References
- Aksimentiev, A., & Schulten, K. (2005). Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map . Biophysical Journal, 88(6), 3745–3761. https://doi.org/https://doi.org/10.1529/biophysj.104.058727
- Alberga, D., Nicolotti, O., Lattanzi, G., Nicchia, G. P., Frigeri, A., Pisani, F., Benfenati, V., & Mangiatordi, G. F. (2014). A new gating site in human aquaporin-4: Insights from molecular dynamics simulations. Biochimica et Biophysica Acta, 1838(12), 3052–3060. https://doi.org/https://doi.org/10.1016/j.bbamem.2014.08.015
- Berezhkovskii, A., & Hummer, G. (2002). Single-file transport of water molecules through a carbon nanotube. Physical Review Letters, 89(6), 064503. https://doi.org/https://doi.org/10.1103/PhysRevLett.89.064503
- Binesh, A. R., & Kamali, R. (2015). Molecular dynamics insights into human aquaporin 2 water channel. Biophysical Chemistry, 207, 107–113. https://doi.org/https://doi.org/10.1016/j.bpc.2015.10.002
- Calvanese, L. (2018). Structural Basis for mutations of human aquaporins associated to genetic diseases. International Journal of Molecular Sciences, 19(6), 1577–1594.
- Contreras-Riquelme, S., Garate, J.-A., Perez-Acle, T., & Martin, A. J. M. (2018). RIP-MD: A tool to study residue interaction networks in protein molecular dynamics. PeerJ., 6, e5998. https://doi.org/https://doi.org/10.7717/peerj.5998
- Cui, Y., & Bastien, D. A. (2011). Water transport in human aquaporin-4: Molecular dynamics (MD) simulations. Biochemical and Biophysical Research Communications, 412(4), 654–659. https://doi.org/https://doi.org/10.1016/j.bbrc.2011.08.019
- de Groot, B. L., & Grubmüller, H. (2001). Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science (New York, N.Y.), 294(5550), 2353–2357. https://doi.org/https://doi.org/10.1126/science.1062459
- DeLano, W. L. (2002). The PyMOL molecular graphics system. .
- Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/https://doi.org/10.1063/1.470117
- Fallah, Z., Jamali, Y., & Rafii-Tabar, H. (2016). Structural and functional effect of an oscillating electric field on the Dopamine-D3 receptor: A molecular dynamics simulation study. PloS One, 11(11), e0166412. https://doi.org/https://doi.org/10.1371/journal.pone.0166412
- Feller, S. E., & MacKerell, A. D. (2000). An improved empirical potential energy function for molecular simulations of phospholipids. The Journal of Physical Chemistry B, 104(31), 7510–7515. https://doi.org/https://doi.org/10.1021/jp0007843
- Feller, S. E., Zhang, Y., Pastor, R. W., & Brooks, B. R. (1995). Constant pressure molecular dynamics simulation: The Langevin piston method. The Journal of Chemical Physics, 103(11), 4613–4621. https://doi.org/https://doi.org/10.1063/1.470648
- Frick, A., Eriksson, U. K., de Mattia, F., Oberg, F., Hedfalk, K., Neutze, R., de Grip, W. J., Deen, P. M. T., & Törnroth-Horsefield, S. (2014). X-ray structure of human aquaporin 2 and its implications for nephrogenic diabetes insipidus and trafficking. Proceedings of the National Academy of Sciences of the United States of America, 111(17), 6305–6310. https://doi.org/https://doi.org/10.1073/pnas.1321406111
- Garate, J. A., English, N. J., & MacElroy, J. M. D. (2011). Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study. The Journal of Chemical Physics, 134(5), 055110https://doi.org/https://doi.org/10.1063/1.3529428
- Gowers, R. J. (2019). MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. Los Alamos National Lab.(LANL).
- Grossfield, A., & Zuckerman, D. M. (2009). Quantifying uncertainty and sampling quality in biomolecular simulations. Annual Reports in Computational Chemistry, 5, 23–48. https://doi.org/https://doi.org/10.1016/S1574-1400(09)00502-7
- Hashido, M., Ikeguchi, M., & Kidera, A. (2005). Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF. FEBS Letters, 579(25), 5549–5552. https://doi.org/https://doi.org/10.1016/j.febslet.2005.09.018
- Hoekstra, J. A., van Lieburg, A. F., Monnens, L. A. H., Hulstijn-Dirkmaat, G. M., & Knoers, V. V. A. M. (1996). Cognitive and psychosocial functioning of patients with congenital nephrogenic diabetes insipidus. American Journal of Medical Genetics, 61(1), 81–88. https://doi.org/https://doi.org/10.1002/(SICI)1096-8628(19960102)61:1<81::AID-AJMG17>3.0.CO;2-S
- Hub, J. S., & De Groot, B. L. (2008). Mechanism of selectivity in aquaporins and aquaglyceroporins. Proceedings of the National Academy of Sciences of the United States of America, 105(4), 1198–1203. https://doi.org/https://doi.org/10.1073/pnas.0707662104
- Hub, J. S., Grubmuller, H., & de Groot, B. L. (2008). Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations?. Handbook of Experimental Pharmacology., (190), 57–76.
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/https://doi.org/10.1016/0263-7855(96)00018-5
- Ishibashi, K., Hara, S., & Kondo, S. (2009). Aquaporin water channels in mammals. Clinical and Experimental Nephrology, 13(2), 107–117. https://doi.org/https://doi.org/10.1007/s10157-008-0118-6
- Janosi, L., & Ceccarelli, M. (2013). The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations. PLoS One, 8(4), e59897https://doi.org/https://doi.org/10.1371/journal.pone.0059897
- Jensen, M. O., & Mouritsen, O. G. (2006). Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF. Biophysical Journal, 90(7), 2270–2284. https://doi.org/https://doi.org/10.1529/biophysj.105.073965
- Jensen, M., Tajkhorshid, E., & Schulten, K. (2003). Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels, in. Biophysical Journal, 85(5), 2884–2899. https://doi.org/https://doi.org/10.1016/S0006-3495(03)74711-0
- Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/https://doi.org/10.1063/1.445869
- Kreida, S., & Törnroth-Horsefield, S. (2015). Structural insights into aquaporin selectivity and regulation. Current Opinion in Structural Biology, 33, 126–134. https://doi.org/https://doi.org/10.1016/j.sbi.2015.08.004
- Kučerka, N., Tristram-Nagle, S., & Nagle, J. F. (2005). Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. The Journal of Membrane Biology, 208(3), 193–202. https://doi.org/https://doi.org/10.1007/s00232-005-7006-8
- Lancaster, J. R. (1994). Simulation of the diffusion and reaction of endogenously produced nitric oxide. Proceedings of the National Academy of Sciences of the United States of America, 91(17), 8137–8141. https://doi.org/https://doi.org/10.1073/pnas.91.17.8137
- MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., … Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B, 102(18), 3586–3616. https://doi.org/https://doi.org/10.1021/jp973084f
- Marr, N., Kamsteeg, E. J., van Raak, M., van Os, C. H., & Deen, P. M. (2001). Functionality of aquaporin-2 missense mutants in recessive nephrogenic diabetes insipidus. Pflugers Archiv: European Journal of Physiology, 442(1), 73–77. https://doi.org/https://doi.org/10.1007/s004240000498
- Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/https://doi.org/10.1002/jcc.540130805
- Moeller, H. B., Rittig, S., & Fenton, R. A. (2013). Nephrogenic diabetes insipidus: Essential insights into the molecular background and potential therapies for treatment. Endocrine Reviews, 34(2), 278–301. https://doi.org/https://doi.org/10.1210/er.2012-1044
- Murata, K., Mitsuoka, K., Hirai, T., Walz, T., Agre, P., Heymann, J. B., Engel, A., & Fujiyoshi, Y. (2000). Structural determinants of water permeation through aquaporin-1. Nature, 407(6804), 599–605.
- Oliva, R., Calamita, G., Thornton, J. M., & Pellegrini-Calace, M. (2010). Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity. Proceedings of the National Academy of Sciences of the United States of America, 107(9), 4135–4140. https://doi.org/https://doi.org/10.1073/pnas.0910632107
- Padhi, S., & Priyakumar, U. D. (2017). Microsecond simulation of human aquaporin 2 reveals structural determinants of water permeability and selectivity. Biochimica et Biophysica Acta. Biomembranes, 1859(1), 10–16. https://doi.org/https://doi.org/10.1016/j.bbamem.2016.10.011
- Payne, J. A., & Forbush, B. (1994). Alternatively spliced isoforms of the putative renal Na-K-Cl cotransporter are differentially distributed within the rabbit kidney. Proceedings of the National Academy of Sciences of the United States of America, 91(10), 4544–4548. https://doi.org/https://doi.org/10.1073/pnas.91.10.4544
- Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/https://doi.org/10.1002/jcc.20289
- Plesnar, E., Subczynski, W. K., & Pasenkiewicz-Gierula, M. (2012). Saturation with cholesterol increases vertical order and smoothes the surface of the phosphatidylcholine bilayer: A molecular simulation study. Biochimica et Biophysica Acta, 1818(3), 520–529. https://doi.org/https://doi.org/10.1016/j.bbamem.2011.10.023
- Release, S. (2017). 1: Maestro. Schrödinger, LLC.
- Robben, J. H., Knoers, N. V., & Deen, P. M. (2006). Cell biological aspects of the vasopressin type-2 receptor and aquaporin 2 water channel in nephrogenic diabetes insipidus. American Journal of Physiology. Renal Physiology, 291(2), F257–70. https://doi.org/https://doi.org/10.1152/ajprenal.00491.2005
- Sasseville, L. J., Cuervo, J. E., Lapointe, J.-Y., & Noskov, S. Y. (2011). The structural pathway for water permeation through sodium-glucose cotransporters. Biophysical Journal, 101(8), 1887–1895. https://doi.org/https://doi.org/10.1016/j.bpj.2011.09.019
- Smart, O. S., Goodfellow, J. M., & Wallace, B. A. (1993). The pore dimensions of gramicidin A. Biophysical Journal, 65(6), 2455–2460. https://doi.org/https://doi.org/10.1016/S0006-3495(93)81293-1
- Sui, H., Han, B. G., Lee, J. K., Walian, P., & Jap, B. K. (2001). Structural basis of water-specific transport through the AQP1 water channel. Nature, 414(6866), 872–878. https://doi.org/https://doi.org/10.1038/414872a
- Tajkhorshid, E., Nollert, P., Jensen, M. Ø., Miercke, L. J. W., O'Connell, J., Stroud, R. M., & Schulten, K. (2002). Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science (New York, N.Y.), 296(5567), 525–530. https://doi.org/https://doi.org/10.1126/science.1067778
- Verkman, A. S. (2012). Aquaporins in clinical medicine. Annual Review of Medicine, 63, 303–316. https://doi.org/https://doi.org/10.1146/annurev-med-043010-193843
- Wang, Y., & Tajkhorshid, E. (2010). Nitric oxide conduction by the brain aquaporin AQP4. Proteins, 78(3), 661–670. https://doi.org/https://doi.org/10.1002/prot.22595
- Wesche, D., Deen, P. M. T., & Knoers, N. V. A. M. (2012). Congenital nephrogenic diabetes insipidus: The current state of affairs. Pediatric Nephrology (Berlin, Germany), 27(12), 2183–2204. https://doi.org/https://doi.org/10.1007/s00467-012-2118-8
- Xin, L., Su, H., Nielsen, C. H., Tang, C., Torres, J., & Mu, Y. (2011). Water permeation dynamics of AqpZ: A tale of two states. Biochim. Biophys. Acta, 1808(6), 1581–1586. https://doi.org/https://doi.org/10.1016/j.bbamem.2011.02.001
- Yamamoto, E., Akimoto, T., Hirano, Y., Yasui, M., & Yasuoka, K. (2014). 1/ f Fluctuations of amino acids regulate water transportation in aquaporin 1 . Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 89(2), 022718https://doi.org/https://doi.org/10.1103/PhysRevE.89.022718
- Yang, B., & Verkman, A. S. (1997). Water and glycerol permeabilities of aquaporins 1-5 and MIP determined quantitatively by expression of epitope-tagged constructs in Xenopus oocytes . The Journal of Biological Chemistry, 272(26), 16140–16146. https://doi.org/https://doi.org/10.1074/jbc.272.26.16140
- Zhu, F., Tajkhorshid, E., & Schulten, K. (2004b). Collective diffusion model for water permeation through microscopic channels. Phys. Rev. Lett, 93(22), 224501https://doi.org/https://doi.org/10.1103/PhysRevLett.93.224501
- Zhu, F., Tajkhorshid, E., & Schulten, K. (2004a). Theory and simulation of water permeation in aquaporin-1. Biophysical Journal, 86(1 Pt 1), 50–57. https://doi.org/https://doi.org/10.1016/S0006-3495(04)74082-5