A gate-free pathway for substrate release from the inward-facing state of the Na +-galactose transporter

Biochimica et Biophysica Acta - Biomembranes

Volumn 1818, Issue 2, 2012, Pages 263-271

  Li, Jing ^a   Tajkhorshid, Emad ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Inward facing state; LeuT fold secondary transporter; Membrane transporters; Molecular dynamics simulation; Sodium coupled transporter; Substrate unbinding

Indexed keywords

MEMBRANE PROTEIN; SODIUM GALACTOSE TRANSPORTER; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; CYTOPLASM; ENZYME RELEASE; MOLECULAR DYNAMICS; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SIMULATION; STRUCTURAL HOMOLOGY;

BACTERIA; BACTERIAL PROTEINS; BINDING SITES; BIOLOGICAL TRANSPORT; GALACTOSE; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; SODIUM; SODIUM-GLUCOSE TRANSPORT PROTEINS;

EID: 84855427590     PISSN: 00052736     EISSN: 18792642     Source Type: Journal    
DOI: 10.1016/j.bbamem.2011.09.011     Document Type: Article

References (54)

1. B.I. Kanner Bioenergetics of neurotransmitter transport Biochim. Biophys. Acta 726 1983 293 316 (Pubitemid 14168688)
2. B.I. Kanner, and S. Schuldiner Mechanism of transport and storage of neurotransmitters CRC Crit. Rev. Biochem. 22 1987 1 39
3. B.I. Kanner Ion-coupled neurotransmitter transport Curr. Opin. Cell Biol. 1 1989 735 738 (Pubitemid 19225791)
4. B. Poolman, and W. Konings Secondary solute transport in bacteria Biochim. Biophys. Acta 1183 1993 5 39 (Pubitemid 23322953)
5. L.R. Forrest, R. Krämer, and C. Ziegler The structural basis of secondary active transport mechanisms Biochim. Biophys. Acta 1807 2011 167 188
6. I.C. West Ligand conduction and the gated-pore mechanism of transmembrane transport Biochim. Biophys. Acta 1331 1997 213 234 (Pubitemid 28015515)
7. L.J. DeFelice Transporter structure and mechanism Trends Neurosci. 27 2004 352 359
8. --dependent neurotransmitter transporters Nature 437 2005 215 233
9. Z. Zhou, J. Zhen, N.K. Karpowich, R.M. Goetz, C.J. Law, M.E.A. Reith, and D.-N. Wang LeuT-Desipramine structure reveals how antidepressants block neurotransmitter reuptake Science 317 2007 1390 1393 (Pubitemid 47417479)
10. S.K. Singh, C.L. Piscitelli, A. Yamashita, and E. Gouaux A competitive inhibitor traps LeuT in an open-to-out conformation Science 322 2008 1655 1661
11. +/sugar symport Science 321 2008 810 814
12. A. Watanabe, S. Choe, V. Chaptal, J.M. Rosenberg, E.M. Wright, M. Grabe, and J. Abramson The mechanism of sodium and substrate release from the binding pocket of vSGLT Nature 468 2010 988 991
13. S. Weyand, T. Shimamura, S. Yajima, S. Suzuki, O. Mirza, K. Krusong, E.P. Carpenter, N.G. Rutherford, J.M. Hadden, J. O'Reilly, P. Ma, M. Saidijam, S.G. Patching, R.J. Hope, H.T. Norbertczak, P.C.J. Roach, S. Iwata, P.J.F. Henderson, and A.D. Cameron Structure and molecular mechanism of a Nucleobase-Cation- Symport-1 family transporter Science 322 2008 709 713
14. T. Shimamura, S. Weyand, O. Beckstein, N.G. Rutherford, J.M. Hadden, D. Sharples, M.S.P. Sansom, S. Iwata, P.J.F. Henderson, and A.D. Cameron Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1 Science 328 2010 470 473
15. +/betaine symporter BetP Nature 458 2009 47 52
16. L. Tang, L. Bai, W.-H. Wang, and T. Jiang Crystal structure of the carnitine transporter and insights into the antiport mechanism Nat. Struct. Mol. Biol. 17 2010 492 496
17. +-independent and cooperative substrate/product antiport in CaiT Nature 467 2010 233 237
18. +-independent amino acid transporter Science 325 2009 1010 1014
19. Y. Fang, H. Jayaram, T. Shane, L. Kolmakova-Partensky, F. Wu, C. Williams, Y. Xiong, and C. Miller Structure of a prokaryotic virtual proton pump at 3.2 Å resolution Nature 460 2009 1040 1043
20. X. Gao, F. Lu, L. Zhou, S. Dang, L. Sun, X. Li, J. Wang, and Y. Shi Structure and mechanism of an amino acid antiporter Science 324 2009 1565 1568
21. X. Gao, L. Zhou, X. Jiao, F. Lu, C. Yan, X. Zeng, J. Wang, and Y. Shi Mechanism of substrate recognition and transport by an amino acid antiporter Nature 463 2010 828 832
22. L. Kowalczyk, M. Ratera, A. Paladino, P. Bartoccioni, E. Errasti-Murugarren, E. Valencia, G. Portella, S. Bial, A. Zorzano, I. Fita, M. Orozco, X. Carpena, J.L. Vázquez-Ibar, and M. Palacín Molecular basis of substrate-induced permeation by an amino acid antiporter Proc. Natl. Acad. Sci. U. S. A. 108 2011 3935 3940
23. H. Krishnamurthy, C.L. Piscitelli, and E. Gouaux Unlocking the molecular secrets of sodium-coupled transporters Nature 459 2009 347 355
24. +-symporters with inverted repeats Curr. Opin. Struct. Biol. 19 2009 425 432
25. +/betaine symporter BetP EMBO J. 30 2011 1221 1229
26. +/galactose cotransporter Biochemistry 43 2004 3620 3627 (Pubitemid 38391717)
27. +/glucose cotransporter: I. voltage-clamp studies JMB 125 1992 49 62
28. +/glucose cotransporter: part II. A transport model under non rapid equilibrium conditions JMB 125 1992 63 79
29. J. Li, and E. Tajkhorshid Ion-releasing state of a secondary membrane transporter Biophys. J. 97 2009 L29 L31
30. E. Zomot, and I. Bahar The sodium/galactose symporter crystal structure is a dynamic, not so occluded state Mol. Biosyst. 6 2010 1040 1046
31. O. Boudker, and G. Verdon Structural perspectives on secondary active transporters Trends Pharmacol. Sci. 31 2010 418 426
32. M. Sujatha, and P.V. Balaji Identification of common structural features of binding sites in galactose-specific proteins Proteins 55 2009 44 65 (Pubitemid 38292833)
33. J. Abramson, I. Smirnova, V. Kasho, G. Verner, H.R. Kaback, and S. Iwata Structure and mechanism of the lactose permease of Escherichia coli Science 301 2003 610 615 (Pubitemid 36927939)
34. as and adding missing hydrogens to macromolecules Nucleic Acids Res. 33 2005 W368 W371
35. W. Humphrey, A. Dalke, and K. Schulten VMD - Visual Molecular Dynamics J. Mol. Graphics 14 1996 33 38
36. A.D. MacKerell Jr., D. Bashford, M. Bellott, J.R.L. Dunbrack, J. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations FASEB J. 6 1992 A143-A143
37. A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, I.W.E. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B. 102 1998 3586 3616 (Pubitemid 128576688)
38. A.D. MacKerell Jr., M. Feig, and C.L. Brooks III Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comp. Chem. 25 2004 1400 1415
39. L. Zhang, and J. Hermans Hydrophilicity of cavities in proteins Proteins: Struct., Funct., Gen. 24 1996 433 438 (Pubitemid 26122057)
40. M.A. Lomize, A.L. Lomize, L.D. Pogozheva, and H.I. Mosberg OPM: orientations of proteins in membranes database Bioinformatics 22 2006 623 625 (Pubitemid 43372827)
41. H. Grubmüller Solvate 1.0 1996
42. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, and K. Schulten Scalable molecular dynamics with NAMD J. Comp. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
43. M. Kuttel, J.W. Brandy, and K.J. Naidoo Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations J. Comp. Chem. 23 2002 1236 1243 (Pubitemid 35017037)
44. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
45. J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comp. Phys. 23 1977 327 341
46. B. Isralewitz, M. Gao, and K. Schulten Steered molecular dynamics and mechanical functions of proteins Curr. Opin. Struct. Biol. 11 2001 224 230 (Pubitemid 32289426)
47. S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten Molecular dynamics study of unbinding of the avidin-biotin complex Biophys. J. 72 1997 1568 1581 (Pubitemid 27133097)
48. G.J. Martyna, D.J. Tobias, and M.L. Klein Constant pressure molecular dynamics algorithms J. Chem. Phys. 101 1994 4177 4189
49. S.E. Feller, Y. Zhang, R.W. Pastor, and B.R. Brooks Constant pressure molecular dynamics simulation: the Langevin piston method J. Chem. Phys. 103 1995 4613 4621
50. T. Darden, D. York, and L.G. Pedersen Particle mesh Ewald: an N log (N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
51. +/glucose cotransporter SGLT1 J. Biol. Chem. 271 1996 1925 1934 (Pubitemid 26047772)
52. B.A. Hirayama, D.D.F. Loo, A. Díez-Sampedro, D.W. Leung, A.-K. Meinild, M. Lai-Bing, E. Turk, and E.M. Wright Sodium-dependent reorganization of the sugar-binding site of SGLT1 Biochemistry 46 2007 13391 13406 (Pubitemid 350136378)
53. +/glucose cotransporter J. Gen. Physiol. 125 2005 13 36 (Pubitemid 40130095)
54. +/glucose cotransporter (SGLT1) turnover rate using the ion-trap technique Biophys. J. 100 2011 52 59