Protonation of Glu135 Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter

Biophysical Journal

Volumn 109, Issue 3, 2015, Pages 542-551

  Liu, Yufeng ^a   Ke, Meng ^a   Gong, Haipeng ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE TRANSPORTER; GLUTAMIC ACID; PROTON;

AMINO ACID SEQUENCE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS;

AMINO ACID SEQUENCE; GLUTAMIC ACID; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MONOSACCHARIDE TRANSPORT PROTEINS; PROTONS;

EID: 84938514705     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2015.06.037     Document Type: Article

References (50)

1. S.S. Pao, I.T. Paulsen, and M.H. Saier Jr. Major facilitator superfamily Microbiol. Mol. Biol. Rev. 62 1998 1 34
2. A.R. Walmsley, and M.P. Barrett G.W. Gould Sugar transporters from bacteria, parasites and mammals: structure-activity relationships Trends Biochem. Sci. 23 1998 476 481
3. M.D. Marger, and M.H. Saier Jr. A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport Trends Biochem. Sci. 18 1993 13 20
4. N. Yan Structural advances for the major facilitator superfamily (MFS) transporters Trends Biochem. Sci. 38 2013 151 159
5. A.G. Murzin, and S.E. Brenner C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
6. L. Sun, and X. Zeng N. Yan Crystal structure of a bacterial homologue of glucose transporters GLUT1-4 Nature 490 2012 361 366
7. E.O. Davis, and P.J. Henderson The cloning and DNA sequence of the gene xylE for xylose-proton symport in Escherichia coli K12 J. Biol. Chem. 262 1987 13928 13932
8. S. Newstead, and D. Drew S. Iwata Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2 EMBO J. 30 2011 417 426
9. N. Solcan, and J. Kwok S. Newstead Alternating access mechanism in the POT family of oligopeptide transporters EMBO J. 31 2012 3411 3421
10. S. Doki, and H.E. Kato O. Nureki Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT Proc. Natl. Acad. Sci. USA 110 2013 11343 11348
11. D.L. Foster, M. Boublik, and H.R. Kaback Structure of the lac carrier protein of Escherichia coli J. Biol. Chem. 258 1983 31 34
12. Y. Huang, and M.J. Lemieux D.N. Wang Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli Science 301 2003 616 620
13. J. Abramson, and I. Smirnova S. Iwata Structure and mechanism of the lactose permease of Escherichia coli Science 301 2003 610 615
14. Y. Yin, and X. He G. Chang Structure of the multidrug transporter EmrD from Escherichia coli Science 312 2006 741 744
15. J. Vasur, and R. Kawai J. Ståhlberg X-ray crystal structures of Phanerochaete chrysosporium Laminarinase 16A in complex with products from lichenin and laminarin hydrolysis FEBS J. 276 2009 3858 3869
16. D. Deng, and C. Xu N. Yan Crystal structure of the human glucose transporter GLUT1 Nature 510 2014 121 125
17. S. Radestock, and L.R. Forrest The alternating-access mechanism of MFS transporters arises from inverted-topology repeats J. Mol. Biol. 407 2011 698 715
18. M.G. Madej, and S. Dang H.R. Kaback Evolutionary mix-and-match with MFS transporters Proc. Natl. Acad. Sci. USA 110 2013 5870 5874
19. L.S. Stelzl, and P.W. Fowler O. Beckstein Flexible gates generate occluded intermediates in the transport cycle of LacY J. Mol. Biol. 426 2014 735 751
20. S. Wada, and M. Tsuda H. Endou Rat multispecific organic anion transporter 1 (rOAT1) transports zidovudine, acyclovir, and other antiviral nucleoside analogs J. Pharmacol. Exp. Ther. 294 2000 844 849
21. N. Fluman, and E. Bibi Bacterial multidrug transport through the lens of the major facilitator superfamily Biochim. Biophys. Acta 1794 2009 738 747
22. J.M. Pascual, and D. Wang D.C. De Vivo GLUT1 deficiency and other glucose transporter diseases Eur. J. Endocrinol 150 2004 627 633
23. F. Jacob, and J. Monod Genetic regulatory mechanisms in the synthesis of proteins J. Mol. Biol. 3 1961 318 356
24. V. Chaptal, and S. Kwon J. Abramson Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition Proc. Natl. Acad. Sci. USA 108 2011 9361 9366
25. S. Dang, and L. Sun N. Yan Structure of a fucose transporter in an outward-open conformation Nature 467 2010 734 738
26. G. Wisedchaisri, and M.S. Park T. Gonen Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE Nat. Commun. 5 2014 4521
27. + symporter revealed by fluorescence spectroscopy Proc. Natl. Acad. Sci. USA 109 2012 14847 14851
28. M.G. Madej, and L. Sun H.R. Kaback Functional architecture of MFS D-glucose transporters Proc. Natl. Acad. Sci. USA 111 2014 E719 E727
29. C. Zhang, and J. Ma Enhanced sampling and applications in protein folding in explicit solvent J. Chem. Phys. 132 2010 244101
30. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graphics 14 1996 27 38
31. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802
32. A.D. MacKerell Jr., M. Feig, and C.L. Brooks 3rd 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 2004 1400 1415
33. A.D. MacKerell, and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
34. A.D. MacKerell Jr., N. Banavali, and N. Foloppe Development and current status of the CHARMM force field for nucleic acids Biopolymers 56 2000-2001 257 265
35. P. Ewald Die berechnung optischer und elektrostatischer gitterpotentiale [The computation of optical and electrostatic lattice potentials] Ann. Phys. 369 1921 253 287
36. J. Kolafa, and J.W. Perram Cutoff errors in the Ewald summation formulas for point-charge systems Mol. Simul. 9 1992 351 368
37. H.D. Herce, A.E. Garcia, and T. Darden The electrostatic surface term: (I) periodic systems J. Chem. Phys. 126 2007 124106
38. A. Bakan, L.M. Meireles, and I. Bahar PRODY: protein dynamics inferred from theory and experiments Bioinformatics 27 2011 1575 1577
39. O.S. Smart, J.M. Goodfellow, and B.A. Wallace The pore dimensions of gramicidin A Biophys. J. 65 1993 2455 2460
40. O.S. Smart, and J.G. Neduvelil M.S.P. Sansom HOLE: a program for the analysis of the pore dimensions of ion channel structural models J. Mol. Graph. 14 1996 354 376
41. a values J. Chem. Theory Comput. 7 2011 2284 2295
42. a predictions J. Chem. Theory Comput. 7 2011 525 537
43. H.M. Berman, and J. Westbrook P.E. Bourne The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
44. + selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation Biophys. J. 104 2013 2401 2409
45. E. Darve, D. Rodríguez-Gómez, and A. Pohorille Adaptive biasing force method for scalar and vector free energy calculations J. Chem. Phys. 128 2008 144120
46. B. Ensing, and A. Laio M.L. Klein A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions J. Phys. Chem. B 109 2005 6676 6687
47. N. Akyuz, and R.B. Altman O. Boudker Transport dynamics in a glutamate transporter homologue Nature 502 2013 114 118
48. N. Akyuz, and E.R. Georgieva S.C. Blanchard Transport domain unlocking sets the uptake rate of an aspartate transporter Nature 518 2015 68 73
49. M.D. Diaz, and M.D. Fernandez-Alonso J. Jimenez-Barbero On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates: a 3D view by using NMR Pure Appl. Chem. 80 2008 1827 1835
50. H. Eyring The activated complex in chemical reactions J. Chem. Phys. 3 1935 107 115