[1]
|
[1] Chen, K., Iribarren, P., Gong, W. and Wang, J.M. (2005) The essential role of phosphoinositide 3-kinases (PI3Ks) in regulating pro-inflammatory responses and the progression of cancer. Cellular & Molecular Immunology, 2, 241-252.
|
[2]
|
Shymanets, A., Ahmadian, M.R., Kossmeier, K.T., Wetzker, R., Harteneck, C. and Nurnberg, B. (2012) The p101 subunit of PI3Kgamma restores activation by Gbeta mutants deficient in stimulating p110gamma. The Journal of Biological Chemistry, 441, 851-858.
doi:10.1042/BJ20111664
|
[3]
|
Brock, C., Schaefer, M., Reusch, H.P., Czupalla, C., Michalke, M., Spicher, K., Schultz, G. and Nurnberg, B. (2003) Roles of G beta gamma in membrane recruitment and activation of p110 gamma/p101 phosphoinositide 3-kinase gamma. The Journal of Cell Biology, 160, 89-99.
doi:10.1083/jcb.200210115
|
[4]
|
Osaki, M., Oshimura, M. and Ito, H. (2004) PI3K-Akt pathway: Its functions and alterations in human cancer. Apoptosis, 9, 667-676.
doi:10.1023/B:APPT.0000045801.15585.dd
|
[5]
|
Zhao, L. and Vogt, P.K. (2008) Class I PI3K in oncogenic cellular transformation. Oncogene, 27, 5486-5496.
doi:10.1038/onc.2008.244
|
[6]
|
Vanhaesebroeck, B. and Alessi, D.R. (2000) The PI3K-PDK1 connection: More than just a road to PKB. The Journal of Biological Chemistry, 346, 561-576.
doi:10.1042/0264-6021:3460561
|
[7]
|
Walker, E.H., Perisic, O., Ried, C., Stephens, L. and Williams, R.L. (1999) Structural insights into phosphoinositide 3-kinase catalysis and signalling. Nature, 402, 313-320. doi:10.1038/46319
|
[8]
|
Voigt, P., Brock, C., Nurnberg, B. and Schaefer, M. (2005) Assigning functional domains within the p101 regulatory subunit of phosphoinositide 3-kinase gamma. The Journal of Biological Chemistry, 280, 5121-5127.
doi:10.1074/jbc.M413104200
|
[9]
|
Skorski, T., Bellacosa, A., Nieborowska-Skorska, M., Majewski, M., Martinez, R., Choi, J.K., Trotta, R., Wlodarski, P., Perrotti, D., Chan, T.O., et al (1997) Transformation of hematopoietic cells by BCR/ABL requires activation of a PI-3k/Akt-dependent pathway. EMBO Journal, 16, 6151-6161. doi:10.1093/emboj/16.20.6151
|
[10]
|
Benistant, C., Chapuis, H. and Roche, S. (2000) A specific function for phosphatidylinositol 3-kinase alpha (p85al-pha-p110alpha) in cell survival and for phosphatidylinositol 3-kinase beta (p85alpha-p110beta) in de novo DNA synthesis of human colon carcinoma cells. Oncogene, 19, 5083-5090. doi:10.1038/sj.onc.1203871
|
[11]
|
Knobbe, C.B., Trampe-Kieslich, A. and Reifenberger, G. (2005) Genetic alteration and expression of the phosphorinositol-3-kinase/Akt pathway genes PIK3CA and PIKE in human glioblastomas. Neuropathology and Applied Neurobiology, 31, 486-490.
doi:10.1111/j.1365-2990.2005.00660.x
|
[12]
|
Mizoguchi, M., Nutt, C.L., Mohapatra, G. and Louis, D.N. (2004) Genetic alterations of phosphoinositide 3-kinase subunit genes in human glioblastomas. Brain Pathology, 14, 372-377. doi:10.1111/j.1750-3639.2004.tb00080.x
|
[13]
|
Al Tassan, N., Khalil, D., Shinwari, J., Al Sharif, L., Bavi, P., Abduljaleel, Z., Abu Dhaim, N., Magrashi, A., Bobis, S., Ahmed, H., et al. (2012) A missense mutation in PIK3R5 gene in a family with ataxia and oculomotor apraxia. Human Mutation, 33, 351-354. doi:10.1002/humu.21650
|
[14]
|
Moreira, M.C., Klur, S., Watanabe, M., Nemeth, A.H., Le Ber, I., Moniz, J.C., Tranchant, C., Aubourg, P., Tazir, M., Schols, L., et al. (2004) Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2. Nature Genetics, 36, 225-227. doi:10.1038/ng1303
|
[15]
|
Amouri, R., Moreira, M.C., Zouari, M., El Euch, G., Barhoumi, C., Kefi, M., Belal, S., Koenig, M. and Hentati, F. (2004) Aprataxin gene mutations in Tunisian families. Neurology, 63, 928-929.
doi:10.1212/01.WNL.0000137044.06573.46
|
[16]
|
Fernet, M., Gribaa, M., Salih, M.A., Seidahmed, M.Z., Hall, J. and Koenig, M. (2005) Identification and functional consequences of a novel MRE11 mutation affecting 10 Saudi Arabian patients with the ataxia telangiectasia-like disorder. Human Molecular Genetics, 14, 307-318.
doi:10.1093/hmg/ddi027
|
[17]
|
Zhang, Z., Miteva, M.A., Wang, L. and Alexov, E. (2012) Analyzing effects of naturally occurring missense mutations. Computational and Mathematical Methods in Medicine, 2012, 805827. doi:10.1155/2012/805827
|
[18]
|
Roy, A., Kucukural, A. and Zhang, Y. (2010) I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5, 725-738.
doi:10.1038/nprot.2010.5
|
[19]
|
Zhang, Y. (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins: Structure, Function, and Bioinformatics, 69, 108-117.
doi:10.1002/prot.21702
|
[20]
|
Wu, S. and Zhang, Y. (2007) LOMETS: A local metathreading-server for protein structure prediction. Nucleic Acids Research, 35, 3375-3382. doi:10.1093/nar/gkm251
|
[21]
|
Sali, A. and Blundell, T.L. (1994) Comparative protein modelling by satisfaction of spatial restraints. Protein Structure by Distance Analysis, 64, C86.
doi:10.1006/jmbi.1993.1626
|
[22]
|
Tuncbag, N., Gursoy, A. and Keskin, O. (2009) Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics, 25, 1513-1520. doi:10.1093/bioinformatics/btp240
|
[23]
|
Pontius, J., Richelle, J. and Wodak, S.J. (1996) Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology, 264, 121-136. doi:10.1006/jmbi.1996.0628
|
[24]
|
Luthy, R., Bowie, J.U. and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85. doi:10.1038/356083a0
|
[25]
|
Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283-291.
doi:10.1107/S0021889892009944
|
[26]
|
Lovell, S.C., Davis, I.W., Arendall, W.B., de Bakker, P.I., Word, J.M., Prisant, M.G., Richardson, J.S. and Richardson, D.C. (2003) Structure validation by Calpha geometry: Phi,psi and Cbeta deviation. Proteins, 50, 437-450.
doi:10.1002/prot.10286
|
[27]
|
Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
doi:10.1002/elps.1150181505
|
[28]
|
Roger, S. and Milner-White, E.J. (1995) RasMol: Biomolecular graphics for all. Trends in Biochemical Sciences (TIBS), 20, 374. doi:10.1016/S0968-0004(00)89080-5
|
[29]
|
Ritchie, D.W. and Venkatraman, V. (2010) Ultra-fast FFT protein docking on graphics processors. Bioinformatics, 26, 2398-2405. doi:10.1093/bioinformatics/btq444
|
[30]
|
Dombkowski, A.A. (2003) Disulfide by DesignTM: A computational method for the rational design of disulfide bonds in proteins. Bioinformatics, 19, 1852-1853.
doi:10.1093/bioinformatics/btg231
|
[31]
|
Herbert, J.B. (2000) Recent changes to RasMol, recombining the variants. Trends in Biochemical Sciences, 25, pp. 453-455. doi:10.1016/S0968-0004(00)01606-6
|
[32]
|
Chen, V.B., Arendall 3rd, W.B., Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S. and Richardson, D.C. (2010) MolProbity: Allatom structure validation for macromolecular crystallography. Acta Crystallographica Section D: Biological Crystallography, 66, 12-21.
doi:10.1107/S0907444909042073
|
[33]
|
Chen, V.B., Davis, I.W. and Richardson, D.C. (2009) KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program. Protein Science, 18, 2403-2409. doi:10.1002/pro.250
|
[34]
|
Colovos, C. and Yeates, T.O. (1993) Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2, 1511-1519.
doi:10.1002/pro.5560020916
|
[35]
|
Olson, A.J. and Goodsell, D.S. (2007) A semiempirical free energy force field with charge-based desolvation. Journal of Computational Chemistry, 28, 1145-1152.
doi:10.1002/jcc.20634
|
[36]
|
Koukouritaki, S.B., Poch, M.T., Henderson, M.C., Siddens, L.K., Krueger, S.K., VanDyke, J.E., Williams, D.E., Pajewski, N.M., Wang, T. and Hines, R.N. (2007) Identification and functional analysis of common human flavincontaining monooxygenase 3 genetic variants. Journal of Pharmacology and Experimental Therapeutics, 320, 266-273. doi:10.1124/jpet.106.112268
|
[37]
|
Tang, K.E. and Dill, K.A. (1998) Native protein fluctuations: The conformational-motion temperature and the inverse correlation of protein flexibility with protein stability. Journal of Biomolecular Structure & Dynamics, 16, 397-411. doi:10.1080/07391102.1998.10508256
|
[38]
|
Board, P.G., Pierce, K. and Coggan, M. (1990) Expression of functional coagulation factor XIII in Escherichia coli. Journal of Thrombosis and Haemostasis, 63, 235-240.
|
[39]
|
Deber, C.M., Brodsky, B. and Rath, A. (2010) Proline residues in proteins. John Wiley & Sons Ltd., Chichester.
|
[40]
|
Williamson, M.P. (1994) The structure and function of proline-rich regions in proteins. Biochemical Journal, 297, 249-260.
|
[41]
|
Kini, R.M. and Evans, H.J. (1995) A hypothetical structural role for proline residues in the flanking segments of protein-protein interaction sites. Biochemical and Biophysical Research Communications, 212, 1115-1124.
doi:10.1006/bbrc.1995.2084
|
[42]
|
Kay, B.K., Williamson, M.P. and Sudol, M. (2000) The importance of being proline: The interaction of prolinerich motifs in signaling proteins with their cognate domains. The FASEB Journal, 14, 231-241.
|