Structural analysis of a peptide fragment of transmembrane transporter protein bilitranslocase

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Perdih, Andrej ^a   Choudhury, Amrita ^a   Župerl, Špela ^a   Sikorska, Emilia ^b   Zhukov, Igor ^a,c,d   Solmajer, Tom ^a   Novič, Marjana ^a  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b UNIVERSITY OF GDA SK   (Poland)

^c EN FIST Center of Excellence   (Slovenia)

^d INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BILITRANSLOCASE; CARRIER PROTEIN; DODECYL SULFATE SODIUM; MEMBRANE PROTEIN; PEPTIDE; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CELL MEMBRANE; CHEMOMETRIC ANALYSIS; MICELLE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDE ANALYSIS; PREDICTION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; MAGNETIC RESONANCE SPECTROSCOPY; MEMBRANE PROTEINS; MEMBRANE TRANSPORT PROTEINS; MICELLES; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SODIUM DODECYL SULFATE;

EID: 84862637480     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038967     Document Type: Article

References (55)

1. Passamonti S, Battiston L, Sottocasa GL, (1977) Arylsulfonylation of bilitranslocase in plasma membranes from rat liver enables to discriminate between natural and artificial substrates. Biochim Biophys Acta 1323: 130-136.
2. Passamonti S, Sottocasa GL, (1988) The quinoid structure is the molecular requirement for recognition of phthaleins by the organic anion carrier at the sinusoidal plasma membrane level in the liver. Biochim Biophys Acta 943: 119-125.
3. Battiston L, Passamonti S, Macagno A, Sottocasa GL, (1998) The bilirubin-binding motif of bilitranslocase and its relation to conserved motifs in ancient biliproteins. Biochem Bioph Res Co 247: 687-692.
4. Torres AM, Lunazzi GC, Stremmel W, Tiribelli C, (1993) Bilitranslocase and sulfobromophthalein/bilirubin-binding protein are both involved in the hepatic uptake of organic anions. Proc Natl Acad Sci USA 90: 8136-8139.
5. Brandoni A, Di Giusto G, Franca R, Passamonti S, Torres AM, (2010) Expression of kidney and liver bilitranslocase in response to acute biliary obstruction. Nephron Physiol 114: 35-40.
6. Passamonti S, Terdoslavich M, Franca R, Vanzo A, Tramer F, et al. (2009) Bioavailability of flavonoids: A review of their membrane transport and the function of bilitranslocase in animal and plant organisms. Curr Drug Metab 10: 369-394.
7. Maestro A, Terdoslavich M, Vanzo A, Kuku A, Tramer F, et al. (2010) Expression of bilitranslocase in the vascular endothelium and its function as a flavonoid transporter. Cardiovasc Res 85: 175-183.
8. Ziberna L, Lunder M, Tramer F, Drevensek G, Passamonti S, (2011) The endothelial plasma membrane transporter bilitranslocase mediates rat aortic vasodilation induced by anthocyanins. Nutr Metab Cardiovasc Dis doi: 10.1016/j.numecd.2011.02.005.
9. Ziberna L, Tramer F, Moze S, Vrhovsek U, Mattivi F, et al. (2012) Transport and bioactivity of cyanidin 3-glucoside into the vascular endothelium. Free Radical Bio Med 52: 1750-1759.
10. Nicolin V, Grill V, Micali F, Narducci P, Passamonti S, (2005) Immunolocalisation of bilitranslocase in mucosecretory and parietal cells of the rat gastric mucosa. J Mol Hist 36: 45-50.
11. Vanzo A, Terdoslavich M, Brandoni A, Torres AM, Vrhovsek U, et al. (2008) Uptake of grape anthocyanins into the rat kidney and the involvement of bilitranslocase. Mol Nutr Food Res 52: 1106-1116.
12. Karawajczyk A, Drgan V, Medic N, Oboh G, Passamonti S, et al. (2007) Properties of flavonoids influencing the binding to bilitranslocase investigated by neural network modelling. Biochem Pharmacol 73: 308-320.
13. Župerl Š, Fornasaro S, Novič M, Passamonti S, (2011) Experimental determination and prediction of bilitranslocase transport activity. Anal Chim Acta 705: 322-333.
14. Dobson PD, Kell DB, (2008) Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule? Nat Rev Drug Discov 7: 205-220.
15. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucl Acids Res 28: 235-242. Available:http://www.pdb.org/pdb/home/home.do. Accessed 22 December 2011.
16. Tusnady GE, Dosztanyi Z, Simon I, (2004) Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics 20: 2964-2972. Available:http://pdbtm.enzim.hu/. Accessed 22 December 2011.
17. Opella SJ, Marassi FM, (2004) Structure determination of membrane proteins by NMR spectroscopy. Chem. Rev. 104: 3587-3606.
18. Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR, (2009) Recent advances in the application of solution NMR spectroscopy to multi-span integral membrane proteins. Prog Nucl Magn Reson Spectrosc 55: 335-360.
19. Linser R, Dasari M, Hiller M, Higman V, Fink U, et al. (2011) Proton-detected solid-state NMR spectroscopy of fibrillar and membrane proteins. Angew Chem Int Ed Engl 50: 4508-4512.
20. Lunazzi G, Tiribelli C, Gazzin B, Sottocasa GL, (1982) Further studies on bilitranslocase, a plasma membrane protein involved in hepatic organic anion uptake. BBA-Biomembranes 685: 117-122.
21. Passamonti S, Battiston L, Sottocasa GL, (1999) On the mechanism of bilitranslocase transport inactivation by phenylmethylsulphonyl fluoride. Mol Membr Biol 16: 167-172.
22. Passamonti S, Cocolo A, Braidot E, Petrussa E, Peresson C, et al. (2005) Characterization of electrogenic bromosulfophthalein transport in carnation petal microsomes and its inhibition by antibodies against bilitranslocase. FEBS J 272: 3282-3296.
23. Roy Choudhury A, Novič M, (2009) Data-driven model for the prediction of protein transmembrane regions. SAR QSAR Environ Res 20: 741-754.
24. Passamonti S, Terdoslavich M, Margon A, Cocolo A, Medic N, et al. (2005) Uptake of bilirubin into HepG2 cells assayed by thermal lens spectroscopy. FEBS J 272: 5522-5535.
25. Elofsson A, von Heijne G, (2007) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76: 125-140.
26. Perdih A, Kotnik M, Hodoscek M, Solmajer T, (2007) Targeted molecular dynamics simulation studies of binding and conformational changes in E.Coli MurD. Proteins 68: 243-254.
27. Shea JM, Brooks CL III, (2001) From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu Rev Phys Chem 52: 499-535.
28. Bu L, Brooks CL III, (2008) De novo prediction of the structures of M. tuberculosis membrane proteins. J Am Chem Soc 130: 5384-5385.
29. Duong TH, Mehler EL, Weinstein H, (1999) Molecular dynamics simulation of membranes and a transmembrane helix. J Comput Phys 151: 358-387.
30. Kelly L, Pieper U, Eswar N, Hays FA, Li M, et al. (2009) A survey of integral α-helical membrane proteins. J Struct Funct Genomics 10: 269-280.
31. Frishman D, Argos P, (1995) Knowledge-based protein secondary structure assignment. Proteins 23: 566-579.
32. Richardson JS, (1981) The anatomy and taxonomy of proteins. Adv Protein Chem 34: 167-339.
33. Wüthrich K, (1986) NMR of proteins and nucleic acids. New York: John Wiley & Sons.
34. Sharma D, Rajarathnam K, (2000) 13C NMR chemical shifts can predict disulfide bond formation. J Biomol NMR 18: 165-171.
35. Shen Y, Delaglio F, Cornilescu G, Bax A, (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44: 213-223.
36. Güntert P, Mumenthaler C, Wüthrich K, (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273: 283-298.
37. Koradi R, Billeter M, Wüthrich K, (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14: 51-55.
38. Passamonti S, Vrhovsek U, Mattivi F, (2002) The interaction of anthocyanins with bilitranslocase. Biochem. Biophys. Res. Commun 296: 631-636.
39. Brooks BR, Brooks III CL, MacKerell AD Jr, Nilsson L, Roux B, et al. (2009) CHARMM: The Biomolecular Simulation Program. J Comp Chem 30: 1545-1615.
40. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
41. MacKerell AD Jr, Feig M, Brooks III CL, (2004) 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 Comput Chem 25: 1400-1415.
42. Foloppe N, MacKerell AD Jr, (2004) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 25: 86-104.
43. MacKerell AD Jr, Banavali NK, (2004) All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 25: 105-120.
44. Li C, Gao P, Qin H, Chase R, Gorkov PL, et al. (2007) Uniformly aligned full-length membrane proteins in liquid crystalline bilayers for structural characterization. J Am Chem Soc 129: 5304-5305.
45. Jo S, Kim T, Iyer VG, Im W, (2008) CHARMM-GUI: A web-based graphical user interface for CHARMM. J Comput Chem 29: 1859-1865.
46. Zidar J, Merzel F, Hodošček M, Rebolj K, Sepčić K, et al. (2009) Liquid-ordered phase formation in cholesterol/sphingomyelin bilayers: All-atom molecular dynamics simulations. J Phys Chem B 113: 15795-15802.
47. Humphrey W, Dalke A, Schulten K, (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-38.
48. 30 September (2011) Gnuplot software. Accessed http://www.gnuplot.info.
49. Wishart DS, Bigam CG, Yao J, Abilgaad F, Dyson HJ, et al. (1995) 1H, 13C, and 15N chemical shifts referencing in biomolecular NMR. J Biomol NMR 6: 135-140.
50. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277-293.
51. Goddard TD, Kneller DG, Sparky 3. University of California, San Francisco.
52. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, et al. (2010) AMBER 11. San Francisco: University of California.
53. Schweighofer KJ, Essman U, Berkowitz M, (1997) Simulation of sodium dodecyl sulfate at the water-vapor and water-carbon tetrachloride interfaces at low surface coverage. J Phys Chem B 101: 3793-3799.
54. Rodziewicz-Motowidło S, Sikorska E, Oleszczuk M, Czaplewski C, (2008) Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: Studies in the SDS micelle. J Pept Sci 14: 85-96.
55. Bruce CD, Berkowitz ML, Perera L, Forbes MDE, (2002) Molecular dynamics simulation of sodium dodecyl sulfate micelle in water: Micellar structural characteristics and counterion distribution. J Phys Chem B 106: 3788-3793.