Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations? (original) (raw)
Beitz E, Wu B, Holm LM, Schultz JE, Zeuthen T (2006) Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons. Proc Natl Acad Sci USA 103:269–274 ArticlePubMedCAS Google Scholar
Blank ME, Ehmke H (2003) Aquaporin-1 and HCO3(−)−Cl(−) transporter-mediated transport of CO2 across the human erythrocyte membrane. J Physiol 550:2:419–429 ArticlePubMedCAS Google Scholar
Borgnia MJ, Agre P (2001) Recontitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Eschericia coli. Proc Natl Acad Sci USA 98:2888–2893 ArticlePubMedCAS Google Scholar
Burykin A, Warshel A (2003) What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals. Biophys1 J 85:3696–3706 CAS Google Scholar
Burykin A, Warshel A (2004) On the origin of the electrostatic barrier for proton transport in aquaporin. FEBS Lett 570:41–46 ArticlePubMedCAS Google Scholar
Chakrabarti N, Roux B, Pomes R (2004a) Structural determinants of proton blockage in aquapor-ins. J Mol Biol 343:493–510 ArticleCAS Google Scholar
Chakrabarti N, Tajkhorshid E, Roux B, Pomes R (2004b) Molecular basis of proton blockage in aquaporins. Structure 12:65–74 ArticleCAS Google Scholar
Chen H, Wu Y, Voth GA (2006) Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel. Biophys J 90:L73–L75 ArticlePubMedCAS Google Scholar
Cooper GJ, Boron WF (1998) Effect of PCMBS on CO2 permeability of Xenopus oocytes expressing aquaporin 1 or its C189S mutant. Am J Physiol 275:C1481–C1486 PubMedCAS Google Scholar
de Groot BL, Grubmüller H (2001) Water permeation across biological membranes:mechanism and dynamics of aquaporin-1 and GlpF. Science 294:2353–2357 ArticlePubMed Google Scholar
de Groot BL, Grubmüller H (2005) The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr Opin Struct Biol 15:176–183 ArticlePubMedCAS Google Scholar
de Groot BL, Engel A, Grubmüller H (2001) A refined structure of human Aquaporin-1. FEBS Lett 504:206–211 ArticlePubMed Google Scholar
de Groot BL, Tieleman DP, Pohl P, Grubmüller H (2002) Water permeation through gramicidin A:desformylation and the double helix; a molecular dynamics study. Biophys J. 82:2934–2942 PubMed Google Scholar
de Groot BL, Frigato T, Helms V, Grubmüller H (2003) The mechanism of proton exclusion in the aquaporin-1 water channel. J Mol Biol 333:279–293 ArticlePubMedCAS Google Scholar
de Grotthuss CJT (1806) Sur la décomposition de l'eau et des corps qu'elle tient en dissolution à l'aide de l'électricité galvanique. Ann Chim LVIII:54–74 Google Scholar
Endeward V, Musa-Aziz R, Cooper GJ, Chen L-M, Pelletier MF, Virkki LV, Supuran CT, King LS, Boron WF, Gros G (2006) Evidence that aquaporin 1 is a major pathway for CO2 transport across the human erythrocyte membrane. FASEB J 20:1974–1981 ArticlePubMedCAS Google Scholar
Engel A, Stahlberg H (2002) Aquaglyceroporins: channel proteins with a conserved core, multiple functions and variable surfaces. Int. Rev. Cytol.215:75–104 ArticlePubMedCAS Google Scholar
Fang X, Yang B, Matthay MA, Verkman AS (2002) Evidence against aquaporin-1-dependent CO2 permeability in lung and kidney. J Physiol 542:63–69 ArticlePubMedCAS Google Scholar
Finkelstein A (1987) Water movement through lipid bilayers, pores, and plasma membranes. Wiley, New York Google Scholar
Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, Krucinski J, Stroud RM (2000) Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290:481–486 ArticlePubMedCAS Google Scholar
Gonen T, Sliz P, Kistler J, Cheng Y, Walz T (2004) Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429:193–197 ArticlePubMedCAS Google Scholar
Hashido M, Ikeguchi M, Kidera A (2005) Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF. FEBS Lett 579:5549–5552 ArticlePubMedCAS Google Scholar
Hashido M, Kidera A, Ikeguchi M (2007) Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations. Biophys J 93:373–385 ArticlePubMedCAS Google Scholar
Heller KB, Lin EC, Wilson TH (1980) Substrate-specificity and transport-properties of the glycerol facilitator of Eschericia coli. J Bacteriol 144:274–278 PubMedCAS Google Scholar
Hénin J, Tajkhorshid E, Schulten K, Chipot C (2008) Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys J 94:832–839 ArticlePubMedCAS Google Scholar
Heymann JB, Engel A (2000) Structural clues in the sequences of the aquaporins. J Mol Biol 295:1039–1053 ArticlePubMedCAS Google Scholar
Hiroaki Y, Tani K, Kamegawa A, Gyobu N, Nishikawa K, Suzuki H, Walz T, Sasaki S, Mitsuoka K, Kimura K, Mizoguchi A, Fujiyoshi Y (2006) Implications of the aquaporin-4 structure on array formation and cell adhesion. J Mol Biol 355:625–639 ArticleCAS Google Scholar
Holm LM, Jahn TP, Møller ALB, Schjoerring JK, Ferri D, Klaerke DA, Zeuthen T (2005) NH3 and NH4 + permeability in aquaporin-expressing Xenopus oocytes. Pflugers Arch 450:415–428 ArticlePubMedCAS Google Scholar
Hub JS, de Groot BL (2008) Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci USA 105:1198–1203 ArticlePubMedCAS Google Scholar
Ilan B, Tajkhorshid E, Schulten K, Voth GA (2004) The mechanism of proton exclusion in aqua-porin channels. Proteins 55:223–228 ArticlePubMedCAS Google Scholar
Jensen MØ, Mouritsen OG (2006) Single-channel water permeabilities of Escherichia coli aqua-porins AqpZ and GlpF. Biophys J 90:2270–2284 ArticlePubMedCAS Google Scholar
Jensen MØ, Tajkhorshid E, Schulten K (2001) The mechanism of glycerol conduction in aquaglyc-eroporins. Structure 9:1083–1093 ArticlePubMedCAS Google Scholar
Jensen MØ, Park S, Tajkhorshid E, Schulten K (2002) Energetics of glycerol conduction through aquaglyceroporin GlpF. Proc Natl Acad Sci USA 99:6731–6736 ArticlePubMedCAS Google Scholar
Jensen MØ, Tajkhorshid E, Schulten K (2003) Electrostatic tuning of permeation and selectivity in aquaporin water channels. Biophys J 85:2884–2899 ArticlePubMedCAS Google Scholar
Jung JS, Preston GM, Smith BL, Guggino WB, Agre P (1994) Molecular structure of the water channel through aquaporin CHIP — the hourglass model. J Biol Chem 269:14648–14654 PubMedCAS Google Scholar
Kato M, Pisliakov AV, Warshel A (2006) The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations. Proteins 64:829–844 ArticlePubMedCAS Google Scholar
Lee JK, Kozono D, Remis J, Kitagawa Y, Agre P, Stroud RM (2005) Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A. Proc Natl Acad Sci USA 102:18932–18937 ArticlePubMedCAS Google Scholar
Maurel C, Reizer J, Schroeder JI, Chrispeels MJ, Saier MH (1994) Functional characterization of the Eschericia coli glycerol facilitator, GlpF, in Xenopus oocytes. J Biol Chem 269: 11869–11872 PubMedCAS Google Scholar
Murata K, Mitsuoka K, Walz T, Agre P, Heymann JB, Engel A, Fujiyoshi Y (2000) Structural determinants of water permeation through aquaporin-1. Nature 407:599–605 ArticlePubMedCAS Google Scholar
Nakhoul NL, Davis BA, Romero MF, Boron WF (1998) Effect of expressing the water channel aquaporin-1 on the CO2 permeability of Xenopus oocytes. Am J Physiol Cell Physiol 274:C543–C548 CAS Google Scholar
Prasad GVR, Coury LA, Finn F, Zeidel ML (1998) Reconstituted aquaporin 1 water channels transport co2 across membranes. J Biol Chem 273:33123–33126 ArticlePubMedCAS Google Scholar
Preston GM, Carroll TP, Guggino WB, Agre P (1992) Appearance of water channels in Xenopus oocytes expressing red-cell CHIP28 protein. Science 256:385–387 ArticlePubMedCAS Google Scholar
Savage DF, Egea PF, Robles-Colmenares Y, O'Connell JDI, Stroud RM (2003) Architecture and selectivity in aquaporins:2.5Å X-ray structure of aquaporin Z. PLoS Biol. 1:e72 ArticlePubMed Google Scholar
Sui H, Han B-G, Lee JK, Walian P, Jap BK (2001) Structural basis of water-specific transport through the AQP1 water channel. Nature 414:872–878 ArticlePubMedCAS Google Scholar
Tajkhorshid E, Nollert P, Jensen MØ, Miercke LJW, O'Connell J, Stroud RM, Schulten K (2002) Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296:525–530 ArticlePubMedCAS Google Scholar
Törnroth-Horsefield S, Wang Y, Hedfalk K, Johanson U, Karlsson M, Tajkhorshid E, Neutze R, Kjellbom P (2006) Structural mechanism of plant aquaporin gating. Nature 439:688–694 ArticlePubMedCAS Google Scholar
Torrie GM, Valleau JP (1974) Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem Phys Lett 28:578–581 ArticleCAS Google Scholar
Uehlein N, Lovisolo C, Siefritz F, Kaldenhoff R (2003) The tobacco aquaporin NtAQP1 is a membrane CO2 pore with physiological functions. Nature 425:734–737 ArticlePubMedCAS Google Scholar
Wang Y, Schulten K, Tajkhorshid E (2005) What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF. Structure 13:1107–1118 ArticlePubMedCAS Google Scholar
Wang Y, Cohen J, Boron WF, Schulten K, Tajkhorshid E (2007) Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. J Struct Biol 157: 534–544 ArticlePubMedCAS Google Scholar
Yang B, Fukuda N, van Hoek A, Matthay MA, Ma T, Verkman AS (2000) Carbon dioxide permeability of aquaporin-1 measured in erythrocytes and lung of aquaporin-1 null mice and in reconstituted proteoliposomes. J Biol Chem 275:2686–2692 ArticlePubMedCAS Google Scholar
Zardoya R (2005) Phylogeny and evolution of the major intrinsic protein family. Biol Cell 97: 397–414 ArticlePubMedCAS Google Scholar
Zeidel ML, Ambudkar SV, Smith BL, Agre P (1992) Reconstitution of functional water channels in liposomes containing purified red-cell CHIP28 protein. Biochemistry 31:7436–7440 ArticlePubMedCAS Google Scholar
Zeidel ML, Nielsen S, Smith BL, Ambudkar SV, Maunsbach AB, Agre P (1994) Ultrastructure, pharmacological inhibition, and transport selectivity of aquaporin channel-forming integral protein in proteoliposomes. Biochemistry 33:1606–1615 ArticlePubMedCAS Google Scholar
Zhu F, Tajkhorshid E, Schulten K (2002) Pressure-induced water transport in membrane channels studied by molecular dynamics. Biophys J 83:154–160 PubMedCAS Google Scholar
Zhu F, Tajkhorshid E, Schulten K (2004a) Collective diffusion model for water permeation through microscopic channels. Phys Rev Lett 93:224501 ArticleCAS Google Scholar
Zhu F, Tajkhorshid E, Schulten K (2004b) Theory and simulation of water permeation in aquaporin-1. Biophys J 86:50–57 CAS Google Scholar