Membrane transporters: Molecular machines coupling cellular energy to vectorial transport across the membrane

Molecular Machines

Volumn , Issue , 2011, Pages 151-182

  Huang, Zhijian ^a   Shaikh, Saher A ^a   Wen, Po Chao ^a   Enkavi, Giray ^a   Li, Jing ^a   Tajkhorshid, Emad ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84973412341     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789814343466_0009     Document Type: Chapter

References (81)

1. L. Celik, B. Schiott and E. Tajkhorshid. 2008. Substrate binding and formation of an occluded state in the leucine transporter. Biophys J 94, 1600-1612.
2. C. J. Law, G. Enkavi, D. N. Wang and E. Tajkhorshid. 2009. Structural basis of substrate selectivity in the glycerol-3-phosphate:phosphate antiporter GlpT. Biophys J 97, 1346-1353.
3. S. A. Shaikh and E. Tajkhorshid. 2008. Potential cation and H+ binding sites in acid sensing ion channel-1. Biophys J 95, 5153-5164.
4. Z. Huang and E. Tajkhorshid. 2008. Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter. Biophys J 95, 2292-2300.
5. P.-C. Wen and E. Tajkhorshid. 2008. Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis. Biophys J 95, 5100-5110.
6. J. Gumbart, M. C. Wiener and E. Tajkhorshid. 2009. Coupling of calcium and substrate binding through loop alignment in the outer membrane transporter BtuB. J Mol Biol 393, 1129-1142.
7. Z. Huang and E. Tajkhorshid. 2010. Identification of the third Na+ site and the sequence of extracellular binding events in the glutamate transporter. Biophys J 99, 1416-1425.
8. J. Jardetzky. 1966. Simple allosteric model for membrane pumps. Nature 211, 2406-2414.
9. Y. Wang and E. Tajkhorshid. 2007. Molecular mechanisms of conduction and selectivity in aquaporin water channels. J Nutr 137, 1509S-1515S.
10. J. Gumbart, M. C. Wiener and E. Tajkhorshid. 2007. Mechanics of force propagation in TonB-dependent outer membrane transport. Biophys J 93, 496-504.
11. Y. Wang and E. Tajkhorshid. 2008. Electrostatic funneling of substrate in mitochondrial inner membrane carriers. Proc Natl Acad Sci U S A 105, 9598-9603.
12. H. Shrivastava, J. Jiang, S. G. Amara and I. Bahar. 2008. Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter. J Biol Chem 283, 28680-28690.
13. J. Li and E. Tajkhorshid. 2009. Ion-releasing state of a secondary membrane transporter. Biophys J 97, L29-L31.
14. F. Khalili-Araghi, J. Gumbart, P. C. Wen, M. Sotomayor, E. Tajkhorshid and K. Schulten. 2009. Molecular dynamics simulations of membrane channels and transporters. Curr Opin Struct Biol 19, 128-137.
15. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale and K. Schulten. 2005. Scalable molecular dynamics with NAMD. J Comp Chem 26, 1781-1802.
16. I. B. Holland, S. P. Cole, K. Kuchler and C. F. Higgins, ABC Proteins: From Bacteria to Man. Academic Press, London, 2003.
17. M. L. Oldham, A. L. Davidson and J. Chen. 2008. Structural insights into ABC transporter mechanism. Curr Opin Struct Biol 18, 726-733.
18. K. P. Locher. 2009. Structure and mechanism of ATP-binding cassette transporters. Phil Trans R Soc Lond B 364, 239-245.
19. V. Kos and R. C. Ford. 2009. The ATP-binding cassette family: A structural perspective. Cell Mol Life Sci 66, 3111-3126.
20. A. Moussatova, C. Kandt, M. L. O’Mara and D. P. Tieleman. 2008. ATP-binding cassette transporters in Escherichia coli. Biochim Biophys Acta 1778, 1757-1771.
21. J. Chen, G. Lu, J. Lin, A. L. Davidson and F. A. Quiocho. 2003. A tweezers-like motion of the ATP-binding cassette dimer in an ABC transport cycle. Mol Cell 12, 651-661.
22. P. M. Jones and A. M. George. 2007. Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette. J Biol Chem 282, 22793-22803.
23. P. M. Jones and A. M. George. 2009. Opening of the ADP-bound active site in the ABC transporter ATPase dimer: Evidence for a constant contact, alternating sites model for the catalytic cycle. Proteins: Struct, Func, Bioinf 75, 387-396.
24. A. S. F. Oliveira, A. M. Baptista and C. M. Soares. 2010. Insights into the molecular mechanism of an ABC transporter: Conformational changes in the NBD dimer of MJ0796. J Phys Chem B 114, 5486-5496.
25. K. Hollenstein, R. J. Dawson and K. P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr Opin Struct Biol 17, 412-418.
26. R. J. Dawson, K. Hollenstein and K. P. Locher. 2007. Uptake or extrusion: Crystal structures of full ABC transporters suggest a common mechanism. Mol Microbiol 65, 250-257.
27. P.-C. Wen and Tajkhorshid T. 2011. Conformational coupling of the nucleotide-binding and the transmembrane domains in the maltose ABC transporter. Submitted.
28. M. L. Oldham, D. Khare, F. A. Quiocho, A. L. Davidson and J. Chen. 2007. Crystal structure of a catalytic intermediate of the maltose transporter. Nature 450, 515-521.
29. D. J. Slotboom, W. N. Konings and J. S. Lolkema. 1999. Structural features of the glutamate transporter family. Microbiol Mol Biol Rev 63, 293-307.
30. D. Yernool, O. Boudker, Y. Jin and E. Gouaux. 2004. Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature 431, 811-818.
31. O. Boudker, R. M. Ryan, D. Yernool, K. Shimamoto and E. Gouaux. 2007. Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature 445, 387-393.
32. N. Reyes, C. Ginter and O. Boudker. 2009. Transport mechanism of a bacterial homologue of glutamate transporters. Nature 462, 880-885.
33. M. P. Kavanaugh, A. Bendahan, N. Zerangue, Y. Zhang and B. I. Kanner. 1997. Mutation of an amino acid residue influencing potassium coupling in the glutamate transporter GLT-1 induces obligate exchange. J Biol Chem 272, 1703-1707.
34. A. Bendahan, A. Armon, N. Madani, M. P. Kavanaugh and B. I. Kanner. 2000. Arginine 447 plays a pivotal role in substrate interactions in a neuronal glutamate transporter. J Biol Chem 275, 37436-37442.
35. Z. Tao, Z. Zhang and C. Grewer. 2006. Neutralization of the aspartic acid residue Asp-367, but not Asp-454, inhibits binding of Na+ to the glutamate-free form and cycling of the glutamate transporter EAAC1. J Biol Chem 281, 10263-10272.
36. P. H. Larsson, A. V. Tzingounis, H. P. Koch and M. P. Kavanaugh. 2004. Fluorometric measurements of conformational changes in glutamate transporters. Proc Natl Acad Sci U S A 101, 3951-3956.
37. D. E. Bergles, A. V. Tzingounis and C. E. Jahr. 2002. Comparison of coupled and uncoupled currents during glutamate uptake by GLT-1 transporters. J Neurosci 22, 10153-10162.
38. H. P. Koch, J. M. Hubbard and H. P. Larsson. 2007. Voltage-independent sodium-binding events reported by the 4B-4C loop in the human glutamate transporter excitatory amino acid transporter 3. J Biol Chem 282, 24547-24553.
39. S. Qu and B. I. Kanner. 2008. Substrates and non-transportable analogues induce structural rearrangements at the extracellular entrance of the glial glutamate transporter GLT-1/EAAT2. Proc Natl Acad Sci U S A 283, 26391-26400.
40. Z. Zhang, Z. Tao, A. Gameiro, S. Barcelona, S. Braams and T. Rauen. 2007. Transport direction determines the kinetics of substrate transport by the glutamate transporter EAAC1. Proc Natl Acad Sci U S A 104, 18025-18030.
41. Y. Huang, M. J. Lemieux, J. Song, M. Auer and D. N. Wang. 2003. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301, 616-620.
42. A. Salasburgos, P. Iserovich, F. Zuniga, J. Vera and J. Fischbarg. 2004. Predicting the three-dimensional structure of the human facilitative glucose transporter Glut1 by a novel evolutionary homology strategy: Insights on the molecular mechanism of substrate migration and binding sites for glucose and inhibitory molecules. Biophys J 87, 2990-2999.
43. M. J. Lemieux, Y. Huang and D. N. Wang. 2004. Glycerol-3-phosphate transporter of Escherichia coli: Structure, function and regulation. Res Microbiol 155, 623-629.
44. J. Holyoake, V. Caulfeild, S. Baldwin and M. Sansom. 2006. Modeling, docking, and simulation of the major facilitator superfamily. Biophys J 91, L84-L86.
45. M. J. Lemieux. 2007. Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure (review). Mol Membr Biol 24, 333-341.
46. S. Pao, I. T. Paulsen and M. H. Saier, Jr. 1998. Major facilitator superfamily. Microbiol Mol Biol Rev 62, 1-34.
47. C. J. Law, P. C. Maloney and D. N. Wang. 2008. Ins and outs of major facilitator superfamily antiporters. Annu Rev Microbiol 62, 289-305.
48. M. Lemieux, Y. Huang and D. Wang. 2004. The structural basis of substrate translocation by the glycerol-3-phosphate transporter: A member of the major facilitator superfamily. Curr Opin Struct Biol 14, 405-412.
49. C. J. Law, J. Almqvist, A. Bernstein, R. M. Goetz, Y. Huang, C. Soudant, A. Laaksonen, S. Hovmlle and D. N. Wang. 2008. Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter glpt. J Mol Biol 378, 828-839.
50. M. C. Fann, A. H. Davies, A. Varadhachary, T. Kuroda, C. Sevier, T. Tsuchiya and P. C. Maloney. 1998. Identification of two essential arginine residues in UhpT, the sugar phosphate antiporter of Escherichia coli. J Membr Biol 164, 187-195.
51. R. M. Stroud. 2007. Transmembrane transporters: An open and closed case. Proc Natl Acad Sci U S A 104, 1445-1446.
52. M. J. Lemieux, Y. Huang and D. N. Wang. 2005. Crystal structure and mechanism of GlpT, the glycerol-3-phosphate transporter from E. coli. J Electron Microsc 54, i43-i46.
53. R. S. G. D’rozario and M. S. P. Sansom. 2008. Helix dynamics in a membrane transport protein: comparative simulations of the glycerol-3-phosphate transporter and its constituent helices. Mol Membr Biol 25, 571-573.
54. I. F. Tsigelny, J. Greenberg, V. Kouznetsova and S. K. Nigam. 2008. Modelling of glycerol-3-phosphate transporter suggests a potential ‘tilt’ mechanism involved in its function. J Bioinformatics Comput Biol 6, 885-904.
55. C. J. Law, Q. Yang, C. Soudant, P. C. Maloney and D. N. Wang. 2007. Kinetic evidence is consistent with the rocker-switch mechanism of membrane transport by GlpT. Biochemistry 46, 12190-12197.
56. G. Enkavi and E. Tajkhorshid. 2010. Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT. Biochemistry 49, 1105-1114.
57. B. I. Kanner and E. Zomot. 2008. Sodium-coupled neurotransmitter transporters. Chem Rev 108, 1654-1668.
58. --dependent neurotransmitter transporters. Nature 437, 215-233.
59. A. Nyola, N. K. Karpowich, J. Zhen, J. Marden, M. E. Reith and D. N. Wang. 2010. Substrate and drug binding sites in LeuT. Curr Opin Struct Biol 20, 415-422.
60. H. Krishnamurthy, C. L. Piscitelli and E. Gouaux. 2009. Unlocking the molecular secrets of sodium-coupled transporters. Nature 459, 347-355.
61. L. R. Forrest, Y. W. Zhang, M. T. Jacobs, J. Gesmonde, L. Xie, B. H. Honig and G. Rudnick. 2008. Mechanism for alternating access in neurotransmitter transporters. Proc Natl Acad Sci U S A 105, 10338-10343.
62. L. Shi, M. Quick, Y. Zhao, H. Weinstein and J. A. Javitch. 2008. The mechanism of a neurotransmitter: sodium symporter-inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell 30, 667-677.
63. -dependent neurotransmitter transporter homologue. PLoS Comput Biol 6(8), e1000905.
64. Y. Zhao, M. Quick, L. Shi, E. L. Mehler, H. Weinstein and J. A. Javitch. 2010. Substrate-dependent proton antiport in neurotransmitter:sodium symporters. Nat Chem Biol 6, 109-116.
65. S. Y. Noskov and B. Roux. 2008. Control of ion selectivity in LeuT: Two Na+ binding sites with two different mechanisms. J Mol Biol 377, 804-818.
66. S. Y. Noskov. 2008. Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT. Proteins 73, 851-863.
67. M. Quick, A.-M. L. Winther, L. Shi, P. Nissen, H. Weinstein and J. A. Javitch. 2009. Binding of an octyl-glucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci U S A 106, 5563-5568.
68. Y. Zhao, D. Terry, L. Shi, H. Weinstein, S. C. Blanchard and J. A. Javitch. 2010. Single-molecule dynamics of gating in a neurotransmitter transporter homologue. Nature 465, 188-193.
69. L. R. Forrest and G. Rudnick. 2009. The rocking bundle: A mechanism for ion-coupled solute flux by symmetrical transporters. Physiology 24, 377-386.
70. S. Faham, A. Watanabe, G. M. Besserer, D. Cascio, A. Specht, B. A. Hirayama, E. M. Wright and J. Abramson. 2008. The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport. Science 321, 810-814.
71. E. Wright and E. Turk. 2004. The sodium/glucose cotransport family slc5. Pflgers Archiv European Journal of Physiology 447, 510-518.
72. S. Yamada, S. Pokutta, F. Drees, W. I. Weis and W. J. Nelson. 2005. Deconstructing the cadherin-catenin-actin complex. Cell 123, 889-901.
73. M. Quick and H. Jung. 1998. A conserved aspartate residue, Asp187, is important for Na+-dependent proline binding and transport by the Na+/proline transporter of Escherichia coli. Biochemistry 37, 3800-13806.
74. M. Quick, D. D. F. Loo and E. M. Wright. 2001. Neutralization of a conserved amino acid residue in the human Na+/glucose transporter (hSGLT1) generates a glucose-gated H1 channel. J Biol Chem 19, 1728-1734.
75. M. Sujatha and P. V. Balaji. 2009. Identification of common structural features of binding sites in galactose-specific proteins. Proteins 55, 44-65.
76. J. Abramson, I. Smirnova, V. Kasho, G. Verner, H. R. Kaback and S. Iwata. 2003. Structure and mechanism of the lactose permease of Escherichia coli. Science 301, 610-615.
77. J. Li and E. Tajkhorshid. 2010. Spontaneous unbinding of the substrate in sodium-glucose transporter Submitted.
78. T. Shimamura, S. Weyand, O. Beckstein, N. G. Rutherford, J. M. Hadden, D. Sharpies, M. S. P. Sansom, S. Iwata, P. J. F. Henderson and A. D. Cameron. 2010. Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhpl. Science 328, 470-473.
79. K. Hollenstein, D. C. Frei and K. P. Locher. 2007. Structure of an ABC transporter in complex with its binding protein. Nature 446, 213-216.
80. A. Ward, C. L. Reyes, J. Yu, C. B. Roth and G. Chang. 2007. Flexibility in the ABC transporter MsbA: Alternating access with a twist. Proc Natl Acad Sci U S A 104, 19005-19010.
81. S. G. Aller, J. Yu, A. Ward, Y. Weng, S. Chittaboina, R. Zhuo, P. M. Harrell, Y. T. Trinh, Q. Zhang, I. L. Urbatsch and G. Chang. 2009. Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science 323, 1718-1722.