Proton-coupled dynamics in lactose permease

Structure

Volumn 20, Issue 11, 2012, Pages 1893-1904

  Andersson, Magnus ^a   Bondar, Ana Nicoleta ^b   Freites, J Alfredo ^a   Tobias, Douglas J ^a   Kaback, H Ronald ^c   White, Stephen H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LACTOSE PERMEASE; PHOSPHATIDYLETHANOLAMINE; PROTON; SUGAR;

ARTICLE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTON TRANSPORT; REACTION ANALYSIS;

ESCHERICHIA COLI; MEMBRANE TRANSPORT PROTEINS; MODELS, MOLECULAR; PROTONS;

ESCHERICHIA COLI;

EID: 84868559590     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.08.021     Document Type: Article

References (56)

1. J. Abramson, I. Smirnova, V. Kasho, G. Verner, H.R. Kaback, and S. Iwata Structure and mechanism of the lactose permease of Escherichia coli Science 301 2003 610 615
2. J. Baker, S.H. Wright, and F. Tama Simulations of substrate transport in the multidrug transporter EmrD Proteins 80 2012 1620 1632
3. M. Bogdanov, P.N. Heacock, and W. Dowhan A polytopic membrane protein displays a reversible topology dependent on membrane lipid composition EMBO J. 21 2002 2107 2116
4. M. Bogdanov, P. Heacock, Z. Guan, and W. Dowhan Plasticity of lipid-protein interactions in the function and topogenesis of the membrane protein lactose permease from Escherichia coli Proc. Natl. Acad. Sci. USA 107 2010 15057 15062
5. A.-N. Bondar, C. del Val, and S.H. White Rhomboid protease dynamics and lipid interactions Structure 17 2009 395 405
6. V. Chaptal, S. Kwon, M.R. Sawaya, L. Guan, H.R. Kaback, and 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
7. S. Dang, L. Sun, Y. Huang, F. Lu, Y. Liu, H. Gong, J. Wang, and N. Yan Structure of a fucose transporter in an outward-open conformation Nature 467 2010 734 738
8. T. Darden, D. York, and L. Pedersen Particle mesh Ewald: An N•log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
9. R.L. Dunten, M. Sahin-Tóth, and H.R. Kaback Role of the charge pair aspartic acid-237-lysine-358 in the lactose permease of Escherichia coli Biochemistry 32 1993 3139 3145
10. G. Enkavi, and E. Tajkhorshid Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT Biochemistry 49 2010 1105 1114
11. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 1995 8577 8593
12. S.E. Feller, Y. Zhang, R.W. Pastor, and B.R. Brooks Constant pressure molecular dynamics simulation: The Langevin piston method J. Chem. Phys. 103 1995 4613 4621
13. S. Frillingos, A. Gonzalez, and H.R. Kaback Cysteine-scanning mutagenesis of helix IV and the adjoining loops in the lactose permease of Escherichia coli: Glu126 and Arg144 are essential. off Biochemistry 36 1997 14284 14290
14. S. Frillingos, M. Sahin-Tóth, J. Wu, and H.R. Kaback Cys-scanning mutagenesis: a novel approach to structure function relationships in polytopic membrane proteins FASEB J. 12 1998 1281 1299
15. J.J. Garcia-Celma, I.N. Smirnova, H.R. Kaback, and K. Fendler Electrophysiological characterization of LacY Proc. Natl. Acad. Sci. USA 106 2009 7373 7378
16. H. Grubmüller, H. Heller, A. Windemuth, and K. Schulten Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions Mol. Simul. 6 1991 121 142
17. L. Guan, and H.R. Kaback Lessons from lactose permease Annu. Rev. Biophys. Biomol. Struct. 35 2006 67 91
18. L. Guan, O. Mirza, G. Verner, S. Iwata, and H.R. Kaback Structural determination of wild-type lactose permease Proc. Natl. Acad. Sci. USA 104 2007 15294 15298
19. M.M. He, and H.R. Kaback Interaction between residues Glu269 (helix VIII) and His322 (helix X) of the lactose permease of Escherichia coli is essential for substrate binding Biochemistry 36 1997 13688 13692
20. J. Holyoake, and M.S.P. Sansom Conformational change in an MFS protein: MD simulations of LacY Structure 15 2007 873 884
21. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28
22. O. Jardetzky Simple allosteric model for membrane pumps Nature 211 1966 969 970
23. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
24. K. Jung, H. Jung, J.H. Wu, G.G. Privé, and H.R. Kaback Use of site-directed fluorescence labeling to study proximity relationships in the lactose permease of Escherichia coli Biochemistry 32 1993 12273 12278
25. K. Jung, H. Jung, and H.R. Kaback Dynamics of lactose permease of Escherichia coli determined by site-directed fluorescence labeling Biochemistry 33 1994 3980 3985
26. K. Jung, H. Jung, P. Colacurcio, and H.R. Kaback Role of glycine residues in the structure and function of lactose permease, an Escherichia coli membrane transport protein Biochemistry 34 1995 1030 1039
27. H.R. Kaback Structure and mechanism of the lactose permease C. R. Biol. 328 2005 557 567
28. H.R. Kaback, M. Sahin-Tóth, and A.B. Weinglass The kamikaze approach to membrane transport Nat. Rev. Mol. Cell Biol. 2 2001 610 620
29. V.N. Kasho, I.N. Smirnova, and H.R. Kaback Sequence alignment and homology threading reveals prokaryotic and eukaryotic proteins similar to lactose permease J. Mol. Biol. 358 2006 1060 1070
30. J.B. Klauda, R.M. Venable, J.A. Freites, J.W. O'Connor, D.J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A.D. MacKerell Jr., and R.W. Pastor Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types J. Phys. Chem. B 114 2010 7830 7843
31. J. le Coutre, L.R. Narasimhan, C.K. Patel, and H.R. Kaback The lipid bilayer determines helical tilt angle and function in lactose permease of Escherichia coli Proc. Natl. Acad. Sci. USA 94 1997 10167 10171
32. Z. Liu, M.G. Madej, and H.R. Kaback Helix dynamics in LacY: helices II and IV J. Mol. Biol. 396 2010 617 626
33. A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, and S. Ha All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
34. G.J. Martyna, D.J. Tobias, and M.L. Klein Constant-pressure molecular-dynamics algorithms J. Chem. Phys. 101 1994 4177 4189
35. O. Mirza, L. Guan, G. Verner, S. Iwata, and H.R. Kaback Structural evidence for induced fit and a mechanism for sugar/H+ symport in LacY EMBO J. 25 2006 1177 1183
36. S. Miyamoto, and P. Kollman An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13 1992 952 962
37. Y. Nie, and H.R. Kaback Sugar binding induces the same global conformational change in purified LacY as in the native bacterial membrane Proc. Natl. Acad. Sci. USA 107 2010 9903 9908
38. M.H.M. Olsson, C.R. Sondergaard, M. Rostkowski, and J.H. Jensen PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions J. Chem. Theory Comput. 7 2011 525 537
39. S.S. Pao, I.T. Paulsen, and M.H. Saier Jr. Major facilitator superfamily Microbiol. Mol. Biol. Rev. 62 1998 1 34
40. P.Y. Pendse, B.R. Brooks, and J.B. Klauda Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation J. Mol. Biol. 404 2010 506 521
41. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, and K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802
42. 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
43. J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J. Comp. Physiol. 23 1977 327 341
44. M. Sahin-Tóth, R.L. Dunten, A. Gonzalez, and H.R. Kaback Functional interactions between putative intramembrane charged residues in the lactose permease of Escherichia coli Proc. Natl. Acad. Sci. USA 89 1992 10547 10551
45. M. Sahin-Tóth, and H.R. Kaback Cysteine scanning mutagenesis of putative transmembrane helices IX and X in the lactose permease of Escherichia coli Protein Sci. 2 1993 1024 1033
46. M. Sahin-Toth, and H.R. Kaback Arg-302 facilitates deprotonation of Glu-325 in the transport mechanism of the lactose permease from Escherichiacoli Proc. Natl. Acad. Sci. USA 98 2001 6068 6073
47. O.S. Smart, J.M. Goodfellow, and B.A. Wallace The pore dimensions of gramicidin A Biophys. J. 65 1993 2455 2460
48. I. Smirnova, V. Kasho, J.-Y. Choe, C. Altenbach, W.L. Hubbell, and H.R. Kaback Sugar binding induces an outward facing conformation of LacY Proc. Natl. Acad. Sci. USA 104 2007 16504 16509
49. a for sugar binding to LacY Biochemistry 48 2009 8852 8860
50. I.N. Smirnova, and H.R. Kaback A mutation in the lactose permease of Escherichia coli that decreases conformational flexibility and increases protein stability Biochemistry 42 2003 3025 3031
51. P.L. Sorgen, Y.L. Hu, L. Guan, H.R. Kaback, and M.E. Girvin An approach to membrane protein structure without crystals Proc. Natl. Acad. Sci. USA 99 2002 14037 14040
52. M.L. Ujwal, M. Sahin-Tóth, B. Persson, and H.R. Kaback Role of glutamate-269 in the lactose permease of Escherichia coli Mol. Membr. Biol. 11 1994 9 16
53. +) symport by the sucrose permease of Escherichia coli relative to lactose permease J. Mol. Biol. 358 2006 1051 1059
54. J.H. Wu, D. Hardy, and H.R. Kaback Transmembrane helix tilting and ligand-induced conformational changes in the lactose permease determined by site-directed chemical crosslinking in situ J. Mol. Biol. 282 1998 959 967
55. Y. Yin, M.O. Jensen, E. Tajkhorshid, and K. Schulten Sugar binding and protein conformational changes in lactose permease Biophys. J. 91 2006 3972 3985
56. W. Zhang, L. Guan, and H.R. Kaback Helices VII and X in the lactose permease of Escherichia coli: proximity and ligand-induced distance changes J. Mol. Biol. 315 2002 53 62