In silico study of human aquaporin AQP11 and AQP12 channels

Protein Science

Volumn 22, Issue 4, 2013, Pages 455-466

  Calvanese, Luisa ^a   Pellegrini Calace, Marialuisa ^b   Oliva, Romina ^a  

^a UNIVERSITY OF NAPLES PARTHENOPE   (Italy)

^b UNIVERSITY OF BARI   (Italy)

Author keywords

Aquaporins; Electrostatics; Molecular modeling; Pore analysis; Water transport

Indexed keywords

AQUAPORIN; AQUAPORIN 11; AQUAPORIN 12; CYSTEINE; UNCLASSIFIED DRUG;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; STATIC ELECTRICITY; WATER PERMEABILITY;

AMINO ACID SEQUENCE; AQUAPORINS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CYSTEINE; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; STATIC ELECTRICITY; WATER;

EID: 84878340752     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2227     Document Type: Article

References (42)

1. Zardoya R (2005) Phylogeny and evolution of the major intrinsic protein family. Biol Cell 97: 397-414. (Pubitemid 40872348)
2. Gomes D, Agasse A, Thiebaud P, Delrot S, Geros H, Chaumont F (2009) Aquaporins are multifunctional water and solute transporters highly divergent in living organisms. Biochim Biophys Acta 1788: 1213-1228.
3. Gonen T, Walz T (2006) The structure of aquaporins. Q Rev Biophys 39: 361-396. (Pubitemid 44950380)
4. 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. (Pubitemid 41111479)
5. Ishibashi K, Hara S, Kondo S (2009) Aquaporin water channels in mammals. Clin Exp Nephrol 13: 107-117.
6. Morishita Y, Sakube Y, Sasaki S, Ishibashi K (2004) Molecular mechanisms and drug development in aquaporin water channel diseases: aquaporin superfamily (superaquaporins): expansion of aquaporins restricted to multicellular organisms. J Pharmacol Sci 96: 276-279. (Pubitemid 40013335)
7. Yakata K, Hiroaki Y, Ishibashi K, Sohara E, Sasaki S, Mitsuoka K, Fujiyoshi Y (2007) Aquaporin-11 containing a divergent NPA motif has normal water channel activity. Biochim Biophys Acta 1768: 688-693. (Pubitemid 46290705)
8. Itoh T, Rai T, Kuwahara M, Ko SB, Uchida S, Sasaki S, Ishibashi K (2005) Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells. Biochem Biophys Res Commun 330: 832-838. (Pubitemid 40462161)
9. Ohta E, Itoh T, Nemoto T, Kumagai J, Ko SB, et al. (2009) Pancreas-specific aquaporin 12 null mice showed increased susceptibility to caerulein-induced acute pancreatitis. Am J Physiol Cell Physiol 297: C1368-1378.
10. Morishita Y, Matsuzaki T, Hara-chikuma M, Andoo A, Shimono M, et al. (2005) Disruption of aquaporin-11 produces polycystic kidneys following vacuolization of the proximal tubule. Mol Cell Biol 25: 7770-7779. (Pubitemid 41170137)
11. Gorelick DA, Praetorius J, Tsunenari T, Nielsen S, Agre P (2006) Aquaporin-11: a channel protein lacking apparent transport function expressed in brain. BMC Biochem 7: 14.
12. Magni F, Sarto C, Ticozzi D, Soldi M, Bosso N, Mocarelli P, Kienle MG (2006) Proteomic knowledge of human aquaporins. Proteomics 6: 5637-5649. (Pubitemid 44683227)
13. Yakata K, Tani K, Fujiyoshi Y (2011) Water permeability and characterization of aquaporin-11. J Struct Biol 174: 315-320.
14. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-W37.
15. Tchekneva EE, Khuchua Z, Davis LS, Kadkina V, Dunn SR, et al. (2008) Single amino acid substitution in aquaporin 11 causes renal failure. J Am Soc Nephrol 19: 1955-1964.
16. Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T (2005) Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438: 633-638. (Pubitemid 41740568)
17. Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M (2010) Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity. Proc Natl Acad Sci USA 107: 4135-4140.
18. Oliva R, Thornton JM, Pellegrini-Calace M (2009) PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins. Bioinformatics 25: 3183-3184.
19. Pellegrini-Calace M, Maiwald T, Thornton JM (2009) PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput Biol 5: e1000440.
20. Calvanese L, Pellegrini-Calace M, Oliva R (2010) Mutations at key pore-lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates. FEBS Lett 584: 4797-4801.
21. de Groot BL, Grubmuller H (2001) Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 294: 2353-2357. (Pubitemid 33140559)
22. Tajkhorshid E, Nollert P, Jensen MO, 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. (Pubitemid 34413590)
23. Mariani V, Kiefer F, Schmidt T, Haas J, Schwede T (2011) Assessment of template based protein structure predictions in CASP9. Proteins 79 Suppl 10: 37-58.
24. Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33: W244-W248. (Pubitemid 44529917)
25. Nugent T, Jones DT (2010) Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm. PLoS Comput Biol 6: e1000714.
26. Forrest LR, Tang CL, Honig B (2006) On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 91: 508-517.
27. Harries WE, Akhavan D, Miercke LJ, Khademi S, Stroud RM (2004) The channel architecture of aquaporin 0 at a 2.2-A resolution. Proc Natl Acad Sci USA 101: 14045-14050. (Pubitemid 39305027)
28. Sui H, Han BG, Lee JK, Walian P, Jap BK (2001) Structural basis of water-specific transport through the AQP1 water channel. Nature 414: 872-878. (Pubitemid 34024731)
29. 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. (Pubitemid 43122390)
30. Beitz E, Pavlovic-Djuranovic S, Yasui M, Agre P, Schultz JE (2004) Molecular dissection of water and glycerol permeability of the aquaglyceroporin from Plasmodium falciparum by mutational analysis. Proc Natl Acad Sci USA 101: 1153-1158. (Pubitemid 38182658)
31. Jensen MO, Dror RO, Xu H, Borhani DW, Arkin IT, Eastwood MP, Shaw DE (2008) 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: 14430-14435.
32. Qiu H, Ma S, Shen R, Guo W (2010) Dynamic and energetic mechanisms for the distinct permeation rate in AQP1 and AQP0. Biochim Biophys Acta 1798: 318-326.
33. Virkki LV, Cooper GJ, Boron WF (2001) Cloning and functional expression of an MIP (AQP0) homolog from killifish (Fundulus heteroclitus) lens. Am J Physiol Regul Integr Comp Physiol 281: R1994-R2003.
34. Ikeda M, Andoo A, Shimono M, Takamatsu N, Taki A, et al. (2011) The NPC motif of aquaporin-11, unlike the NPA motif of known aquaporins, is essential for full expression of molecular function. J Biol Chem 286: 3342-3350.
35. Newby ZER, O'Connell J, 3rd, Robles-Colmenares Y, Khademi S, Miercke LJ, Stroud RM (2008) Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum. Nat Struct Mol Biol 15: 619-625. (Pubitemid 351799138)
36. Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann JB, Engel A, Fujiyoshi Y (2000) Structural determinants of water permeation through aquaporin-1. Nature 407: 599-605.
37. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32: D115-D119. (Pubitemid 38081617)
38. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815. (Pubitemid 24007801)
39. Wallner B, Elofsson A (2006) Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 15: 900-913.
40. Benkert P, Kunzli M, Schwede T (2009) QMEAN server for protein model quality estimation. Nucleic Acids Res 37: W510-W514.
41. Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23: 205-211.
42. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98: 10037-10041. (Pubitemid 32802969)