Skip to main content
SpringerLink
Log in

In silico characterization of residues essential for substrate binding of human cystine transporter, xCT

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

xCT is a sodium-independent amino acid antiporter that imports L-cystine and exports L-glutamate in a 1:1 ratio. It is a component of heterodimeric amino acid transporter system Xc- working at the cross-roads of maintaining neurological processes and regulating antioxidant defense. The transporter has 12 transmembrane domains with intracellular N- and C-termini, and like other transporter proteins can undergo various conformational changes while switching the ligand accessibilities from intracellular to extracellular site. In the present study, we generated two homology models of human xCT in two distinct conformations: inward-facing occluded state and outward-facing open state. Our results indicated the substrate translocation channel composed of transmembrane helices TMs 1, 3, 6, 8, and 10. We docked anionic L-cystine and L-glutamate within the cavities to assess the two distinct binding scenarios for xCT as antiporter. We also assessed the interactions between the ligands and transporter and observed that ligands bind to similar residues within the channel. Using MM-PBSA/MM-GBSA approach, we computed the binding energies of these ligands to different conformational states. Cystine and glutamate bind xCT with favorable binding energies, with more favorable binding observed in inward occluded state than in outward open state. We further computed the residue-wise decomposition of these binding energies and identified the residues as essential for substrate binding/permeation. Filtering the residues that form favorable energetic contributions to the ligand binding in both the states, our studies suggest T56, A60, R135, A138, V141, Y244, A247, F250, S330, L392, and R396 as critical residues for ligand binding as well as ligand transport for any conformational state adopted by xCT during its transport cycle.

.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. Bannai S, Kitamura E (1980) Transport interaction of L-cystine and L-glutamate in human diploid fibroblasts in culture. J Biol Chem 255:2372–2376

    CAS  PubMed  Google Scholar 

  2. Makowske M, Christensen HN (1982) Contrasts in transport systems for anionic amino acids in hepatocytes and a hepatoma cell line HTC. J Biol Chem 257:5663–5670

    CAS  PubMed  Google Scholar 

  3. Albrecht P, Lewerenz J, Dittmer S et al (2010) Mechanisms of oxidative glutamate toxicity: the glutamate/cystine antiporter system xc- as a neuroprotective drug target. CNS Neurol Disord Drug Targets 9:373–382

    Article  CAS  PubMed  Google Scholar 

  4. Domercq M, Sánchez-Gómez MV, Sherwin C et al (2007) System xc- and glutamate transporter inhibition mediates microglial toxicity to oligodendrocytes. J Immunol 178:6549–6556

    Article  CAS  PubMed  Google Scholar 

  5. Lewerenz J, Hewett SJ, Huang Y et al (2013) The cystine/glutamate antiporter system xc− in health and disease: from molecular mechanisms to novel therapeutic opportunities. Antioxid Redox Signal 18:522–555. https://doi.org/10.1089/ars.2011.4391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Bassi MT, Gasol E, Manzoni M et al (2001) Identification and characterisation of human xCT that co-expresses, with 4F2 heavy chain, the amino acid transport activity system xc. Pflugers Arch 442:286–296

    Article  CAS  PubMed  Google Scholar 

  7. Sato H, Tamba M, Kuriyama-Matsumura K et al (2000) Molecular cloning and expression of human xCT, the light chain of amino acid transport system xc. Antioxid Redox Signal 2:665–671. https://doi.org/10.1089/ars.2000.2.4-665

    Article  CAS  PubMed  Google Scholar 

  8. Reig N, Chillarón J, Bartoccioni P et al (2002) The light subunit of system b(o,+) is fully functional in the absence of the heavy subunit. EMBO J 21:4906–4914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Sato H, Shiiya A, Kimata M et al (2005) Redox imbalance in cystine/glutamate transporter-deficient mice. J Biol Chem 280:37423–37429. https://doi.org/10.1074/jbc.M506439200

    Article  CAS  PubMed  Google Scholar 

  10. Bannai S (1986) Exchange of cystine and glutamate across plasma membrane of human fibroblasts. J Biol Chem 261:2256–2263

    CAS  PubMed  Google Scholar 

  11. Cho Y, Bannai S (1990) Uptake of glutamate and cysteine in C-6 glioma cells and in cultured astrocytes. J Neurochem 55:2091–2097

    Article  CAS  PubMed  Google Scholar 

  12. Kato S, Ishita S, Sugawara K, Mawatari K (1993) Cystine/glutamate antiporter expression in retinal mu¨ller glial cells: Implications fordl-alpha-aminoadipate toxicity. Neuroscience 57:473–482. https://doi.org/10.1016/0306-4522(93)90080-Y

    Article  CAS  PubMed  Google Scholar 

  13. Kato S, Negishi K, Mawatari K, Kuo C-H (1992) A mechanism for glutamate toxicity in the C6 glioma cells involving inhibition of cystine uptake leading to glutathione depletion. Neuroscience 48:903–914. https://doi.org/10.1016/0306-4522(92)90278-A

    Article  CAS  PubMed  Google Scholar 

  14. Bridges CC, Kekuda R, Wang H et al (2001) Structure, function, and regulation of human cystine/glutamate transporter in retinal pigment epithelial cells. Invest Ophthalmol Vis Sci 42:47–54

    CAS  PubMed  Google Scholar 

  15. Lin C-H, Lin P-P, Lin C-Y et al (2016) Decreased mRNA expression for the two subunits of system xc(-), SLC3A2 and SLC7A11, in WBC in patients with schizophrenia: evidence in support of the hypo-glutamatergic hypothesis of schizophrenia. J Psychiatr Res 72:58–63. https://doi.org/10.1016/j.jpsychires.2015.10.007

    Article  PubMed  Google Scholar 

  16. Fournier M, Monin A, Ferrari C et al (2017) Implication of the glutamate–cystine antiporter xCT in schizophrenia cases linked to impaired GSH synthesis. NPJ Schizophr 3:31. https://doi.org/10.1038/s41537-017-0035-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Mesci P, Zaïdi S, Lobsiger CS et al (2015) System xC- is a mediator of microglial function and its deletion slows symptoms in amyotrophic lateral sclerosis mice. Brain 138:53–68. https://doi.org/10.1093/brain/awu312

    Article  PubMed  Google Scholar 

  18. Pampliega O, Domercq M, Soria FN et al (2011) Increased expression of cystine/glutamate antiporter in multiple sclerosis. J Neuroinflammation 8:63. https://doi.org/10.1186/1742-2094-8-63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Massie A, Schallier A, Mertens B et al (2008) Time-dependent changes in striatal xCT protein expression in hemi-Parkinson rats. Neuroreport 19:1589–1592. https://doi.org/10.1097/WNR.0b013e328312181c

    Article  CAS  PubMed  Google Scholar 

  20. Lo M, Ling V, Wang YZ, Gout PW (2008) The xc − cystine/glutamate antiporter: a mediator of pancreatic cancer growth with a role in drug resistance. Br J Cancer 99:464–472. https://doi.org/10.1038/sj.bjc.6604485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Habib E, Linher-Melville K, Lin H-X, Singh G (2015) Expression of xCT and activity of system xc(-) are regulated by NRF2 in human breast cancer cells in response to oxidative stress. Redox Biol 5:33–42. https://doi.org/10.1016/j.redox.2015.03.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ruiu R, Rolih V, Bolli E et al (2018) Fighting breast cancer stem cells through the immune-targeting of the xCT cystine-glutamate antiporter. Cancer Immunol Immunother. https://doi.org/10.1007/s00262-018-2185-1

    Article  PubMed  Google Scholar 

  23. Ye P, Mimura J, Okada T et al (2014) Nrf2- and ATF4-dependent upregulation of xCT modulates the sensitivity of T24 bladder carcinoma cells to proteasome inhibition. Mol Cell Biol 34:3421–3434. https://doi.org/10.1128/MCB.00221-14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ji X, Qian J, Rahman SMJ et al (2018) xCT (SLC7A11)-mediated metabolic reprogramming promotes non-small cell lung cancer progression. Oncogene. https://doi.org/10.1038/s41388-018-0307-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Sugano K, Maeda K, Ohtani H et al (2015) Expression of xCT as a predictor of disease recurrence in patients with colorectal cancer. Anticancer Res 35:677–682

    PubMed  Google Scholar 

  26. Dai L, Noverr MC, Parsons C, et al (2015) xCT, not just an amino-acid transporter: a multi-functional regulator of microbial infection and associated diseases. Front Microbiol 6:. https://doi.org/10.3389/fmicb.2015.00120

  27. Okuno S, Sato H, Kuriyama-Matsumura K et al (2003) Role of cystine transport in intracellular glutathione level and cisplatin resistance in human ovarian cancer cell lines. Br J Cancer 88:951–956. https://doi.org/10.1038/sj.bjc.6600786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Yang P, Ebbert JO, Sun Z, Weinshilboum RM (2006) Role of the glutathione metabolic pathway in lung cancer treatment and prognosis: a review. J Clin Oncol 24:1761–1769. https://doi.org/10.1200/JCO.2005.02.7110

    Article  CAS  PubMed  Google Scholar 

  29. Kaleeba JAR, Berger EA (2006) Kaposi’s sarcoma-associated herpesvirus fusion-entry receptor: cystine transporter xCT. Science 311:1921–1924. https://doi.org/10.1126/science.1120878

    Article  CAS  PubMed  Google Scholar 

  30. Qin Z, Freitas E, Sullivan R et al (2010) Upregulation of xCT by KSHV-encoded microRNAs facilitates KSHV dissemination and persistence in an environment of oxidative stress. PLoS Pathog 6:e1000742. https://doi.org/10.1371/journal.ppat.1000742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Chandran B (2010) Early Events in Kaposi’s sarcoma-associated herpesvirus infection of target cells. J Virol 84:2188–2199. https://doi.org/10.1128/JVI.01334-09

    Article  CAS  PubMed  Google Scholar 

  32. Dai Z, Huang Y, Sadee W, Blower P (2007) Chemoinformatics analysis identifies cytotoxic compounds susceptible to chemoresistance mediated by glutathione and cystine/glutamate transport system xc. J Med Chem 50:1896–1906. https://doi.org/10.1021/jm060960h

    Article  CAS  PubMed  Google Scholar 

  33. Dai L, Noverr MC, Parsons C, et al (2015) xCT, not just an amino-acid transporter: a multi-functional regulator of microbial infection and associated diseases. Front Microbiol 6:. https://doi.org/10.3389/fmicb.2015.00120

  34. Shin C-S, Mishra P, Watrous JD et al (2017) The glutamate/cystine xCT antiporter antagonizes glutamine metabolism and reduces nutrient flexibility. Nat Commun 8:15074. https://doi.org/10.1038/ncomms15074

    Article  PubMed  PubMed Central  Google Scholar 

  35. Koppula P, Zhang Y, Zhuang L, Gan B (2018) Amino acid transporter SLC7A11/xCT at the crossroads of regulating redox homeostasis and nutrient dependency of cancer. Cancer Commun (Lond) 38:12. https://doi.org/10.1186/s40880-018-0288-x

    Article  Google Scholar 

  36. Lewerenz J, Albrecht P, Tien M-LT et al (2009) Induction of Nrf2 and xCT are involved in the action of the neuroprotective antibiotic ceftriaxone in vitro. J Neurochem 111:332–343. https://doi.org/10.1111/j.1471-4159.2009.06347.x

    Article  CAS  PubMed  Google Scholar 

  37. Savaskan NE, Fan Z, Broggini T et al (2015) Neurodegeneration in the brain tumor microenvironment: glutamate in the limelight. Curr Neuropharmacol 13:258–265. https://doi.org/10.2174/1570159X13666150122224158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Gout PW, Buckley AR, Simms CR, Bruchovsky N (2001) Sulfasalazine, a potent suppressor of lymphoma growth by inhibition of the x(c)- cystine transporter: a new action for an old drug. Leukemia 15:1633–1640

    Article  CAS  PubMed  Google Scholar 

  39. Sehm T, Fan Z, Ghoochani A et al (2016) Sulfasalazine impacts on ferroptotic cell death and alleviates the tumor microenvironment and glioma-induced brain edema. Oncotarget 7:36021–36033. https://doi.org/10.18632/oncotarget.8651

    Article  PubMed  PubMed Central  Google Scholar 

  40. Gasol E, Jiménez-Vidal M, Chillarón J et al (2004) Membrane topology of system Xc- light subunit reveals a re-entrant loop with substrate-restricted accessibility. J Biol Chem 279:31228–31236. https://doi.org/10.1074/jbc.M402428200

    Article  CAS  PubMed  Google Scholar 

  41. Jiménez-Vidal M, Gasol E, Zorzano A et al (2004) Thiol modification of cysteine 327 in the eighth transmembrane domain of the light subunit xCT of the heteromeric cystine/glutamate antiporter suggests close proximity to the substrate binding site/permeation pathway. J Biol Chem 279:11214–11221. https://doi.org/10.1074/jbc.M309866200

    Article  CAS  PubMed  Google Scholar 

  42. Kim JY, Kanai Y, Chairoungdua A et al (2001) Human cystine/glutamate transporter: cDNA cloning and upregulation by oxidative stress in glioma cells. Biochim Biophys Acta Biomembr 1512:335–344. https://doi.org/10.1016/S0005-2736(01)00338-8

    Article  CAS  Google Scholar 

  43. Deshpande AA, Sharma M, Bachhawat AK (2017) Insights into the molecular basis for substrate binding and specificity of the fungal cystine transporter CgCYN1. Biochim Biophys Acta 1859:2259–2268. https://doi.org/10.1016/j.bbamem.2017.08.020

    Article  CAS  Google Scholar 

  44. Drew D, Boudker O (2016) Shared molecular mechanisms of membrane transporters. Annu Rev Biochem 85:543–572. https://doi.org/10.1146/annurev-biochem-060815-014520

    Article  CAS  PubMed  Google Scholar 

  45. Forrest LR, Zhang Y-W, Jacobs MT et al (2008) Mechanism for alternating access in neurotransmitter transporters. Proc Natl Acad Sci U S A 105:10338–10343. https://doi.org/10.1073/pnas.0804659105

    Article  PubMed  PubMed Central  Google Scholar 

  46. Latorraca NR, Fastman NM, Venkatakrishnan AJ et al (2017) Mechanism of substrate translocation in an alternating access transporter. Cell 169:96-107.e12. https://doi.org/10.1016/j.cell.2017.03.010

    Article  PubMed  PubMed Central  Google Scholar 

  47. LeVine MV, Cuendet MA, Khelashvili G, Weinstein H (2016) Allosteric mechanisms of molecular machines at the membrane: transport by sodium-coupled symporters. Chem Rev 116:6552–6587. https://doi.org/10.1021/acs.chemrev.5b00627

    Article  CAS  PubMed  Google Scholar 

  48. Locher KP (2016) Mechanistic diversity in ATP-binding cassette (ABC) transporters. Nat Struct Mol Biol 23:487–493. https://doi.org/10.1038/nsmb.3216

    Article  CAS  PubMed  Google Scholar 

  49. Palmgren MG, Nissen P (2011) P-type ATPases. Annu Rev Biophys 40:243–266. https://doi.org/10.1146/annurev.biophys.093008.131331

    Article  CAS  PubMed  Google Scholar 

  50. Quistgaard EM, Löw C, Guettou F, Nordlund P (2016) Understanding transport by the major facilitator superfamily (MFS): structures pave the way. Nat Rev Mol Cell Biol 17:123–132. https://doi.org/10.1038/nrm.2015.25

    Article  CAS  PubMed  Google Scholar 

  51. Weyand S, Shimamura T, Beckstein O et al (2011) The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1. J Synchrotron Radiat 18:20–23. https://doi.org/10.1107/S0909049510032449

    Article  CAS  PubMed  Google Scholar 

  52. Yan N (2015) Structural biology of the major facilitator superfamily transporters. Annu Rev Biophys 44:257–283. https://doi.org/10.1146/annurev-biophys-060414-033901

    Article  CAS  PubMed  Google Scholar 

  53. Jardetzky O (1966) Simple allosteric model for membrane pumps. Nature 211:969–970

    Article  CAS  PubMed  Google Scholar 

  54. Mitchell P (1957) A general theory of membrane transport from studies of bacteria. Nature 180:134–136

    Article  CAS  PubMed  Google Scholar 

  55. Adelman JL, Ghezzi C, Bisignano P et al (2016) Stochastic steps in secondary active sugar transport. Proc Natl Acad Sci U S A 113:E3960–E3966. https://doi.org/10.1073/pnas.1525378113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Dror RO, Dirks RM, Grossman JP et al (2012) Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys 41:429–452. https://doi.org/10.1146/annurev-biophys-042910-155245

    Article  CAS  PubMed  Google Scholar 

  57. Faraldo-Gómez JD, Forrest LR (2011) Modeling and simulation of ion-coupled and ATP-driven membrane proteins. Curr Opin Struct Biol 21:173–179. https://doi.org/10.1016/j.sbi.2011.01.013

    Article  CAS  PubMed  Google Scholar 

  58. Fukuda M, Takeda H, Kato HE et al (2015) Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK. Nat Commun 6:7097. https://doi.org/10.1038/ncomms8097

    Article  CAS  PubMed  Google Scholar 

  59. Lee S, Swanson JMJ, Voth GA (2016) Multiscale simulations reveal key aspects of the proton transport mechanism in the ClC-ec1 antiporter. Biophys J 110:1334–1345. https://doi.org/10.1016/j.bpj.2016.02.014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Li J, Wen P-C, Moradi M, Tajkhorshid E (2015) Computational characterization of structural dynamics underlying function in active membrane transporters. Curr Opin Struct Biol 31:96–105. https://doi.org/10.1016/j.sbi.2015.04.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Watanabe A, Choe S, Chaptal V et al (2010) The mechanism of sodium and substrate release from the binding pocket of vSGLT. Nature 468:988–991. https://doi.org/10.1038/nature09580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Dobson L, Reményi I, Tusnády GE (2015) CCTOP: a Consensus Constrained TOPology prediction web server. Nucleic Acids Res 43:W408–W412. https://doi.org/10.1093/nar/gkv451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Shaffer PL, Goehring A, Shankaranarayanan A, Gouaux E (2009) Structure and mechanism of a Na+-independent amino acid transporter. Science 325:1010–1014. https://doi.org/10.1126/science.1176088

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Ilgü H, Jeckelmann J-M, Gapsys V et al (2016) Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proc Natl Acad Sci U S A 113:10358–10363. https://doi.org/10.1073/pnas.1605442113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Zimmermann L, Stephens A, Nam S-Z et al (2018) A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol 430:2237–2243. https://doi.org/10.1016/j.jmb.2017.12.007

    Article  CAS  PubMed  Google Scholar 

  66. Ma D, Lu P, Yan C et al (2012) Structure and mechanism of a glutamate-GABA antiporter. Nature 483:632–636. https://doi.org/10.1038/nature10917

    Article  CAS  PubMed  Google Scholar 

  67. Eswar N, Webb B, Marti-Renom MA, et al (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics 0 5:Unit-5.6. https://doi.org/10.1002/0471250953.bi0506s15

    Article  Google Scholar 

  68. Jo S, Cheng X, Lee J et al (2017) CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem 38:1114–1124. https://doi.org/10.1002/jcc.24660

    Article  CAS  PubMed  Google Scholar 

  69. Huang J, MacKerell AD (2013) CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34:2135–2145. https://doi.org/10.1002/jcc.23354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Lomize MA, Pogozheva ID, Joo H et al (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res 40:D370–D376. https://doi.org/10.1093/nar/gkr703

    Article  CAS  PubMed  Google Scholar 

  71. Campbell SD, Regina KJ, Kharasch ED (2014) Significance of lipid composition in a blood-brain barrier-mimetic PAMPA assay. J Biomol Screen 19:437–444. https://doi.org/10.1177/1087057113497981

    Article  CAS  PubMed  Google Scholar 

  72. Phillips JC, Braun R, Wang W et al (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802. https://doi.org/10.1002/jcc.20289

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092. https://doi.org/10.1063/1.464397

    Article  CAS  Google Scholar 

  74. Lovell SC, Davis IW, Arendall WB et al (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50:437–450. https://doi.org/10.1002/prot.10286

    Article  CAS  PubMed  Google Scholar 

  75. Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J Comput Chem 31:455–461. https://doi.org/10.1002/jcc.21334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Seeliger D, de Groot BL (2010) Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des 24:417–422. https://doi.org/10.1007/s10822-010-9352-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Smart OS, Neduvelil JG, Wang X et al (1996) HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph 14:354–360. https://doi.org/10.1016/S0263-7855(97)00009-X

    Article  CAS  PubMed  Google Scholar 

  78. Kim S, Lee J, Jo S et al (2017) CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. J Comput Chem 38:1879–1886. https://doi.org/10.1002/jcc.24829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(33–38):27–28

    Google Scholar 

  80. Smart OS, Goodfellow JM, Wallace BA (1993) The pore dimensions of gramicidin A. Biophys J 65:2455–2460

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Stelzl LS, Fowler PW, Sansom MSP, Beckstein O (2014) Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol 426:735–751. https://doi.org/10.1016/j.jmb.2013.10.024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O (2011) MD Analysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem 32:2319–2327. https://doi.org/10.1002/jcc.21787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Roe DR, Cheatham TE (2013) PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9:3084–3095. https://doi.org/10.1021/ct400341p

    Article  CAS  PubMed  Google Scholar 

  84. Kollman PA, Massova I, Reyes C et al (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897

    Article  CAS  PubMed  Google Scholar 

  85. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discovery 10:449–461. https://doi.org/10.1517/17460441.2015.1032936

    Article  CAS  Google Scholar 

  86. Studer G, Biasini M, Schwede T (2014) Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Bioinformatics 30:i505–i511. https://doi.org/10.1093/bioinformatics/btu457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Yamashita A, Singh SK, Kawate T et al (2005) Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters. Nature 437:215–223. https://doi.org/10.1038/nature03978

    Article  CAS  PubMed  Google Scholar 

  88. Cheng MH, Bahar I (2014) Complete mapping of substrate translocation highlights the role of LeuT N-terminal segment in regulating transport cycle. PLoS Comput Biol 10:e1003879. https://doi.org/10.1371/journal.pcbi.1003879

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Sonne J, Kandt C, Peters GH et al (2007) Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD. Biophys J 92:2727–2734. https://doi.org/10.1529/biophysj.106.097972

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Selvam B, Yu Y-C, Chen L-Q, Shukla D (2019) Molecular basis of the glucose transport mechanism in plants. ACS Cent Sci 5:1085–1096. https://doi.org/10.1021/acscentsci.9b00252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Coudray NL, Seyler S, Lasala R et al (2017) Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein Sci 26:130–145. https://doi.org/10.1002/pro.3061

    Article  CAS  PubMed  Google Scholar 

  92. Cain NE, Kaiser CA (2011) Transport activity–dependent intracellular sorting of the yeast general amino acid permease. Mol Biol Cell 22:1919–1929. https://doi.org/10.1091/mbc.E10-10-0800

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Ghaddar K, Krammer E-M, Mihajlovic N et al (2014) Converting the yeast arginine can1 permease to a lysine permease. J Biol Chem 289:7232–7246. https://doi.org/10.1074/jbc.M113.525915

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Deshpande AA, Sharma M, Bachhawat AK (2017) Insights into the molecular basis for substrate binding and specificity of the fungal cystine transporter CgCYN1. Biochim Biophys Acta Biomembr 1859:2259–2268. https://doi.org/10.1016/j.bbamem.2017.08.020

    Article  CAS  PubMed  Google Scholar 

  95. Bridges RJ, Natale NR, Patel SA (2012) System xc- cystine/glutamate antiporter: an update on molecular pharmacology and roles within the CNS. Br J Pharmacol 165:20–34. https://doi.org/10.1111/j.1476-5381.2011.01480.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

MS thanks the Department of Science and Technology (DST), India, for INSPIRE Award and research grant (IFA14-CH-165).

Author information

Authors and Affiliations

  1. Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS, Nagar, Punjab, India

    Monika Sharma & C. R. Anirudh

Authors
  1. Monika Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. R. Anirudh
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.S. conceived, designed, and performed the experiments. A.C.R performed initial experiments. M.S. analyzed the data and wrote the paper. M.S. and A.C.R contributed the literature materials and reviewed the manuscript.

Corresponding author

Correspondence to Monika Sharma.

Ethics declarations

Competing interests

The authors declare that they have no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

ESM 1

(PDF 3775 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sharma, M., Anirudh, C.R. In silico characterization of residues essential for substrate binding of human cystine transporter, xCT. J Mol Model 25, 336 (2019). https://doi.org/10.1007/s00894-019-4233-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-019-4233-y

Keywords

Search

Navigation