Topology scanning and putative three-dimensional structure of the extracellular binding domains of the apical sodium-dependent bile acid transporter (SLC10A2)

Biochemistry

Volumn 43, Issue 36, 2004, Pages 11380-11392

  Zhang, Eric Y ^c,d   Phelps, Mitch A ^a   Banerjee, Antara ^c   Khantwal, Chandra M ^c   Chang, Cheng ^a   Helsper, Freek ^c   Swaan, Peter W ^a,b,c  

^a OHIO STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c UNIVERSITY OF MARYLAND   (United States)

^d PFIZER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HOMOLOGY; MEMBRANE TOPOLOGY;

CELLS; CHOLESTEROL; COMPUTER SIMULATION; METABOLISM; MOLECULAR DYNAMICS; MUTAGENESIS; SALTS; SCANNING;

BIOCHEMISTRY;

APICAL SODIUM DEPENDENT BILE ACID TRANSPORTER PROTEIN; BACTERIORHODOPSIN; BILE SALT; CHOLESTEROL; CHOLIC ACID; PROTEIN; UNCLASSIFIED DRUG;

APICAL MEMBRANE; ARTICLE; BINDING DOMAIN; BINDING SITE; C TERMINAL DOMAIN; CHEMICAL MODEL; CHOLESTEROL METABOLISM; CONSENSUS SEQUENCE; CONSENSUS TOPOGRAPHY ANALYSIS; CRYSTAL STRUCTURE; ENTEROHEPATIC CIRCULATION; EXTRACELLULAR BINDING DOMAIN; EXTRAMEMBRANOUS DOMAIN; GEOMETRY; GLYCOSYLATION; HOMOLOGY MODEL; MEMBRANE STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; MUTAGENESIS; N GLYCOSYLATION MUTAGENESIS; N TERMINAL DOMAIN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; RAMACHANDRAN SCORE; SCORING SYSTEM; SILICO MUTAGENESIS; SITE DIRECTED MUTAGENESIS; THREE DIMENSIONAL MODEL; THREE DIMENSIONAL STRUCTURE; TOPOGRAPHY; TRANSMEMBRANE DOMAIN; VALIDATION PROCESS;

AMINO ACID SEQUENCE; BINDING SITES; CARBOHYDRATE CONFORMATION; COMPUTER SIMULATION; CONSENSUS SEQUENCE; EXTRACELLULAR SPACE; GLUTAMIC ACID; GLYCOSYLATION; HUMANS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; ORGANIC ANION TRANSPORTERS, SODIUM-DEPENDENT; PEPTIDE FRAGMENTS; POLYMORPHISM, GENETIC; PROLINE; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SERINE; SYMPORTERS;

EID: 4444299420     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049270a     Document Type: Article

References (43)

1. Wong, M. H., Oelkers, P., Craddock, A. L., and Dawson, P. A. (1994) Expression cloning and characterization of the hamster ileal sodium-dependent bile acid transporter, J. Biol. Chem. 269, 1340-1347.
2. Shneider, B. L., Dawson, P. A., Christie, D. M., Hardikar, W., Wong, M. H., and Suchy, F. J. (1995) Cloning and molecular characterization of the ontogeny of a rat ileal sodium-dependent bile acid transporter, J. Clin. Invest. 95, 745-754.
3. Wong, M. H., Oelkers, P., and Dawson, P. A. (1995) Identification of a mutation in the ileal sodium-dependent bile acid transporter gene that abolishes transport activity, J. Biol. Chem. 270, 27228-27234.
4. Lazaridis, K. N., Pham, L., Tietz, P., Marinelli, R. A., deGroen, P. C., Levine, S., Dawson, P. A., and LaRusso, N. F. (1997) Rat cholangiocytes absorb bile acids at their apical domain via the ileal sodium-dependent bile acid transporter, J. Clin. Invest. 100, 2714-2721.
5. Dawson, P. A., and Oelkers, P. (1995) Bile acid transporters, Curr. Opin. Lipidol. 6, 109-114.
6. + bile acid cotransporter, J. Clin. Invest. 93, 1326-1331.
7. +/bile acid cotransport system, Proc. Natl. Acad. Sci. U.S.A. 88, 10629-10633.
8. Meier, P. J., Jacquemin, E., and Hagenbuch, B. (1992) in Bile Acids and the Hepatobiliary System. Falk Symposium 68 (Paumgartner, G., Stiehl, A., and Gerok, W., Eds.) pp 95-102, Kluwer Academic Publishers, Dordrecht, The Netherlands.
9. Hallén, S., Branden, M., Dawson, P. A., and Sachs, G. (1999) Membrane insertion scanning of the human ileal sodium/bile acid co-transporter, Biochemistry 38, 11379-11388.
10. +/glucose cotransporter SGLT1, J. Biol. Chem. 271, 1925-1934.
11. Covitz, K. M., Amidon, G. L., and Sadee, W. (1998) Membrane topology of the human dipeptide transporter, hPEPT1, determined by epitope insertions, Biochemistry 37, 15214-15221.
12. Sun, A. Q., Salkar, R., Sachchidanand, Xu, S., Zheng, L., Zhou, M. M., and Suchy, F. J. (2003) A 14 amino acid sequence with a β-turn structure is required for apical membrane sorting of the rat ileal bile acid transporter, J. Biol. Chem. 278, 4000-4009.
13. Hallen, S., Bjorquist, A., Ostlund-Lindqvist, A. M., and Sachs, G. (2002) Identification of a region of the ileal-type sodium/bile acid cotransporter interacting with a competitive bile acid transport inhibitor, Biochemistry 41, 14916-14924.
14. von Heijne, G. (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule, J. Mol. Biol. 225, 487-494.
15. Ikeda, M., Arai, M., Lao, D. M., and Shimizu, T. (2002) Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally characterized transmembrane topologies, In Silico Biol. 2, 19-33.
16. Kimura, Y., Vassylyev, D. G., Miyazawa, A., Kidera, A., Matsushima, M., Mitsuoka, K., Murata, K., Hirai, T., and Fujiyoshi, Y. (1997) Surface of bacteriorhodopsin revealed by high-resolution electron crystallography, Nature 389, 206-211.
17. Morris, G. M., Goodsell, D. S., Huey, R., and Olson, A. J. (1996) Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4, J. Comput.-Aided Mol. Des. 10, 293-304.
18. Jones, D. T., Tress, M., Bryson, K., and Hadley, C. (1999) Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure, Proteins 37, 104-111.
19. Moro, S., Hoffmann, C., and Jacobson, K. A. (1999) Role of the extracellular loops of G protein-coupled receptors in ligand recognition: A molecular modeling study of the human P2Y1 receptor, Biochemistry 38, 3498-3507.
20. Lucke, C., Zhang, F., Ruterjans, H., Hamilton, J. A., and Sacchettini, J. C. (1996) Flexibility is a likely determinant of binding specificity in the case of ileal lipid binding protein, Structure 4, 785-800.
21. Oelkers, P., Kirby, L. C., Heubi, J. E., and Dawson, P. A. (1997) Primary bile acid malabsorption caused by mutations in the ileal sodium-dependent bile acid transporter gene (SLC10A2), J. Clin. Invest. 99, 1880-1887.
22. Nilsson, I. M., and von Heijne, G. (1993) Determination of the distance between the oligosaccharyltransferase active site and the endoplasmic reticulum membrane, J. Biol. Chem. 268, 5798-5801.
23. Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., and Thornton, J. M. (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR, J. Biomol. NMR 8, 477-486.
24. +/glucose cotransporters is determined by the carboxyl-terminal half of the protein, J. Biol. Chem. 271, 10029-10034.
25. Sanchez, R., and Sali, A. (1997) Evaluation of comparative protein structure modeling by MODELLER-3, Proteins, Suppl 1, 50-58.
26. +/bile acid cotransporter, J. Lipid Res. 40, 2158-2168.
27. Zhang, E. Y., Phelps, M. A., Cheng, C., Ekins, S., and Swaan, P. W. (2002) Modeling of active transport systems, Adv. Drug Delivery Rev. 54, 329-354.
28. +/bile-salt-cotransport system, Eur. J. Biochem. 249, 456-464.
29. Craddock, A. L., Love, M. W., Daniel, R. W., Kirby, L. C., Walters, H. C., Wong, M. H., and Dawson, P. A. (1998) Expression and transport properties of the human ileal and renal sodium-dependent bile acid transporter, Am. J. Physiol. 274, G157-G169.
30. Buchwald, H., Varco, R. L., Matts, J. P., Long, J. M., Fitch, L. L., Campbell, G. S., Pearce, M. B., Yellin, A. E., Edmiston, W. A., Smink, R. D., Jr., et al. (1990) Effect of partial ileal bypass surgery on mortality and morbidity from coronary heart disease in patients with hypercholesterolemia. Report of the Program on the Surgical Control of the Hyperlipidemias (POSCH), N. Engl. J. Med. 323, 946-955.
31. Takashima, K., Kohno, T., Mori, T., Ohtani, A., Hirakoso, K., and Takeyama, S. (1994) The hypocholesterolemic action of TA-7552 and its effects on cholesterol metabolism in the rat, Atherosclerosis 107, 247-257.
32. Hallén, S., Fryklund, J., and Sachs, G. (2000) Inhibition of the human sodium/bile acid cotransporters by side-specific methanethiosulfonate sulfhydryl reagents: Substrate-controlled accessibility of site of inactivation, Biochemistry 39, 6743-6750.
33. Slotboom, D. J., Sobczak, I., Konings, W. N., and Lolkema, J. S. (1999) A conserved serine-rich stretch in the glutamate transporter family forms a substrate-sensitive reentrant loop, Proc. Natl. Acad. Sci. U.S.A. 96, 14282-14287.
34. Hallen, S., Mareninova, O., Branden, M., and Sachs, G. (2002) Organization of the membrane domain of the human liver sodium/bile acid cotransporter, Biochemistry 41, 7253-7266.
35. Swaan, P. W., Szoka, F. C., Jr., and Oie, S. (1997) Molecular modeling of the intestinal bile acid carrier: A comparative molecular field analysis study, J. Comput.-Aided Mol. Des. 11, 581-588.
36. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Le Trong, I., Teller, D. C., Okada, T., Stenkamp, R. E., Yamamoto, M., and Miyano, M. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor, Science 289, 739-745.
37. Doak, D. G., Mulvey, D., Kawaguchi, K., Villalain, J., and Campbell, I. D. (1996) Structural studies of synthetic peptides dissected from the voltage-gated sodium channel, J. Mol. Biol. 258, 672-687.
38. Ren, G., Reddy, V. S., Cheng, A., Melnyk, P., and Mitra, A. K. (2001) Visualization of a water-selective pore by electron crystallography in vitreous ice, Proc. Natl. Acad. Sci. U.S.A. 98, 1398-1403.
39. + conduction and selectivity, Science 280, 69-77.
40. Zuniga, F. A., Shi, G., Haller, J. F., Rubashkin, A., Flynn, D. R., Iserovich, P., and Fischbarg, J. (2001) A three-dimensional model of the human facultative glucose transporter Glut1, J. Biol. Chem. 276, 44970-44975.
41. Koradi, R., Billeter, M., and Wuthrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures, J. Mol Graphics 14, 51-55, 29-32.
42. Abramson, J., Smirnova, I., Kasho, V., Verner, G., Kaback, H. R., and Iwata, S. (2003) Structure and mechanism of the lactose permease of Escherichia coli, Science 301, 610-615.
43. Huang, Y., Lemieux, M. J., Song, J., Auer, M., and Wang, D. N. (2003) Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli, Science 301, 616-620.