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Original Article

Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure (Review)

Pages 333-341 | Received 29 Jan 2007, Published online: 15 Dec 2009

References

  • Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, Iwata S. Structure and mechanism of the lactose permease of Escherichia coli. Science 2003; 301(5633)610–615
  • Almqvist J, Huang Y, Hovmoller S, Wang DN. Homology modeling of the human microsomal glucose 6-phosphate transporter explains the mutations that cause the glycogen storage disease type Ib. Biochemistry 2004; 43: 9289–9297
  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389–3402
  • Chang AB, Lin R, Keith Studley W, Tran CV, Saier MH, Jr. Phylogeny as a guide to structure and function of membrane transport proteins. Mol Membr Biol 2004; 21: 171–181
  • Cohen GH. ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions. J Appl Cryst 1997; 30: 1160–1161
  • Eisenberg D, Luthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997; 277: 396–404
  • Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003; 374: 461–491
  • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003; 19: 1015–1018
  • Gorboulev V, Shatskaya N, Volk C, Koepsell H. Subtype-specific affinity for corticosterone of rat organic cation transporters rOCT1 and rOCT2 depends on three amino acids within the substrate binding region. Mol Pharmacol 2005; 67: 1612–1619
  • Gorboulev V, Volk C, Arndt P, Akhoundova A, Koepsell H. Selectivity of the polyspecific cation transporter rOCT1 is changed by mutation of aspartate 475 to glutamate. Mol Pharmacol 1999; 56: 1254–1261
  • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992; 89: 10915–10919
  • Heymann JA, Hirai T, Shi D, Subramaniam S. Projection structure of the bacterial oxalate transporter OxlT at 3.4A resolution. J Struct Biol 2003; 144: 320–326
  • Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673–4680
  • Hirai T, Subramaniam S. Structure and transport mechanism of the bacterial oxalate transporter OxlT. Biophys J 2004; 87: 3600–3607
  • Hooft RWW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996; 381: 272
  • Hruz PW, Mueckler MM. Structural analysis of the GLUT1 facilitative glucose transporter (review). Mol Membr Biol 2001; 18: 183–193
  • Huang Y, Lemieux MJ, Song J, Auer M, Wang DN. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 2003; 301(5633)616–620
  • Lagerstedt JO, Voss JC, Wieslander A, Persson BL. Structural modeling of dual-affinity purified Pho84 phosphate transporter. FEBS Lett 2004; 578: 262–268
  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993; 26: 283–291
  • McKusick V. Mendelian inheritance in man: A catalog of human genes and genetic disorders. Johns Hopkins University Press, Baltimore, MD 1998
  • Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000; 302: 205–217
  • Pan CJ, Lin B, Chou JY. Transmembrane topology of human glucose 6-phosphate transporter. J Biol Chem 1999; 274: 13865–13869
  • Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 1996; 264: 121–136
  • Popp C, Gorboulev V, Muller TD, Gorbunov D, Shatskaya N, Koepsell H. Amino acids critical for substrate affinity of rat organic cation transporter 1 line the substrate binding region in a model derived from the tertiary structure of lactose permease. Mol Pharmacol 2005; 67: 1600–1611
  • Salas-Burgos A, Iserovich P, Zuniga F, Vera JC, Fischbarg J. 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 2004; 87: 2990–2999
  • van Gunsteren, WF, Kruger, P, Billeter, SR, Mark, AE, Eising, AA, Scott, WRP, Huneberger, PH, Tironi, IG. 1996. Biomolecular simulation: the GROMOS96 manual and user guide. BiomosrHochschulverlag AG an der ETH Zurich, Switzerland.
  • Vriend G. WHAT IF: A molecular modeling and drug design program. J Mol Graph 1990; 8: 52–56
  • Wang D, Kranz-Eble P, De Vivo DC. Mutational analysis of GLUT1 (SLC2A1) in Glut-1 deficiency syndrome. Hum Mutat 2000; 16: 224–231
  • Wood NJ, Alizadeh T, Richardson DJ, Ferguson SJ, Moir JW. Two domains of a dual-function NarK protein are required for nitrate uptake, the first step of denitrification in Paracoccus pantotrophus. Mol Microbiol 2002; 44: 157–170
  • Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001; 311: 421–430
  • Yang Q, Wang X, Ye L, Mentrikoski M, Mohammadi E, Kim YM, Maloney PC. Experimental tests of a homology model for OxlT, the oxalate transporter of Oxalobacter formigenes. Proc Natl Acad Sci USA 2005; 102: 8513–8518
  • Yin Y, He X, Szewczyk P, Nguyen T, Chang G. Structure of the multidrug transporter EmrD from Escherichia coli. Science 2006; 312(5774)741–744
  • Zhang X, Shirahatti NV, Mahadevan D, Wright SH. A conserved glutamate residue in transmembrane helix 10 influences substrate specificity of rabbit OCT2 (SLC22A2). J Biol Chem 2005; 280: 34813–34822

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