MD) simulations in lipid bilayers were performed to investigate the combination of the alternate and multisite transport mechanism of glucose with GLUT1 in atomic detail. To explore the substrate recognition mechanism, the outward-open state human GLUT1 homology model was generated based on the template of xylose transporter XylE (PDB ID: 4GBZ), which shares up to 29% sequence identity and 49% similarity with GLUT1. Through the MD simulation study of glucose across lipid bilayer with both the outward-open GLUT1 and the GLUT1 inward-open crystal structure, we investigated six different conformational states and identified four key binding sites in both exofacial and endofacial loops that are essential for glucose recognition and transport. The study further revealed that four flexible gates consisting of W65/Y292/Y293-M420/TM10b-W388 might play important roles in the transport cycle. The study showed that some side chains close to the central ligand binding site underwent larger position changes. These conformational interchanges formed gated networks within an S-shaped central channel that permitted staged ligand diffusion across the transporter. This study provides new inroads for the understanding of GLUT1 ligand recognition paradigm and configurational features which are important for molecular, structural, and physiological research of the MFS members, especially for GLUT1-targeted drug design and discovery.
Collapse
Affiliation(s)
- Xuegang Fu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University , Tianjin, 300072, P. R. China
| | - Gang Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University , Tianjin, 300072, P. R. China
| | - Ran Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University , Tianjin, 300072, P. R. China
| | - Jing Wei
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University , Tianjin, 300072, P. R. China
| | - Daisy Zhang-Negrerie
- Concordia International School , 999 Mingyue Road, Shanghai, 201206, P. R. China
| | - Xiaodong Jian
- National Supercomputing Center in Tianjin , TEDA Service Outsourcing Industrial Park, Binhai New Area, Tianjin, 300457, P. R. China
| | - Qingzhi Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University , Tianjin, 300072, P. R. China.,Tianjin University Collaborative Innovation Center of Chemical Science and Engineering , Tianjin, 300072, P. R. China
| |
Collapse
|
7
|
Diallinas G. Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters. Front Pharmacol 2014; 5:207. [PMID: 25309439 PMCID: PMC4162363 DOI: 10.3389/fphar.2014.00207] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/22/2014] [Indexed: 12/12/2022] Open
Abstract
Transporters are ubiquitous proteins mediating the translocation of solutes across cell membranes, a biological process involved in nutrition, signaling, neurotransmission, cell communication and drug uptake or efflux. Similarly to enzymes, most transporters have a single substrate binding-site and thus their activity follows Michaelis-Menten kinetics. Substrate binding elicits a series of structural changes, which produce a transporter conformer open toward the side opposite to the one from where the substrate was originally bound. This mechanism, involving alternate outward- and inward-facing transporter conformers, has gained significant support from structural, genetic, biochemical and biophysical approaches. Most transporters are specific for a given substrate or a group of substrates with similar chemical structure, but substrate specificity and/or affinity can vary dramatically, even among members of a transporter family that show high overall amino acid sequence and structural similarity. The current view is that transporter substrate affinity or specificity is determined by a small number of interactions a given solute can make within a specific binding site. However, genetic, biochemical and in silico modeling studies with the purine transporter UapA of the filamentous ascomycete Aspergillus nidulans have challenged this dogma. This review highlights results leading to a novel concept, stating that substrate specificity, but also transport kinetics and transporter turnover, are determined by subtle intramolecular interactions between a major substrate binding site and independent outward- or cytoplasmically-facing gating domains, analogous to those present in channels. This concept is supported by recent structural evidence from several, phylogenetically and functionally distinct transporter families. The significance of this concept is discussed in relationship to the role and potential exploitation of transporters in drug action.
Collapse
|
8
|
Cunningham P, Naftalin RJ. Reptation-induced coalescence of tunnels and cavities in Escherichia Coli XylE transporter conformers accounts for facilitated diffusion. J Membr Biol 2014; 247:1161-79. [PMID: 25163893 PMCID: PMC4207944 DOI: 10.1007/s00232-014-9711-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/15/2014] [Indexed: 11/30/2022]
Abstract
Structural changes and xylose docking to eight conformers of Escherichia Coli XylE, a xylose transporter similar to mammalian passive glucose transporters GLUTs, have been examined. Xylose docks to inward and outward facing conformers at a high affinity central site (Ki 4–20 µM), previously identified by crystallography and additionally consistently docks to lower affinity sites in the external and internal vestibules (Ki 12–50 µM). All these sites lie within intramolecular tunnels and cavities. Several local regions in the central transmembrane zone have large positional divergences of both skeleton carbon Cα positions and side chains. One such in TM 10 is the destabilizing sequence G388-P389-V390-C391 with an average RMSD (4.5 ± 0.4 Å). Interchange between conformer poses results in coalescence of tunnels with adjacent cavities, thereby producing a transitory channel spanning the entire transporter. A fully open channel exists in one inward-facing apo-conformer, (PDB 4ja4c) as demonstrated by several different tunnel-finding algorithms. The conformer interchanges produce a gated network within a branched central channel that permits staged ligand diffusion across the transporter during the open gate periods. Simulation of this model demonstrates that small-scale conformational changes required for sequentially opening gate with frequencies in the ns-μs time domain accommodate diffusive ligand flow between adjacent sites with association–dissociation rates in the μs-ms domain without imposing delays. This current model helps to unify the apparently opposing concepts of alternate access and multisite models of ligand transport.
Collapse
Affiliation(s)
- Philip Cunningham
- Department of Bioinformatics, School of Medicine, King’s College London, Waterloo Campus, Franklin–Wilkins Building, London, SE1 9NH UK
| | - Richard J. Naftalin
- Department of Physiology, School of Medicine, King’s College London, Waterloo Campus, Franklin–Wilkins Building, London, SE1 9NH UK
- BHF Centre of Research Excellence, School of Medicine, King’s College London, Waterloo Campus, Franklin–Wilkins Building, London, SE1 9NH UK
| |
Collapse
|