Computational Analysis of the MembraneTargeting Domains of Plant-specific PRAF Proteins

Autor:	Wywial, Ewa, Shaneen M. Singh
Jazyk:	angličtina
Rok vydání:	2009
Předmět:	PRAF proteins homology modeling Arabidopsisthaliana
DOI:	10.5281/zenodo.1062154
Popis:	The PRAF family of proteins is a plant specific family of proteins with distinct domain architecture and various unique sequence/structure traits. We have carried out an extensive search of the Arabidopsis genome using an automated pipeline and manual methods to verify previously known and identify unknown instances of PRAF proteins, characterize their sequence and build 3D structures of their individual domains. Integrating the sequence, structure and whatever little known experimental details for each of these proteins and their domains, we present a comprehensive characterization of the different domains in these proteins and their variant properties. {"references":["G.C. Briggs, C.F. Mouchel, C.S. Hardtke, Plant Physiol, 140 (2006)\n1306.","C.F. Mouchel, G.C. Briggs, C.S. Hardtke, Genes Dev, 18 (2004) 700.","B. Heras, B.K. Drobak, J Exp Bot, 53 (2002) 565.","R.B. Jensen, T. La Cour, J. Albrethsen, M. Nielsen, K. Skriver, Biochem\nJ, 359 (2001) 165.","C.D. Knox, A.E. Belous, J.M. Pierce, A. Wakata, I.B. Nicoud, C.D.\nAnderson, C.W. Pinson, R.S. Chari, Am J Physiol Gastrointest Liver\nPhysiol, 287 (2004) G533.","P. Garcia, R. Gupta, S. Shah, A.J. Morris, S.A. Rudge, S. Scarlata, V.\nPetrova, S. McLaughlin, M.J. Rebecchi, Biochemistry, 34 (1995) 16228.","F.M. Flesch, J.W. Yu, M.A. Lemmon, K.N. Burger, Biochem J, 389\n(2005) 435.","M.A. Lemmon, K.M. Ferguson, R. O'Brien, P.B. Sigler, J. Schlessinger,\nProc Natl Acad Sci U S A, 92 (1995) 10472.","A. Hayakawa, S.J. Hayes, D.C. Lawe, E. Sudharshan, R. Tuft, K.\nFogarty, D. Lambright, S. Corvera, J Biol Chem, 279 (2004) 5958.\n[10] W. van Leeuwen, L. Okresz, L. Bogre, T. Munnik, Trends Plant Sci, 9\n(2004) 378.\n[11] B.K. Drobak, B. Heras, Trends Plant Sci, 7 (2002) 132.\n[12] M. Lemmon, Biochem Soc Trans. , 32 (2004) 707.\n[13] T. Gibson, M. Hyvonen, A. Musacchio, M. Saraste, E. Birney, Trends\nBiochem Sci. , 19 (1994) 349.\n[14] J.M. Kavran, D.E. Klein, A. Lee, M. Falasca, S.J. Isakoff, E.Y. Skolnik,\nM.A. Lemmon, J Biol Chem, 273 (1998) 30497.\n[15] M.A. Lemmon, K.M. Ferguson, Biochem J, 350 (2000) 1.\n[16] A. Musacchio, T. Gibson, P. Rice, J. Thompson, M. Saraste, Trends\nBiochem Sci. , 18 (1993) 343.\n[17] A. Petiot, J. Faure, H. Stenmark, J. Gruenberg, J. Cell Biol., 162 (2003)\n971.\n[18] A.E. Wurmser, J.D. Gary, S.D. Emr, J. Biol. Chem., 274 (1999) 9129.\n[19] A. Simonsen, R. Lippe, S. Christoforidis, J.M. Gaullier, A. Brech, J.\nCallaghan, B.H. Toh, C. Murphy, M. Zerial, H. Stenmark, Nature, 394\n(1998) 494.\n[20] W. Moore, C. Zhang, P.R. Clarke, Curr Biol, 12 (2002) 1442.\n[21] N. Mirkovic, Z. Li, A. Parnassa, D. Murray, Proteins, 66 (2006) 766.\n[22] H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H.\nWeissig, I.N. Shindyalov, P.E. Bourne, Nucleic Acids Res, 28 (2000)\n235.\n[23] H. Berman, K. Henrick, H. Nakamura, Nat Struct Biol, 10 (2003) 980.\n[24] M. Kanehisa, Novartis Found Symp, 247 (2002) 91.\n[25] M. Kanehisa, S. Goto, M. Hattori, K.F. Aoki-Kinoshita, M. Itoh, S.\nKawashima, T. Katayama, M. Araki, M. Hirakawa, Nucl. Acids Res., 34\n(2006) D354.\n[26] J. Schultz, R.R. Copley, T. Doerks, C.P. Ponting, P. Bork, Nucleic Acids\nRes, 28 (2000) 231.\n[27] J. Schultz, F. Milpetz, P. Bork, C.P. Ponting, PNAS, 95 (1998) 5857.\n[28] I. Letunic, R.R. Copley, B. Pils, S. Pinkert, J. Schultz, P. Bork, Nucleic\nAcids Res, 34 (2006) D257.\n[29] A. Bairoch, B. Boeckmann, Nucleic Acids Res, 22 (1994) 3578.\n[30] B. Boeckmann, M.C. Blatter, L. Famiglietti, U. Hinz, L. Lane, B.\nRoechert, A. Bairoch, C R Biol, 328 (2005) 882.\n[31] D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, D.L. Wheeler,\nNucleic Acids Res, 34 (2006) D16.\n[32] D.L. Wheeler, T. Barrett, D.A. Benson, S.H. Bryant, K. Canese, V.\nChetvernin, D.M. Church, M. DiCuccio, R. Edgar, S. Federhen, L.Y.\nGeer, W. Helmberg, Y. Kapustin, D.L. Kenton, O. Khovayko, D.J.\nLipman, T.L. Madden, D.R. Maglott, J. Ostell, K.D. Pruitt, G.D.\nSchuler, L.M. Schriml, E. Sequeira, S.T. Sherry, K. Sirotkin, A.\nSouvorov, G. Starchenko, T.O. Suzek, R. Tatusov, T.A. Tatusova, L.\nWagner, E. Yaschenko, Nucleic Acids Res, 34 (2006) D173.\n[33] R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, S.\nFerro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M.J. Martin, D.A.\nNatale, C. O'Donovan, N. Redaschi, L.S. Yeh, Nucleic Acids Res, 32\n(2004) D115.\n[34] A. Bairoch, R. Apweiler, C.H. Wu, W.C. Barker, B. Boeckmann, S.\nFerro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M.J. Martin, D.A.\nNatale, C. O'Donovan, N. Redaschi, L.S. Yeh, Nucleic Acids Res, 33\n(2005) D154.\n[35] C.H. Wu, R. Apweiler, A. Bairoch, D.A. Natale, W.C. Barker, B.\nBoeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane,\nM.J. Martin, R. Mazumder, C. O'Donovan, N. Redaschi, B. Suzek,\nNucleic Acids Res, 34 (2006) D187.\n[36] S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W.\nMiller, D.J. Lipman, Nucleic Acids Res, 25 (1997) 3389.\n[37] A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-\nJones, A. Khanna, M. Marshall, S. Moxon, E.L. Sonnhammer, D.J.\nStudholme, C. Yeats, S.R. Eddy, Nucleic Acids Res, 32 (2004) D138.\n[38] A. Marchler-Bauer, J.B. Anderson, P.F. Cherukuri, C. DeWeese-Scott,\nL.Y. Geer, M. Gwadz, S. He, D.I. Hurwitz, J.D. Jackson, Z. Ke, C.J.\nLanczycki, C.A. Liebert, C. Liu, F. Lu, G.H. Marchler, M. Mullokandov,\nB.A. Shoemaker, V. Simonyan, J.S. Song, P.A. Thiessen, R.A.\nYamashita, J.J. Yin, D. Zhang, S.H. Bryant, Nucleic Acids Res, 33\n(2005) D192.\n[39] A. Marchler-Bauer, J.B. Anderson, M.K. Derbyshire, C. DeWeese-Scott,\nN.R. Gonzales, M. Gwadz, L. Hao, S. He, D.I. Hurwitz, J.D. Jackson, Z.\nKe, D. Krylov, C.J. Lanczycki, C.A. Liebert, C. Liu, F. Lu, S. Lu, G.H.\nMarchler, M. Mullokandov, J.S. Song, N. Thanki, R.A. Yamashita, J.J.\nYin, D. Zhang, S.H. Bryant, Nucleic Acids Res, 35 (2007) D237.\n[40] A. Marchler-Bauer, J.B. Anderson, C. DeWeese-Scott, N.D. Fedorova,\nL.Y. Geer, S. He, D.I. Hurwitz, J.D. Jackson, A.R. Jacobs, C.J.\nLanczycki, C.A. Liebert, C. Liu, T. Madej, G.H. Marchler, R.\nMazumder, A.N. Nikolskaya, A.R. Panchenko, B.S. Rao, B.A.\nShoemaker, V. Simonyan, J.S. Song, P.A. Thiessen, S. Vasudevan, Y.\nWang, R.A. Yamashita, J.J. Yin, S.H. Bryant, Nucleic Acids Res, 31\n(2003) 383.\n[41] A. Marchler-Bauer, S.H. Bryant, Nucleic Acids Res, 32 (2004) W327.\n[42] A. Marchler-Bauer, A.R. Panchenko, B.A. Shoemaker, P.A. Thiessen,\nL.Y. Geer, S.H. Bryant, Nucleic Acids Res, 30 (2002) 281.\n[43] R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin,\nE.V. Koonin, D.M. Krylov, R. Mazumder, S.L. Mekhedov, A.N.\nNikolskaya, B.S. Rao, S. Smirnov, A.V. Sverdlov, S. Vasudevan, Y.I.\nWolf, J.J. Yin, D.A. Natale, BMC Bioinformatics, 4 (2003) 41.\n[44] R.L. Tatusov, E.V. Koonin, D.J. Lipman, Science, 278 (1997) 631.\n[45] J.A. Cuff, G.J. Barton, Proteins, 40 (2000) 502.\n[46] J.A. Cuff, G.J. Barton, Proteins, 34 (1999) 508.\n[47] J.A. Cuff, M.E. Clamp, A.S. Siddiqui, M. Finlay, G.J. Barton,\nBioinformatics, 14 (1998) 892.\n[48] K. Bryson, L.J. McGuffin, R.L. Marsden, J.J. Ward, J.S. Sodhi, D.T.\nJones, Nucleic Acids Res, 33 (2005) W36.\n[49] D.T. Jones, J Mol Biol, 292 (1999) 195.\n[50] L.J. McGuffin, K. Bryson, D.T. Jones, Bioinformatics, 16 (2000) 404.\n[51] B. Rost, Methods Enzymol, 266 (1996) 525.\n[52] M. Ouali, R.D. King, Protein Sci, 9 (2000) 1162.\n[53] K. Karplus, C. Barrett, R. Hughey, Bioinformatics, 14 (1998) 846.\n[54] K. Karplus, S. Katzman, G. Shackleford, M. Koeva, J. Draper, B.\nBarnes, M. Soriano, R. Hughey, Proteins, 61 Suppl 7 (2005) 135.\n[55] K. Karplus, B. Hu, Bioinformatics, 17 (2001) 713.\n[56] Y. Guermeur, PhD thesis (1997).\n[57] P. Baldi, S. Brunak, P. Frasconi, G. Soda, G. Pollastri, Bioinformatics,\n15 (1999) 937.\n[58] J. Cheng, A.Z. Randall, M.J. Sweredoski, P. Baldi, Nucleic Acids Res,\n33 (2005) W72.\n[59] C. Cole, J.D. Barber, G.J. Barton, Nucleic Acids Res, 36 (2008) W197.\n[60] O. Dor, Y. Zhou, Proteins, 66 (2007) 838.\n[61] B. Wallner, A. Elofsson, Protein Sci, 14 (2005) 1315.\n[62] D. Petrey, B. Honig, Mol Cell, 20 (2005) 811.\n[63] S.M. Singh, D. Murray, Protein Sci, 12 (2003) 1934.\n[64] Z. Xiang, C.S. Soto, B. Honig, Proc Natl Acad Sci U S A, 99 (2002)\n7432.\n[65] A.A. Canutescu, A.A. Shelenkov, R.L. Dunbrack, Jr., Protein Sci, 12\n(2003) 2001.\n[66] Z. Xiang, P.J. Steinbach, M.P. Jacobson, R.A. Friesner, B. Honig,\nProteins (2007).\n[67] Z. Xiang, B. Honig, J Mol Biol, 311 (2001) 421.\n[68] M.P. Jacobson, R.A. Friesner, Z. Xiang, B. Honig, J Mol Biol, 320\n(2002) 597.\n[69] J.L. Sussman, D. Lin, J. Jiang, N.O. Manning, J. Prilusky, O. Ritter, E.E.\nAbola, Acta Crystallogr D Biol Crystallogr, 54 (1998) 1078.\n[70] N.N. Alexandrov, R. Nussinov, R.M. Zimmer, Pac Symp Biocomput\n(1996) 53.\n[71] J. Shi, T.L. Blundell, K. Mizuguchi, J Mol Biol, 310 (2001) 243.\n[72] J. Meller, R. Elber, Proteins, 45 (2001) 241.\n[73] O. Teodorescu, T. Galor, J. Pillardy, R. Elber, Proteins, 54 (2004) 41.\n[74] D. Tobi, R. Elber, Proteins, 41 (2000) 40.\n[75] L.A. Kelley, R.M. MacCallum, M.J. Sternberg, J Mol Biol, 299 (2000)\n499.\n[76] S.F. Altschul, E.V. Koonin, Trends Biochem Sci, 23 (1998) 444.\n[77] A.A. Schaffer, L. Aravind, T.L. Madden, S. Shavirin, J.L. Spouge, Y.I.\nWolf, E.V. Koonin, S.F. Altschul, Nucleic Acids Res, 29 (2001) 2994.\n[78] A.A. Schaffer, Y.I. Wolf, C.P. Ponting, E.V. Koonin, L. Aravind, S.F.\nAltschul, Bioinformatics, 15 (1999) 1000.\n[79] P.A. Bates, L.A. Kelley, R.M. MacCallum, M.J. Sternberg, Proteins,\nSuppl 5 (2001) 39.\n[80] P.A. Bates, M.J. Sternberg, Proteins, Suppl 3 (1999) 47.\n[81] B. Contreras-Moreira, P.A. Bates, Bioinformatics, 18 (2002) 1141.\n[82] S.C.E. Tosatto, (Submitted).\n[83] S.C.E. Tosatto, Journal of Computational Biology, 12 (2005) 1316.\n[84] O. Lund, M. Nielsen, C. Lundegaard, P. Worning, Abstract at the\nCASP5 conference A102 (2002).\n[85] K. Nicholas, H. Nicholas, D. Deerfield, EMBNEW.NEWS, 14 (1997).\n[86] R. Bonneau, C.E. Strauss, C.A. Rohl, D. Chivian, P. Bradley, L. \nMalmstrom, T. Robertson, D. Baker, J Mol Biol, 322 (2002) 65. \n[87] R. Bonneau, J. Tsai, I. Ruczinski, D. Chivian, C. Rohl, C.E. Strauss, D. \nBaker, Proteins, Suppl 5 (2001) 119. \n[88] D. Chivian, D.E. Kim, L. Malmstrom, P. Bradley, T. Robertson, P. \nMurphy, C.E. Strauss, R. Bonneau, C.A. Rohl, D. Baker, Proteins, 53 \nSuppl 6 (2003) 524. \n[89] D. Chivian, D.E. Kim, L. Malmstrom, J. Schonbrun, C.A. Rohl, D. \nBaker, Proteins, 61 Suppl 7 (2005) 157. \n[90] D.E. Kim, D. Chivian, D. Baker, Nucl. Acids Res., 32 (2004) W526. \n[91] K.T. Simons, C. Kooperberg, E. Huang, D. Baker, J Mol Biol, 268 \n(1997) 209. \n[92] K.T. Simons, I. Ruczinski, C. Kooperberg, B.A. Fox, C. Bystroff, D. \nBaker, Proteins, 34 (1999) 82. \n[93] J. Moult, Curr Opin Struct Biol, 15 (2005) 285. \n[94] C. Sander, R. Schneider, Proteins, 9 (1991) 56. \n[95] M. Pellegrini-Calace, S. Soro, A. Tramontano, Febs J, 273 (2006) 2977. \n[96] A. Fiser, R.K. Do, A. Sali, Protein Sci, 9 (2000) 1753. \n[97] M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali, \nAnnu Rev Biophys Biomol Struct, 29 (2000) 291. \n[98] U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. \nStuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. \nGreenblatt, C.C. Huang, T.E. Ferrin, A. Sali, Nucleic Acids Res, 32 \n(2004) D217. \n[99] A. Sali, T.L. Blundell, J Mol Biol, 234 (1993) 779. \n[100]D. Petrey, Z. Xiang, C.L. Tang, L. Xie, M. Gimpelev, T. Mitros, C.S. \nSoto, S. Goldsmith-Fischman, A. Kernytsky, A. Schlessinger, I.Y. Koh, \nE. Alexov, B. Honig, Proteins, 53 Suppl 6 (2003) 430. \n[101]J.U. Bowie, R. Luthy, D. Eisenberg, Science, 253 (1991) 164. \n[102]D. Eisenberg, R. Luthy, J.U. Bowie, Methods Enzymol, 277 (1997) 396. \n[103]R. Luethy, J.U. Bowie, D. Eisenberg, Nature, 356 (1992) 83. \n[104]M.J. Sippl, J Comput Aided Mol Des, 7 (1993) 473. \n[105]A. Nicholls, K.A. Sharp, B. Honig, Proteins, 11 (1991) 281. \n[106]J.C. Gordon, J.B. Myers, T. Folta, V. Shoja, L.S. Heath, A. Onufriev, \nNucleic Acids Res, 33 (2005) W368. \n[107]J. Myers, G. Grothaus, S. Narayanan, A. Onufriev, Proteins, 63 (2006) \n928. \n[108]D. Bashford, M. Karplus, Biochemistry, 29 (1990) 10219. \n[109]S.G. Jackson, Y. Zhang, R.J. Haslam, M.S. Junop, BMC Struct Biol, 7 \n(2007) 80. \n[110]T.G. Kutateladze, Biochim Biophys Acta, 1761 (2006) 868. \n[111]E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. \nGreenblatt, E.C. Meng, T.E. Ferrin, J Comput Chem, 25 (2004) 1605. \n[112]I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge, T.E. Ferrin, J Mol \nBiol, 161 (1982) 269. \n[113]F.M. Richards, Annu Rev Biophys Bioeng, 6 (1977) 151. \n[114]T.E. Ferrin, C.C. Huang, L.E. Jarvis, R. Langridge, J. Mol. Graph., 6 \n(1988) 13. \n[115]B.K. Shoichet, D.L. Bodian, I.D. Kuntz, J. Comp. Chem., 13 (1992) 380. \n[116]E.C. Meng, B.K. Shoichet, I.D. Kuntz, J. Comp. Chem., 13 (1992) 505. \n[117]V. Sobolev, A. Sorokine, J. Prilusky, E.E. Abola, M. Edelman, \nBioinformatics, 15 (1999) 327. \n[118]R. Chenna, H. Sugawara, T. Koike, R. Lopez, T.J. Gibson, D.G. \nHiggins, J.D. Thompson, Nucleic Acids Res, 31 (2003) 3497. \n[119]K.M. Ferguson, M.A. Lemmon, J. Schlessinger, P.B. Sigler, Cell, 83 \n(1995) 1037. \n[120]A. Otomo, S. Hadano, T. Okada, H. Mizumura, R. Kunita, H. Nishijima, \nJ. Showguchi-Miyata, Y. Yanagisawa, E. Kohiki, E. Suga, M. Yasuda, \nH. Osuga, T. Nishimoto, S. Narumiya, J.E. Ikeda, Hum Mol Genet, 12 \n(2003) 1671. \n[121]J.L. Rosa, R.P. Casaroli-Marano, A.J. Buckler, S. Vilaro, M. Barbacid, \nEmbo J, 15 (1996) 4262. \n[122]L. Renault, N. Nassar, I. Vetter, J. Becker, C. Klebe, M. Roth, A. \nWittinghofer, Nature, 392 (1998) 97. \n[123]A. Rodrigues, J. Santiago, S. Rubio, A. Saez, K.S. Osmont, J. Gadea, \nC.S. Hardtke, P.L. Rodriguez, Plant Physiol., 149 (2009) 1917."]}
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cfde5024da053b67f1a6e15afa25ff80 Zobrazit plný text záznamu