Water permeation dynamics of AqpZ: A tale of two states

Biochimica et Biophysica Acta - Biomembranes

Volumn 1808, Issue 6, 2011, Pages 1581-1586

  Xin, Lin ^a,b,c   Su, Haibin ^c   Nielsen, Claus Helix ^d,e   Tang, Chuyang ^a,c   Torres, Jaume ^b   Mu, Yuguang ^b  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^d TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^e AQUAPORIN A S   (Denmark)

Author keywords

AqpZ dual permeation states; MD simulations; PMF; Structure permeability relation

Indexed keywords

AQUAPORIN; AQUAPORIN Z; ARGININE; OXYGEN; UNCLASSIFIED DRUG; WATER;

ARTICLE; CELL MEMBRANE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIFFUSION; ESCHERICHIA COLI; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; WATER PERMEABILITY; WATER TRANSPORT;

ALANINE; AMINO ACID SUBSTITUTION; AQUAPORINS; ARGININE; BIOLOGICAL TRANSPORT; CELL MEMBRANE; CELL MEMBRANE PERMEABILITY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; OSMOSIS; OSMOTIC PRESSURE; PROTEIN CONFORMATION; SERINE; WATER;

ESCHERICHIA COLI;

EID: 79954774036     PISSN: 00052736     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamem.2011.02.001     Document Type: Article

References (48)

1. G.M. Preston, T.P. Carroll, W.B. Guggino, and P. Agre Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein Science 256 1992 385 387
2. B. Wu, and E. Beitz Aquaporins with selectivity for unconventional permeants Cell. Mol. Life Sci. 64 2007 2413 2421 (Pubitemid 47402583)
3. L.S. King, D. Kozono, and P. Agre From structure to disease: the evolving tale of aquaporin biology Nat. Rev. Mol. Cell Biol. 5 2004 687 698 (Pubitemid 39208179)
4. Z. Liu, J. Shen, J.M. Carbrey, R. Mukhopadhyay, P. Agre, and B.P. Rosen Arsenite transport by mammalian aquaglyceroporins AQP7 and AQP9 Proc. Natl. Acad. Sci. USA 99 2002 6053 6058 (Pubitemid 34493263)
5. Y.J. Ko, J. Huh, and W.H. Jo Ion exclusion mechanism in aquaporin at an atomistic level Proteins 70 2008 1442 1450 (Pubitemid 351304102)
6. D. Fu, and M. Lu The structural basis of water permeation and proton exclusion in aquaporins Mol. Membr. Biol. 24 2007 366 374 (Pubitemid 47290694)
7. N. Chakrabarti, E. Tajkhorshid, B. Roux, and R. Pomes Molecular basis of proton blockage in aquaporins Structure 12 2004 65 74 (Pubitemid 38114807)
8. H. Sui, B.G. Han, J.K. Lee, P. Walian, and B.K. Jap Structural basis of water-specific transport through the AQP1 water channel Nature 414 2001 872 878 (Pubitemid 34024731)
9. M. Hara-Chikuma, and A.S. Verkman Aquaporin-1 facilitates epithelial cell migration in kidney proximal tubule J. Am. Soc. Nephrol. 17 2006 39 45
10. O. Bloch, M.C. Papadopoulos, G.T. Manley, and A.S. Verkman Aquaporin-4 gene deletion in mice increases focal edema associated with staphylococcal brain abscess J. Neurochem. 95 2005 254 262 (Pubitemid 41384443)
11. P. Agre, and D. Kozono Aquaporin water channels: molecular mechanisms for human diseases FEBS Lett. 555 2003 72 78 (Pubitemid 37431100)
12. A. Tanghe, P. Van Dijck, and J.M. Thevelein Why do microorganisms have aquaporins? Trends Microbiol. 14 2006 78 85 (Pubitemid 43190737)
13. A.S. Verkman Role of aquaporin water channels in eye function Exp. Eye Res. 76 2003 137 143 (Pubitemid 36263339)
14. Y.C. Chen, M.A. Cadnapaphornchai, and R.W. Schrier Clinical update on renal aquaporins Biol. Cell 97 2005 357 371 (Pubitemid 40872345)
15. M. Amiry-Moghaddam, and O.P. Ottersen The molecular basis of water transport in the brain Nat. Rev. Neurosci. 4 2003 991 1001 (Pubitemid 37486675)
16. I. Johansson, M. Karlsson, U. Johanson, C. Larsson, and P. Kjellbom The role of aquaporins in cellular and whole plant water balance Biochim. Biophys. Acta 1465 2000 324 342 (Pubitemid 30169077)
17. C. Maurel, H. Javot, V. Lauvergeat, P. Gerbeau, C. Tournaire, V. Santoni, and J. Heyes Molecular physiology of aquaporins in plants Int. Rev. Cytol. 215 2002 105 148 (Pubitemid 34280293)
18. K. Murata, K. Mitsuoka, T. Hirai, T. Walz, P. Agre, J.B. Heymann, A. Engel, and Y. Fujiyoshi Structural determinants of water permeation through aquaporin-1 Nature 407 2000 599 605
19. S. Törnroth-Horsefield, K. Hedfalk, G. Fischer, K. Lindkvist-Petersson, and R. Neutze Structural insights into eukaryotic aquaporin regulation FEBS Lett. 584 2010 2580 2588
20. D. Fu, A. Libson, L.J. Miercke, C. Weitzman, P. Nollert, J. Krucinski, and R.M. Stroud Structure of a glycerol-conducting channel and the basis for its selectivity Science 290 2000 481 486
21. E. Tajkhorshid, P. Nollert, M.∅. Jensen, L.J.W. Miercke, J. O'Connell, R.M. Stroud, and K. Schulten Control of the selectivity of the aquaporin water channel family by global orientational tuning Science 296 2002 525 530 (Pubitemid 34413590)
22. J. Jiang, B.V. Daniels, and D. Fu Crystal structure of AqpZ tetramer reveals two distinct Arg-189 conformations associated with water permeation through the narrowest constriction of the water-conducting channel J. Biol. Chem. 281 2006 454 460 (Pubitemid 43671207)
23. D.F. Savage, P.F. Egea, Y. Robles-Colmenares, J.D. O'Connell III, and R.M. Stroud Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z PLoS Biol. 1 2003 E72
24. S. Törnroth-Horsefield, Y. Wang, K. Hedfalk, U. Johanson, M. Karlsson, E. Tajkhorshid, R. Neutze, and P. Kjellbom Structural mechanism of plant aquaporin gating Nature 439 2006 688 694 (Pubitemid 43237610)
25. T. Gonen, P. Silz, J. Kistler, Y. Cheng, and T. Walz Aquaporin-0 membrane junctions reveal the structure of a closed water pore Nature 429 2004 193 197 (Pubitemid 38656196)
26. J.K. Lee, D. Kozono, J. Remis, Y. Kitagawa, P. Agre, and R.M. Stroud Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 Å Proc. Natl. Acad. Sci. USA 102 2005 18932 18937 (Pubitemid 43049544)
27. Z.E.R. Newby, J. O'Connell Iii, Y. Robles-Colmenares, S. Khademi, L.J. Miercke, and R.M. Stroud Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum Nat. Struct. Mol. Biol. 15 2008 619 625 (Pubitemid 351799138)
28. R. Horsefield, K. Nordén, M. Fellert, A. Backmark, S. Törnroth-Horsefield, A.C. Terwisscha Van Scheltinga, J. Kvassman, P. Kjellbom, U. Johanson, and R. Neutze High-resolution x-ray structure of human aquaporin 5 Proc. Natl. Acad. Sci. USA 105 2008 13327 13332
29. G. Fischer, U. Kosinska-Eriksson, C. Aponte-Santamaria, M. Palmgren, C. Geijer, K. Hedfalk, S. Hohmann, B.L. de Groot, R. Neutze, and K. Lindkvist-Petersson Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism PLoS Biol. 7 2009 e1000130
30. B.L. De Groot, and H. Grubmüller Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF Science 294 2001 2353 2357 (Pubitemid 33140559)
31. H. Khandelia, M.O. Jensen, and O.G. Mouritsen To gate or not to gate: using molecular dynamics simulations to morph gated plant aquaporins into constitutively open conformations J. Phys. Chem. B 113 2009 5239 5244
32. J.S. Hub, C. Aponte-Santamaría, H. Grubmüller, and B.L. de Groot Voltage-regulated water flux through aquaporin channels in silico Biophys. J. 99 2010 L97 L99
33. R. Zardoya Phylogeny and evolution of the major intrinsic protein family Biol. Cell 97 2005 397 414 (Pubitemid 40872348)
34. M.O. Jensen, and O.G. Mouritsen Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF Biophys. J. 90 2006 2270 2284
35. Y. Wang, K. Schulten, and E. Tajkhorshid What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF Structure 13 2005 1107 1118 (Pubitemid 41111479)
36. F. Zhu, E. Tajkhorshid, and K. Schulten Theory and simulation of water permeation in aquaporin-1 Biophys. J. 86 2004 50 57 (Pubitemid 38071799)
37. M. Hashido, M. Ikeguchi, and A. Kidera Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF FEBS Lett. 579 2005 5549 5552 (Pubitemid 41455629)
38. M.O. Jensen, R.O. Dror, H. Xu, D.W. Borhani, I.T. Arkin, M.P. Eastwood, and D.E. Shaw Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens Proc. Natl. Acad. Sci. USA 105 2008 14430 14435
39. M. Hashido, A. Kidera, and M. Ikeguchi Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations Biophys. J. 93 2007 373 385 (Pubitemid 47057805)
40. A. Berezhkovskii, and G. Hummer Single-file transport of water molecules through a carbon nanotube Phys. Rev. Lett. 89 2002 064503
41. F. Zhu, E. Tajkhorshid, and K. Schulten Collective diffusion model for water permeation through microscopic channels Phys. Rev. Lett. 93 2004 224501
42. W.H. Press, S.A. Teukolsky, W.T. Vetterling, and B.P. Flannery Numerical Recipes in C: The Art of Scientific Computing 1992 The Press Syndicate of the University of Cambridge 663
43. S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules: I. The method J. Comput. Chem. 8 1992 1011 1021
44. O.S. Smart, J.M. Goodfellow, and B.A. Wallace The pore dimensions of gramicidin A Biophys. J. 65 1993 2455 2460 (Pubitemid 24005977)
45. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J. Berendsen GROMACS: fast, flexible, and free J. Comput. Chem. 26 2005 1701 1718 (Pubitemid 43076182)
46. D.M. Alexander Jr., B. Nilesh, and F. Nicolas Development and current status of the CHARMM force field for nucleic acids Biopolymers 56 2000 257 265
47. P. Bjelkmar, P. Larsson, M.A. Cuendet, B. Hess, and E. Lindahl Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models J. Chem. Theory Comput. 6 2010 459 466
48. T. Darden, L. Perera, L. Li, and L. Pedersen New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations Structure 7 1999 R55 R60