Water transport in human aquaporin-4: Molecular dynamics (MD) simulations

Biochemical and Biophysical Research Communications

Volumn 412, Issue 4, 2011, Pages 654-659

  Cui, Yubao ^a   Bastien, David A ^a  

^a UNIVERSITY OF TEXAS AT SAN ANTONIO   (United States)

Author keywords

Aquaporin 4; Asn Pro Ala motifs; Brownian dynamics fluctuation dissipation theorem (BD FDT); Central fourfold axis; Free energy computation; Molecular dynamics simulations

Indexed keywords

AQUAPORIN 4; MONOMER; TETRAMER; WATER;

ARTICLE; HYDROPHOBICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION; WATER FLOW;

AQUAPORIN 4; HUMANS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; POROSITY; PROTEIN CONFORMATION; WATER; WATER-ELECTROLYTE BALANCE;

EID: 80052627790     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2011.08.019     Document Type: Article

References (30)

1. Agre P., King L.S., Yasui M., et al. Aquaporin water channels-from atomic structure to clinical medicine. J. Physiol. 2002, 542:3-16.
2. Arciénega I.I., Brunet J.F., Bloch J., et al. Cell locations for AQP1, AQP4 and AQP9 in the non-human primate brain. Neuroscience 2010, 167:1103-1114.
3. Badaut J., Lasbennes F., Magistretti P.J., et al. Aquaporins in brain: distribution, Physiology and pathophysiology. J. Cereb. Blood Flow Metab. 2002, 22:367-378.
4. Benga G. Water channel proteins (later called aquaporins) and relatives: past, present, and future. IUBMB Life 2004, 61:112-133.
5. Masseguin C., Corcoran M., Carcenac C., et al. Altered gravity downregulates aquaporin-1 protein expression in choroid plexus. J. Appl. Physiol. 2000, 88:843-850.
6. Speake T., Freeman L.J., Brown P.D. Expression of aquaporin 1 and aquaporin 4 water channels in rat choroid plexus. Biochim. Biophys. Acta 2003, 1609:80-86.
7. Brown P.D., Davies S.L., Speake T., et al. Molecular mechanisms of cerebrospinal fluid production. Neuroscience 2004, 129:957-970.
8. Badaut J., Regli L. Distribution, possible roles of aquaporin 9 in the brain. Neuroscience 2004, 129:971-981.
9. Nagelhus E.A., Mathiisen T.M., Ottersen O.P. Aquaporin-4 in the central nervous system: cellular and subcellular distribution and coexpression with KIR4.1. Neuroscience 2004, 129:905-913.
10. Nicchia G.P., Nico B., Camassa L.M., et al. The role of aquaporins-4 in the blood-brain barrier development and integrity: studies in animal and cell culture models. Neuroscience 2004, 129:935-945.
11. Walz T., Fujiyoshi Y., Engel A. The AQP structure and functional implications. Handb. Exp. Pharmacol. 2009, 190:31-56.
12. Wu B., Beitz E. Aquaporins with selectivity for unconventional permeants. Cell Mol. Life Sci. 2007, 64:2413-2421.
13. de Groot B.L., Grubmüller H. Water permeation across biological membrances: mechanism and dynamics of aaquaporin-1 and GlpF. Science 2001, 294:2353-2357.
14. Hub J.S., Grubmüller H., de Groot B.L. Dynamics and energetics of permeation through aquaporins, what do we learn from molecular dynamics simulations ?. Handb. Exp. Pharmacol. 2009, 190:57-76.
15. de Groot B.L., Grubmüller H. The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr. Opin. Struct. Biol. 2005, 15:176-183.
16. Ho J.D., Yeh R., Sandstrom A., et al. Crystal structure of human aquaporin 4 at 1.8Å and its mechanism of conductance. Proc. Natl. Acad. Sci. USA 2009, 106:7437-7442.
17. Humphrey W., Dalke A., Schulten K. VMD-visual molecular dynamics. J. Mol. Graphics 1996, 14:33-38.
18. Grubmüller H. SOLVATE v. 1.0, Theoretical Biophysics Group 1996, Institute for Medical Optics, Ludwig-Maximilians University, Munich.
19. MacKerell A.D., Bashford D., Bellott M., et al. Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations. FASEB J. 1992, 6:A143.
20. MacKerell A.D., Bashford D., Bellott M., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102:3568-3616.
21. Kalé L., Skeel R., Bhandarkar M., et al. NAMD2: greater scalability for parallel molecular dynamics. J. Comp. Phys. 1999, 151:283-312.
22. Essmann U., Perera L., Berkowitz M.L., et al. A smooth Particle Mesh Ewald method. J. Chem. Phys. 1995, 103:8577-8593.
23. Chen L.Y., Bastien D.A., Espejel H.E. Determination of equilibrium free-energy from non-equilibrium work measurements. Phys. Chem. Chem. Phys. 2010, 12:6579-6582.
24. Chen L.Y. Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations. Biophys. Chem. 2010, 151:178-180.
25. de Groot B.L., Frigato T., Helms V., et al. The mechanism of proton exclusion in the aquaporin-1 water channel. J. Mol. Biol. 2003, 333:279-293.
26. Harries W.E., Akhavan D., Miercke L.J., et al. The channel architecture of aquaporin 0 at 2.2-Å resolution. Proc. Natl. Acad. Sci. USA 2004, 101:14045-14050.
27. Hub J.S., de Groot B.L. Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc. Natl. Acad. Sci. USA 2008, 105:1198-1203.
28. Newby Z.E., O'Connell J., Robbes-Colmenares Y., et al. Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum. Nat. Struct. Mol. Biol. 2008, 15:619-625.
29. Savage D.F., Egea P.F., Robles-Colmenares Y., et al. Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z. PLoS Biol. 2003, 1:E72.
30. Hummer G., Szabo A. Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc. Natl. Acad. Sci. USA 2001, 98:3658-3661.