Protein multifunctionality: Principles and mechanisms

Translational Oncogenomics

Volumn 2008, Issue 3, 2008, Pages 99-136

  Zaretsky, Joseph Z ^a   Wreschner, Daniel H ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Function; Multifunctionality; Protein; Structure

Indexed keywords

ABC TRANSPORTER; AMINO ACID TRANSFER RNA LIGASE; BACTERIAL TOXIN; CELL SURFACE RECEPTOR; CHEMOKINE; CHEMOKINE RECEPTOR CXCR1; CHEMOKINE RECEPTOR CXCR2; CHOLINESTERASE; CYTOKINE; FIBROBLAST GROWTH FACTOR; GLUCAN SYNTHASE; GRANULOCYTE COLONY STIMULATING FACTOR; GRANZYME B; GROWTH FACTOR; GROWTH HORMONE; LACTOFERRIN; LOW DENSITY LIPOPROTEIN; MUCIN 1; PROTEASOME; PROTEIN KINASE; PROTEINASE; PROTEOME; TRANSCRIPTION FACTOR; TRANSCRIPTOME; VEGETABLE PROTEIN;

5' UNTRANSLATED REGION; DEGLYCOSYLATION; FUNCTIONAL PROTEOMICS; GENE ACTIVITY; GENE DUPLICATION; GENE MUTATION; GENOME; HUMAN; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; OPEN READING FRAME; PALMITOYLATION; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN GLYCOSYLATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; REVIEW; RIBOSOMAL FRAMESHIFTING; RIBOSOME; STOP CODON; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; TRANSCRIPTION INITIATION;

EID: 74849112945     PISSN: None     EISSN: 11772727     Source Type: Journal    
DOI: None     Document Type: Review

References (382)

1. Acconcia, F., Ascenzi, P., Bocedi, A., Spisni, E., Tomasi, V., Trentalance, A., Visca, P. and Marino, M. 2005. Palmitoylation-dependent estrogen receptor alpha membrane localization: regulation by 17beta-estradiol. Mol. Biol. Cell., 16:231-7.
2. Adamski, F.M., Donly, B.C. and Tate, W.P. 1993. Competition between frameshifting, termination and suppression at the frameshift site in the Escherichia coli release factor-2 mRNA. Nucleic Acids Res., 21:5074-8
3. Agrawal, A., Lingappa, J., Leppla, S.H., Agrawal, S., Jabbar, A., Quinn, C. and Pulendran, B. 2003. Impairment of dendritic cells and adaptive immunity by anthrax lethal toxin. Nature, 424:329-34.
4. Ahmad, I., Hoessli, D.C., Gupta, R., Walker-Nasir, E., Rafik, S.M., Choudhary, M.I. and Shakoori, A.R. 2007. In silico determination of intracellular glycosylation and phosphorylation sites in human selectins: implications for biological function. J. Cell Biochem., 100:1558-72.
5. Allen, S.H., Bennett, J.A., Mizejewski, G.J., Andersen, T.T., Ferraris, S. and Jacobson, H.I. 1993. Puri cation of alpha-fetoprotein from human cord serum with demonstration of its antiestrogenic activity. Biochim. Biophys. Acta., 1202:135-42.
6. Altschuler, Y., Kinlough, C.L., Poland, P.A., Bruns, J.B., Apodaca, G., Weisz, O.A. and Hughey, R.P. 2000. Clathrin-mediated endocytosis of MUC1 is modulated by its glycosylation state. Mol. Biol. Cell., 11:819-31.
7. Anfinsen, C.B. 1973. Principles that govern the folding of protein chains. Science. 181:223-30.
8. Aoyagi, Y., Ikenaka, T. and Ichida, F. 1979. alpha-Fetoprotein as a carrier protein in plasma and its bilirubin-binding ability. Cancer Res., 39:3571-4.
9. Apic, G., Huber, W. and Teichmann, S.A. 2003. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J. Struct. Funct. Genomics. 4:67-78.
10. Arai, R., Wriggers, W., Nishikawa, Y., Nagamune, T. and Fujisawa, T. 2004. Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering. Proteins, 57:829-38.
11. Atkins, J.F., Baranov, P.V., Fayet, O. Herr, A.J., Howard, M.T., Ivanov, I.P., Matsufuji, S., Miller, W.A., Moore, B., Prere, M.F., Wills, N.M., Zhou, J. and Gesteland, R.F. 2001. Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression. Cold Spring Harb Symp. Quant. Biol., 66:217-32.
12. Aussel, C. and Negrel, R. 1986. Effect of alpha-fetoprotein on arachidonic acid metabolism in the preadipocyte cell line OB. 17. Prostaglandins Leukot. Med., 21:69-76.
13. Baird, S.D., Turcotte, M., Korneluk, R.G. and Holcik, M. 2006. Searching for IRES. Rna., 12:1755-85.
14. Balbach, JAS. and FX,. 2000. In Mechanisms of protein folding (R. Pain, Ed.), pp. 212-249, IRL Press, Oxford.
15. Balzi, E. and Goffeau, A. 1994. Genetics and biochemistry of yeast multidrug resistance. Biochem. Biophys. Acta., 1187:152-62
16. Barbato, G., Ikura, M., Kay, L.E., Pastor, R.W. and Bax, A. 1992. Backbone dynamics of calmodulin studied by 15N. relaxation using inverse detected two-dimensional NMR. spectroscopy: the central helix is exible. Biochemistry, 31:5269-78.
17. Barbieri, J.T. and Sun, J. 2004. Pseudomonas aeruginosa ExoS and ExoT. Rev. Physiol. Biochem. Pharmacol., 152:79-92
18. Baruch, A., Hartmann, M., Yoeli, M., Adereth, Y., Greenstein, S., Stadler, Y., Skornik, Y., Zaretsky, J., Smorodinsky, N.I., Keydar, I. and Wreschner, D H. 1999. The breast cancer-associated MUCI gene generates both a receptor and its cognate binding protein. Cancer Res., 59:1552-61.
19. Baruch, A., Hartmann, M., Zrihan-Licht, S., Greenstein, S., Burstein, M., Keydar, I., Weiss, M., Smorodinsky, N. and Wreschner, D.H. 1997. Preferential expression of novel MUCI tumor antigen isoforms in human epithelial tumors and their tumor-potentiating function. Int. J. Cancer. 71:741-9.
20. Basu, S., Binder, R.J., Ramalingam, T. and Srivastava, P.K. 2001. CD91 is a common receptor for heat shock proteins gp96, hsp90, hsp70, and calreticulin. Immunity, 14:303-13
21. Baveye, S., Elass, E., Niazurier, J., Spik, G. and Legrand, D. 1999. Lactoferrin: a multifunctional glycoprotein involved in the modulation of the in ammatory process. Clin. Chem. Lab. Med., 37:281-6.
22. Behm-Ansmant, I., Kashima, I., Rehwinkel, J., Sauliere, J., Wittkopp, N. and Izaurralde, E. 2007. mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons. FEBS Lett, 581:2845-53.
23. Bell, J.K., Goetz, D.H., Mahrus, S., Harris, J.L., Fletterick, R.J. and Craik, C.S. 2003. The oligomeric structure of human granzyme A is a determinant of its extended substrate speci city. Nat. Struct. Biol., 10:527-34.
24. Berry, M.J., Banu, L., Chen, Y.Y., Mandel, S.J., Kieffer, J.D., Harney, J.W. and Larsen, P.R. 1991a. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3' untranslated region. Nature, 353:273-6.
25. Berry, M.J., Banu, L. and Larsen, P.R. 1991b. Type I iodothyronine deiodinase is a selenocysteine-containing enzyme. Nature, 349:438-40.
26. Bijlmakers, M.J. and Marsh, M. 2003. The on-off story of protein palmitoylation. Trends Cell Biol., 13:32-42.
27. Birkenmeier, G., Usbeck, E., Saro, L. and Kopperschlager, G. 1983. Triazine dye binding of human alpha-fetoprotein and albumin. J. Chromatogr., 265:27-35.
28. Black, D.L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem., 72:291-336
29. Bloom, J.W., Madanai, M.S. and Ray, M.K. 1996. Cell. line and site speci c comparative analysis of the N.-linked oligosaccharides on human ICAM-1des454-532 by electrospray ionization mass spectrometry. Biochemistry, 35:1856-64.
30. Bohlen, P. 1989. Fibroblast growth factor. In Macrophage-derived cell regulatory factors. Cytokines (C. Sorg, Ed.), Karger, Basel.
31. Bonetti, B., Fu, L., Moon, J. and Bedwell, D.M. 1995. The efciency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol., 251:334-45.
32. Bork, P. Schultz, J. and Ponting. C.P. 1997. Cytoplasmic signalling domains: the next generation. Trends Biochem. Sci., 22:296-8.
33. Brierley, I. and Pennell, S. 2001. Structure and function of the stimulatory RNAs involved in programmed eukaryotic-1 ribosomal frameshifting. Cold Spring Harb Symp. Quant. Biol., 66:233-48.
34. Brock, J.H. 2002. The physiology of lactoferrin. Biochem. Cell Biol., 80:1-6.
35. Bukau, B. and Horwich, A.L. 1998. The Hsp70 and Hsp60 chaperone machines. Celi., 92:351-66.
36. Burk, R.F., Hill, K.E., Awad, J.A., Morrow, J.D., Kato, T., Cockell, K-A. and Lyons PR. 1995. Pathogenesis of diquat-induced liver necrosis in selenium-de cient rats: assessment of the roles of lipid peroxidation and selenoprotein P. Hepatology, 21: 561-9
37. Buzza, M.S. Zamurs, L., Sun, J., Bird, C.H., Smith, A I., Trapani, J.A., Froelich, C.J., Nice, E.C. and Bird, P.I. 2005. Extracellular matrix remodeling by human granzyme B. via cleavage of vitronectin, bronectin, and lammin. J. Biol. Chem., 280:23549-58
38. Cai, J., Huang, Y., Li, F. and Li, Y. 2006. Alteration of protein subcellular location and domain formation by alternative translational initiation. Proteins. 62.793-9
39. Cai, X. 2007. Molecular evolution and structural analysis of the Ca(2+) release-activated Ca(2+) channel subunit, Orai. J. Mol. Biol., 388: 128-91.
40. Candejas, M.M., Powell, D.J., Roubalova, E., Apcher, S., Bourougaa, K., Vojtesek, B., Bruzzoni-Giovanelli, H. and Fahraeus, R. 2006. Expression of p53 and p53/47 are controlled by alternative mechanisms of messenger RNA translation initiation. Oncogene., 25:6936-17
41. Carrington, D.M., Auffret, A. and Hanke, D.E. 1985. Polypeptide ligation occurs during post-translational modi cation of concanavalin A. Nature, 313:64-7
42. Casey, P.J. and Seabra, M.C. 1996. Protein prenyltransferases. J. Biol. Chem., 271:5289-92.
43. Cesareni, G. 2004. Modular Protein Domains, (Wiley-Verlag).
44. Chen, A., Kao, Y.F. and Brown, C. M. 2005a. Translation of the rst upstream ORF in the hepatitis B. virus pregenomic RNA modulates translation at the core and polymerase initiation codons. Nucleic Acids Res., 33:1169-81.
45. Chen, P. Y., Lin, C C., Chang, Y.T., Lin, S.C. and Chan, S.I. 2002. One O-linked sugar can affect the coil-to-beta structural transition of the prion peptide. Proc. Natl. Acad. Sci. U.S.A., 99:12633-8.
46. Chen, Y.T., Collins, L.L., Uno, H. and Chang, C. 2005b. Deficits in motor coordination with aberrant cerebellar development in mice lacking testicular orphan nuclear receptor 4. Mol. Cell Biol., 25:2722-32.
47. Cheng, X., Cole, R.N,, Zaia, J. and Hart, G.W. 2000 Alternative O-glycosylation/O-phosphorylation of the murine estrogen receptor beta. Biochemistry, 39: 11609-20.
48. Cheng, X. and Hart, G.W. 2001. Alternative O-glycosylation/ O-phosphorylation of serine-16 in murine estrogen receptor beta: post-translational regulation of turnover and transactivation activity. J. Biol. Chem., 276: 10570-5.
49. Cheung, W.Y. 1970. Cyclic 3', 5'- nucleotide phosphodiesterase. Demonstration of an activator. Biochem. Biophys. Res. Commun., 38:533-8.
50. Chittum, H.S., Himeno, S., Hill, K.E. and Burk, R.F. 1996. Multiple forms of selenoprotein P in rat plasma. Arch. Biochem. Biophys., 325:124-8.
51. Chong, S., Williams., K.S., Wotkowicz, C. and Xu, M.Q. 1998. Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein. J. Biol. Chem., 273:10567-77.
52. Chou, C.F. and Omary, M.B. 1994. Mitotic arrest with anti-microtubule agents or okadaic acid is associated with increased glycoprotein terminal GlcNAc's. J. Cell Sci., 107(Pt 7): 1833-43.
53. Chou, T.Y., Dang, C.V. and Hart, G.W. 1995a. Glycosylation of the c-Myc transactivation domain. Proc. Natl. Acad. Sci. U.S.A., 92:4417-21.
54. Chou, T.Y., Hart, G.W. and Dang, C.V. 1995b. c-Myc is glycosylated at threonine 58, a known phosphorylation site and a mutational hot spot in lymphomas. J. Biol. Chem., 270:18961-5.
55. Clerico, A., Del Ry, S. and Giannessi, D. 2000. Measurement of cardiac natriuretic hormones (atrial natriuretic peptide, brain natriuretic peptide, and related peptides) in clinical practice: the need for a new generation of immunoassay methods. Clin. Chem., 46: 1529-34.
56. Cocquerel, L., Duvet, S., Meunier, J.C., Pillez, A., Cacan, R., Wychowski, C. and Dubuisson, J. 1999. The transmembrane domain of hepatitis C virus glycoprotein E1 is a signal for static retention in the endoplasmic reticulum. J. Virol., 73:2641-9.
57. Cocquerel, L., Meunier, J.C., Pillez, A., Wychowski, C. and Dubuisson, J. 1998. A retention signal necessary and suf cient for endoplasmic reticulum localization maps to the transmembrane domain of hepatitis C virus glycoprotein E2. J. Virol., 72 2183-91.
58. Cocquerel, L., Op de Beeck, A., Lambot, M., Roussel, J., Delgrange, D., Pillez, A., Wychowski, C., Penin, F. and Dubuisson, J. 2002. Topological changes in the transmembrane domains of heptitis C virus envelope glycoproteins. Embo. J., 21:2893-902.
59. Cocquerel, L., Wychowski, C., Minner, F., Penin, F. and Dubuisson, J. 2000. Charged residues in the transmembrane domains of hepatitis C virus glycoproteins play a major role in the processing, subcellular localization, and assembly of these envelope proteins J. Virol., 74:3623-33.
60. Cohen, P., Burchell, A., Foulkes, J.G. and Cohen, P.T. 1978. Identi cation of the Ca2+-dependent modulator protiens as the fourth subunit of rabbit skeletal muscle phosphorylase kinase. FEBS Lett., 92:287-93.
61. Collins, L.L., Lee, Y.F., Heinlein, C.A., Liu, N.C., Chen, Y.T., Shyr, C.R., Meshul, C.K., Uno, H., Platt, K.A. and Chang, C. 2004. Growth retardation and abnormal maternal behavior in mice lacking testicular orphan nuclear receptor 4. Proc. Natl. Acad. Sci. U.S.A., 101:15058-63
62. Comer, F.I. and Hart, G.W. 2000. O-Glycosylation of nuclear and cytosolic proteins. Dynamic interplay between O-GlcNAc and O-phosphate J. Biol. Chem., 275:29179-82
63. Cote, F., Boisvert, F.M., Grondin, B., Bazinet, M., Goodyer, C.G., Bazett-Jones, D,P. and Aubry, M. 2001. Alternative promoter usage and splicing of ZNF74 multi nger gene produce protein isoforms with a different repressor activitv and nuclear partitioning. DNA Cell Biol., 20:159-73.
64. Cover, T.L. and Blanke, S.R. 2005. Helicobacter pylori VacA, a paradigm for toxin multifunctionality. Nat. Rev. Microbiol., 3:320-32.
65. Coyle, J.E., Jaeger, J., Gross, M., Robinson, C.V. and Radford, S.E. 1997. Structural and mechanistic consequences of polypeptide binding by GroEL. Fold Des., 2:R.93-104.
66. Creighton, T. 2002. In Mechanisms of protein folding (R. Pain, Ed.), pp. 250-278 IRL Press, Oxford.
67. Cridge, A.G., Major, L.L., Mahagaonkar, A.A., Poole, E.S., Isaksson, L.A. and Tate, W.P. 2006. Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms. Nucleic Acids Res., 34:1959-73.
68. Datta, B., Ray, M.K., Chakrabarti, D., Wylie, D.E. and Gupta, N.K. 1989. Glycosylation of eukaryotic peptide chain initiation factor 2 (eIF-2)-associated 67-kDa polypeptide (p67) and its possible role in the inhibition of eIF-2 kinase-catalyzed phosphorylation of the eIF-2 alpha-subunit. J. Biol. Chem., 264 20620-4
69. Dauphinee, M.J. and Mizejewski, G.J. 2002. Human alpha-fetoprotein contains potential heterodimerization motifs capable of interaction with nuclear receptors and transcription/growth factors. Med. Hypotheses., 58:453-61.
70. David, R., Richter, M.P. and Beck-Sickinger, A.G. 2004. Expressed protein ligation. Method and applications. Eur. J. Biochem., 271:663-77.
71. De Palo, E.F., Gatti, R., Antonelli, G. and Spinella, P. 2006. Growth hormone isoforms, segments/fragments: does a link exist with multifunctionality? Clin. Chim. Acta., 364:77-81.
72. de Souza, S.J., Camargo, A.A., Briones, M.R., Costa, F.F., Nagai M.A., Verjovski-Almeida, S., Zago, M.A., Andrade, L.E., Carrer, H., El-Dorry H.F., Esprea co,E.M., Habr-Gama, A., Giannella-Neto, D., Goldman, G.H., Gruber, A., Hackel, C., Kimura, E.T., Maciel, R.M., Marie, S.K., Martins, E.A., Nobrega, M.P., Paco-Larson, M.L., Pardini, M.I., Pereira, G.G., Pesquero. J.B., Rodrigues, V., Rogatto, S.R, da Silva, I.D., Sogayar, M.C., de Fatima Sonati, M., Tajara, E.H., Valentini, S.R., Acencio, M., Alberto, F.L., Amaral, M.E., Aneas, I., Bengtson, M.H., Carraro, D.M., Carvalho, A.F., Carvalho, L.H., Ceruti, J.M., Correa, M.L., Costa, M.C., Curcio, C., Gushiken, T., Ho, P.L., Kimura, E., Leite, L.C., Maia, G., Majumder, P., Marins, M., Matsukuma, A., Melo, A.S., Mestriner, C.A., Miracca, E.C., Miranda, D.C., Nascimento, A.N., Nobrega, F.G., Ojopi, E.P., Pandol, J.R., Pessoa, L.G., Rahal, P., Rainho, C.A., da Ros, N. de Sa, R.G., Sales, M.M., da Silva N.P., Silva, T.C., da Silva, WJr., Simao, D.F., Sousa, J.F., Stecconi, D., Tsukumo, F., Valente, V., Zalcbeg, H., Brentani, R.R., Reis, F.L., Dias-Neto, E. and Simpson, A.J. 2000 Identi cation of human chromosome 22 transcribed sequences with ORF expressed sequence tags. Proc. Natl. Acad Sci. U.S.A., 97:12690-3.
73. De Vit, M.J., Waddle, J.A. and Johnston, M. 1997 Regulated nuclear translocation of the Migl glucose repressor. Mol. Biol. Cell., 8:1603-18.
74. Dias Neto, E., Correa, R.G., Verjovski-Almeida, S., Briones, M.R., Nagai, M.A., da Silva, WJr., Zago, M.A., Bordin, S., Costa, F.F., Goldman, G.H., Carvalho, A.F., Matsukuma, A., Baia, G.S., Simpson, D.H., Brunstein, A., de Oliveira, P.S., Bitcher, P., Jongencel, C.V., O'Hare, M.J., Soares, F., Brentani, R.R., Reis, L.F., de Souza, S.J. and Simpson, A.J. 2000. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc. Natl. Acad. Sci, U.S.A., 97:3491-6.
75. Dobson, C.M. 1990. Protein conformation. Hinge-bending and folding. Nature, 348:198-9.
76. Dobson, C.M and Karplus, M. 1999. The fundamentals of protein folding: bringing together theory and experiment. Curr. Opin. Struct. Biol., 9:92-101.
77. Dong, D.L. and Hart, G.W. 1994 Puri cation and characterization of an O-GlcNAc selective N.acetyl-beta-D-glucosaminidase from rat spleen cytosol. J. Biol. Chem. 269:19321-30.
78. Doronina, V.A., and Brown, J.D. 2006. [Non-canonical decoding events at stop codons in eukaryotes]. Mol. Biol. (Mosk), 40:731-41.
79. Draper, J.M., Xia, Z. and Smith, C.D. 2007. Cellular palmitoylation and traf cking of lipidated peptides. J. Lipid Res., 48:1873-84.
80. Du, X.L., Edelstein, D., Rossetti, L., Fantus, I.G., Goldberg, H., Ziyadeh, F., Wu, J. and Brownlee, M. 2000. Hyperglycemia-induced mitochondrial superoxide overproduction activates the hexosamine pathway and induces plasminogen activator inhibitor-1 expression by increasing Sp1 glycosylation. Proc. Natl. Acad. Sci. U.S.A., 97:12222-6.
81. Dunphy, J.T. and Linder, M.E. 1998. Signalling functions of protein palmitoylation. Biochim. Biophys. Acta 1436:245-61.
82. Eisenstein, R.S. 2000. Iron regulatory proteins and the molecular control of mammalian iron metabolism. Annu. Rev. Nutr., 20:627-62.
83. el-Husseini Ael, D. and Bredt, D.S. 2002. Protein palmitoylation: a regulator of neuronal development and function. Nat. Rev. Neurosci., 3:791-802.
84. Elass-Rochard, E., Roseanu, A., Legrand, D., Trif, M., Salmon, V., Motas, C., Montreuil, J. and Spik, G. 1995. Lactoferrin-lipopolysaccharide interaction involvement of the 28-34 loop region of human lactoferrin in the high-af nity binding to Escherichia coli 055B5 lipoposaccharide. Biochem. J., 312 (Pt.3):839-45.
85. Ellis, R.J. and Hartl, F.U. 1996. Protein folding in the cell: competing models of chaperonin function. Faseb J., 10:20-6.
86. Evans, T.C Jr, Benner, J. and Xu, M.Q. 1999. The in vitro ligation of bacterially expressed proteins using an intein from Methanobacterium thermoautotrophicum. J. Biol. Chem., 274:3923-6.
87. Evans, T.J.T. and Xu, M.Q. 2002. Mechanistic and kinetic considerations of protein splicing. Chem. Rev., 102:4869-84
88. Fearon, K., McClendon, V., Bonetti, B. and Bedwell, D.M. 1994. Premature translation termination mutations are effeciently suppressed in a highly conserved region of yeast Ste6p, a member of the ATP-binding cassette (ABC) transporter family. J. Biol. Chem., 269:17802-8.
89. Fewell, S.W., Travers, K.J., Weissman, J.S. and Brodsky, J.L. 2001. The action of moleculare chaperones in the early secretory pathway. Annu. Rev. Genet. 35:149-91.
90. Filippou, P.S., Lioliou, E.E., Panagiotidis, C.A.. Athanassopoulos, C. M., Garnelis, T., Papaioannou. D. and Kyriakidis, D.A. 2007. Effect of polyamines and synthetic polyamine-analogues on the expression of antizyme (AtoC) and its regulatory genes. BMC Biochem., 8:1.
91. Finol-Urdaneta, R.K., Struver, N. and Terlau, H. 2006. Molecular and Functional Differences between Heart niKv1.7 Channel Isoforms. J. Gen. Physiol., 128: 133-45.
92. Frand, A.R., Cuozzo, J.W. and Kaiser, C.A. 2000. Pathways for protein disulphide bond formation. Trends Cell Biol., 10:203-10.
93. Friedlander, A.M. 1986. Macrophages; are sensitive to anthrax lethal toxin through an acid-dependent process. J. Biol. Chem., 261:7123-6.
94. Frischmeyer, P.A. and Dietz, H.C. 1999. Nonsense-mediated mRNA decay in health and disease. Hum. Mol. Genet. 8:1893-900.
95. Gandre, S.. Bercovich, Z. and Kahana, C. 2003. Mitochondrial localization of antizyme is determined by context-dependent alternative utilization of two AUG initiation codons. Mitochondrion. 2:245-56.
96. Gasdaska. P.Y., Gasdaska, J.R., Cochran, S, and Powis, G. 1995. Cloning and sequencing of a human thioredoxin reductase. FEBS Lett, 373:5-9.
97. Gesteland, R.F. and Atkins, J.F. 1996 Recoding: dynamic reprogramming of translation. Annu. Rev. Biochem., 65:
98. Gesteland. R. F., Weiss, R.B. and Atkins, J.F. 11392. Recoding: reprogrammed genetic decoding. Science, 257:1640-1.
99. Ghosh, L, Sun, L, and Xu, M.Q. 2001 Zinc inhibition of protein trans-splicing and identification of regions essential for splicing and association of a split intein* J. Biol. Chem., 276:24051-8
100. Gliemann, J. 1998, Receptors of the low density lipoprotein (LDL) receptor family in man. Multiple functions of the large family members via interaction with complex ligands. Biol. Chem., 379:951-64.
101. Goehrung, U.M., Schmidt, G., Pederson, K.J., Aktories, K. and Barbieri, J.T. 1999, The N-terminal domain of Pseudomonas aeruginosa exoenzyme S is a GTPase-activating protein for Rho GTPases. J. Biol. Chem., 274:36369-72
102. Gokdale, R.S. and Khosla, C. 2000. Role of linkers in communication between protein modules. Curr. Opin. Chem. Biol., 4:22-7.
103. Goldstein, J. 2001. Familial hypercholesteremia. In Metabolic and Molecular Bases of Inherited Disease (C. Server, Ed.), pp. 2863-2913, McGraw-Hill.
104. Gopinath, R.M. and Vincenzi, F.F. 1977. Phosphodiesterase protein activator mimics red blood cell cytoplasmic activator of(Ca2+Mg2+) ATPase. Biochem. Biophys. Res. Commun., 71:1203-9.
105. Goto, C., Osaka, T. and Mizutani, T. 2001. A model for Sec incorporation with the regions. upstream of the UGA Sec codon to play a key role. Biofactors, 14:25-35
106. Gottesman, M.M. and Pastan, I. 1993. Biochemistry of multidrug resistance mediated by the multidrug transporter. Annu. Rev. Biochem., 62:385-427.
107. Gotthardt, M., Trommsdorff, M., Nevitt, M.F., Shellon, J., Richardson, J.A., Studkinger, W., Nimpf, J. and Herz, J. 2000. Interactions of the low density lipoprotein receptor gene family with cytosolic adaptor and scaffold prateins suggest diverse biological functions in cellular communication and signal transduction. J. Biol. Chem., 275:25616-24.
108. Graveley, B.R. 2001. Alternative splicing: increasing diversity in the proteomic world. Trends Genet., 17:100-7.
109. Greaves, J. and Chamberlain, L.H. 2007. Palmitoylation-dependent protein sorting. J. Cell Biol., 176:249-54.
110. Gritli-Linde, A., Nilsson, J., Bohlooly, Y.M., Heby, O. and Linde, A. 2001. Nuclear translocation of antizyme and expression of omithine decarboxylase and antizyme are developmentally regulated. Dev. Dyn., 220:250-75.
111. Groisman, I. and Engelberg-Kulka, H. 1995. Translational bypassing: a new reading alternative of the genetic code. Biochem Cell Biol., 73:1055-9.
112. Grothe, C. and Meisinger, C. 1997. The multifunctionality of FGF-2 in the adrenal medulla. Anat. Embryol, (Berli), 195:103-11.
113. Gu, Z., Cavalcanti, A., Chen, F.C., Bouman, P. and Li, W.H. 2002. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol, Evol., 19:256-62.
114. Gutsche, I., Essen, L.O. and Baumeister, W. 1999. Group II chaperonins: new TRX(k)s and turns of a protein folding machine. J. Mol. Biol., 293:295-312.
115. Halliwanger, R.S., Blomberg, M.A. and Hart, G.W. 1992. Glycosylation of nuclear and cytoplasmic proteins. Purification and characterization of a uridine diphospho-N-acetylglucosamine:polypeptide beta-N-acetylglucosaminyltransferase. J. Biol. Chem., 267:9005-13
116. Halliwanger, R.S., Holk G.D. and Hart, G.W 1990. Enzymatic addition of O-GlcNAc to nuclear and cytoplasmic proteins. Identification of a uridine diphospho-N-acetylglucosamine:peptide beta-N-acetylglucosaminyltransferase. J. Biol. Chem., 265:2563-8.
117. Han, I., Oh, E.S. and Kidlow, J.E. 2000. Responsiveness of the state of O-linked N-acetylglucosamine modification of nuclear pore protein. p62 to the extracellular glucose concentration. Biochem. J., 350 Pt 1:409-14.
118. Hanada, K. and Yang, J.C. 2204)5. Novel biochemistry: post-translational protein splicing and other lessons from the school of antigen processing. J. Mol. Med., 83:420-8.
119. Hanada, K., Yewdell, J.W. and Yang, J.C. 2004. Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature, 427:252-6.
120. HanKe, J., Brett, D., Zastrow, I., Aydin, A., Delbruck, S., Lehmann, G., Luft, F., Reich, J. and Bork, P. 199. Alternative splicing of human genes: more the rule than the exception? Trends Genet., 15:389-90.
121. Hanrison, S.C. 1981. Molecular organization of virus particles: implications for assembly. Prog. Clin Biol. Res., 64:3-18.
122. Hart, G. W. 1997. Dynamic O-linked gglycosylation of nuclear and cytoskeletal proteins. Annu Rev. Biochem., 66:315-35.
123. Hart, G. W., Housley, M.P. and Slawson, C. 2007. Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins. Nature, 446:1017-22.
124. Hard, F.U. and Hayer-Hartl, M. 2002. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science, 295:1852-8.
125. He, J. and Furmanski, P. 1995. Sequence specificity and transcriptional activation in the binding of lactoferrin to DNA. Nature, 373:721-4.
126. Hefferng, M.A., Jiang, W.J., Thorburn, A. W. and Ng, F.M., 2000. Effects of oral administration of a synthetic fragment of human growth hormone on lipid metabolism. Am. J. Physiol. Endocrinol. Metab., 279:E501-7.
127. Heller, J.S., Fong, W.E. and Canellakis, E.S. 1976 Induction of a protein inhibitor to ornithine decarboxylase by the end products of its reaction. Proc. Natl. Acad. Sci. U.S.A., 73:1858-62.
128. Henderson. B.R. and Kuhn, L.C. 1995. Differential modulation of the RNA-binding proteins IRP- 1 and IRP-2 in response to iron. IRP-2 inactivation requires translation of another protein. J. Biol. Chem., 270:2509-15.
129. Henikoff, S., Greene, E.A., Pietrokovski, S., Bork, P., Attwood, T.K. and Hood, L. 1997 Gene families: the taxonomy of protein paralogs and chimeras. Science, 278:609-14.
130. Henkel, T., Zabel, U., Yan Zee, K., Mulleer, J.M., Fanning, E. and Baeuerle, P.A. 1992. Intramolecular masking of the nuclear location signal and dimerization domain in the precursor for the p50 NF-kappa B. subunit. Cell, 68:1121-33.
131. Hentze, M.W. and Kuhn, L.C. 1996. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc. Natl. Acad. Sci. U.S.A., 93:8175-82.
132. Hentze, M.W. Muckenthaler, M.U. and Andrews, N.C. 2004, Balancing acts: molecular control of mammalian iron metabolism. Cell, 1177.285-97
133. Herr, A.J., Atkins, J.F. and Gesteland, R.F. 2000a. Coupling of open reading frames by translational bypassing. Annu. Rev. Biochem., 69:343-72
134. Herr, A.J., Gesteland, R.F. and Atkins, J.F. 2000b. One protein from two open reading frames: mechanism of a 50 nt translational bypass. Embo. J., 19:2671-80.
135. Herz, J. and Strickland, D K. 2001. LRP: a multifunctional scavenger and signaling receptor. J Clin. Invest. 108:779-84
136. Higgins, C.F. 1992. ABC transporters: from microorganisms to man. Annu Rev. Cell Biol., 8:67-113
137. Higgins, C.F. 1995. The ABC of channel regulation. Cell, 82 693-6
138. Hilkens, J. and Buijs, F. 1988. Biosynthesis of MAM-6, an epithelial sialomucin. Evidence for involvement of a rare proteolytic cleavage step in the endoplasmic reticolum. J. Biol. Chem., 263 4215-22
139. Hill, K.E., Lloyd, R.S., Yang, J.G., Read. R. and Burk, R.F. 1991. The cDNA for rat selenoprotein P contains 10 TGA codons in the open reading frame. J. Biol. Chem., 266: 10050-3.
140. Hinnebusch, A.G. and Nataralan, K. 2002. Gen4p, a master regulator of gene expression is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot.Cell., 1,22-32.
141. Hironaka, T., Furukawa, K., Esmon, P.C., Yokota, T., Brown, J.E., Sawada, S., Fournel, M.A., Kato, M., Minaga, T and Kobata, A. 1993. Structural study of the sugar chains of porcine factor VIII - issue- and species-specific glycosylation of factor VIII. Arch. Biochem. Biophys., 307:316-30.
142. Hirst, C.E., Buzza, M.S , Sutton, V.R., Trapana, J.A., Loveland, K.L. and Bird, P.I. 2001. Perforin-independent expression of granzyme B. and proteinase inhibitor 9 in human testis and placenta suggests a role for granzyme B-mediated proteolysis in reproduction. Mol. Hum. Reprod., 7 1133-42.
143. Holcik, M., Sonenberg N. and Korneluk, R.G. 2000. Internal ribosome initiation of translation and the control of cell death. Trends Genet. 15: 469-73.
144. Howell. B.W. and Herz, J. 2001. The LDL receptor gene family: signaling functions during development. Curr. Opin. Neurobiol., 11: 74-81
145. Huez, L., Bornes, S., Bresson, D., Creancier, L. and Prats, H. 2001. New vascular endothelial growth factor isoform generated by internal ribosome entry site-driven CUG translation initiation. Mol. Endocrinol. 15: 2197-210.
146. Ruez, I., Creancier, L., Audigier, S., Gensac, M.C., Prats, A.C. and Prats, H. 1998. Two independent internal ribosome entry sites are involved in translation initiation of vascular endothelial growth factor mRNA. Mol. Cell Biol., 18:6178-90.
147. Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J. S. and O'Shea, E.K. 2003. Global analysis of protein localization in budding yeast. Nature, 425: 686-91.
148. Huq, M.D., Gupta, P., Tsai, N.P. and Wei, L.N. 2006. Modulation of testicular receptor 4 activity by mitogen-activated protein kinase-mediated phosphorylation. Mol. Cell. Proteomics, 5: 2072-82.
149. Ichiba, T., Matsufuji, S., Miyazaki, Y., Murakami, Y., Tanaka, K., Ichihara, A. and Hayashi, S. 1994. Functional regions of ornithine decarboxylase antizyme. Biochem. Biophys. Res. Commun. 200: 1721-7.
150. Ichtchenko, K., Hata, V., Nguyen, T., Ullrich, B., Missler, M., Moomaw, C. and Sudhof, T.C. 1995. Neuroligin 1: a splice site-speci e ligand for beta-neurexins Cell, 81 435-43.
151. Ikura, M. and Ames, J.B. 2006. Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality. Proc. Natl. Acad. Sci. U.S.A., 103: 1159-64
152. Ikura, M., Clore, G.M., Gronenborn, A.M., Zhu, G., Klee, C.B. and Bax, A. 1992. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science, 256:
153. Isken, O. and Maquat, L.E. 2007. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev., 21: 1833-56.
154. Iturralde, M., Alava, M.A., Gonzalez, B., Anel, A. and Pineiro, A. 1991. Effect of alpha-fetoprotein and albumin on the uptake of polyunsaturated fatty acids by rat hepatoma cells and fetal rat hepatocytes. Biochim. Biophys. Acta., 1086:81-8
155. Ivakhno, S. S. and Kornellyuk, A.I. 2004. Cytokine-like activities of some aminoacyl-tRNA synthetases and auxiliary p13 cofactor of amino-acylation reaction and their role in oncogenesis. Exp. Oncol., 26:250-5.
156. Jacobson, H.I., Bennett, J.A. and Mizejewski, G.J. 1990. Inhibition of estrogen-dependent breast cancer growth by a reaction product of alpha-fetoprotein and estradiol. Cancer Res., 50:415-20.
157. Janzen, D.M. and Geballe, A.P. 2004. The effect of eukaryotic release factor depletion on translation termination in human cell lines. Nucleic Acids Res., 32:4491-502.
158. Jarrett, H. W. and Penniston, J. T. 1977 Partial puri cation of the Ca2+-Mg2+ ATPase activator from human erythrocytes: its similarity to the activator of 3′:5′ - cyclic nucleotide phosphodiesterase. Biochem. Biophys. Res. Commun., 77:1210-6.
159. Jonhson, G. and Moore, S.W. 2004. Identi cation of a structural site on acetylcholinesterase that promotes neurite outgrowth and binds laminin-1 and collagen IV. Biochem. Biophys. Res. Commun., 319:448-55.
160. Kaiserman, D., Bird, C.H., Sun, J., Matthews, A., Ung, K., Whisstock, J.C., Thompson, P.E., Trapani,J.A. and Bud, P.I. 2006. The major human and mouse granzymes are structurally and functionally divergent. J. Cell Biol., 175:619-30.
161. Kakiuchi, S. and Yamasaki, R. 1970. Calcium dependent phospodiesterase activity and its activating factor (PAF) from brain studies on cyclic 5′, 5′-nucieotide phosphodiesterase (3). Biochem. Biophys. Res. Commun., 41:1104-10.
162. Kanyshkova, T.G., Buneva, V.N. and Nevinsky, G.A. 2001. Lactoferrin and its biological functions. Biochemistry (Mosc), 66:1-7
163. Kapp, L.D. and Lorsch, J.R. 2004. The molecular mechanics of eukaryotic translation. Annu. Rev. Biochem. 73:657-704.
164. Kamiely, S. and Pines, O. 2005. Single translation - dual destination: mechanisms of dual protein targeting in eukaryotes. EMBO Rep., 6:420-5.
165. Karunakaran, K.P., Noguchi, Y., Read, T.D., Cherkasov, A., Kwee, J., Shen, C., Nelson, C.C. and Brunham, R.C. 2003. Molecular analysis of the multiple GroEL proteins of Chlamydiae. J. Bacteriol., 185:1958-66.
166. Kearse, K.P. and Hart, G.W. 1991. Lymphocyte activation induces rapid changes in nuclear and cytoplasmic glycoproteins. Proc. Natl. Acad. Sci. U.S.A., 88:1701-5.
167. Keeling, K.M., Lanier, J., Du, M., Salas-Marco, J., Gao, L., Kaenjak-Angeletti, A. and Bedwell, D.M. 2004. Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae. Rna, 10:691-703.
168. Kelly, A., Powis, S.H., Kerr, L.A., Mockridge, I., Elliott, T., Bastin, J., Uchanska-Ziegler, B., Ziegler, A., Trowsdale, J. and Townsend, A. 1992. Assembly and function of the two ABC transporter proteins encoded in the human major hitocompatibility complex. Nature, 355:641-4.
169. Kelly, W.G., Dahmus, M.E. and Hart, G.W. 1993. RNA polymerase II is a glycoprotein. Modification of the COOH-terminal domain by O-GlcNAc. J. Biol. Chem., 268:10416-24.
170. Kennedy, M.C., Mende-Mueller, L., Blondin, G.A. and Beinert, H. 1992. Puri cation and characterization of cytosolic aconitase from beef liver and its relationship to the iron-responsive element binding protein. Proc. Natl. Acad. Sci. U.S.A., 89:11730-4.
171. Kim, E, Xie, S. Yeh, S.D., Lee, Y.F., Collins, L.L., Hu, Y.C., Shyr, C.R., Mu, X.M., Liu, N.C., Chen, Y.T., Wang, P.H. and Chang, C. 2003. Disruption of TR4 orphan nuclear receptor reduces the expression of liver apolipoprotein E/C-I/C-II gene cluster. J. Biol. Chem., 278:46919-26.
172. Kinlough, C.L., Poland, P.A., Bruns, J.B., Harkleroad, K.L. and Hughey, R.P. 2004. MUC1 membrane trafficking is modulated by multiple
173. Kirby, J.E. 2004. Anthrax lethal toxin induces human endothelial cell apoptosis. Infect. Immun., 72:430-9.
174. Klabunde, T, Sharma, S., Telenti, A., Jacobs, WRJr and Sacchettini, J.C. 1998. Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing. Nat. Struct. Biol., 5:31-6.
175. Kochetov, A.V. 2006. [Alternative translation start sites and their significance for eukaryotic proteome]. Mol. Biol. (Mosk), 40:788-95.
176. Kochetov, A.V., Sarai, A., Rogozin, I.B., Shumny, V.K. and Kolchanov, N. A. 2005. The role of alternative translation start sites in the generation of human protein diversity. Mol. Genet. Genomics, 273:491-6.
177. Komeili, A and O'Shea, E.K. 1999, Roles of phosphorylation sites in regulating activity of the transcription factor Pho4. Science, 284: 977-80.
178. Koritschoner, N.P., Madruga, J., Knespel, S., Blendinger, G., Anzinger, B., Otto, A., Zenke, M. and Bartunek, P. 2001. The nuclear orphan receptor TR4 promotes proliferation of myeloid progenitor cells. Cell. Growth Differ., 12:563-72.
179. Kozak, M. 1980. In uence of mRNA secondary structure on binding and migration of 40S ribosomal subunits. Cell., 19:79-90.
180. Kozak, M. 2002. Pushing the limits of the scanning mechanism for initiation of translation. Gene. 299:1-34.
181. Krebs, E.G. 1993. Nobel Lecture. Protein phosphorylation and cellular regulation I. Biosci. Rep., 13:127-42.
182. Kreppel, L.K., Blomberg, M.A. and Hart, G.W 1997. Dynamic glycosylation of nuclear and cytosolic proteins. Cloning and characterization of a unique O-GlcNAc transferase with multiple tetratricopeptide repeats. J. Biol. Chem. 272:9308-15.
183. Kreppel, L.K. and Hart, G.W. 1999. Regulation of a cytosolic and nuclear O-GlcNAc transferase. Role of the tetratricopeptide repeats. J. Biol. Chem., 274:32015-22.
184. Kretsinger, R.H. and Nockolds, C.E. 1973. Carp muscle calcium-binding protein. II. Structure determination and general description. J. Biol. Chem., 248:3313-26.
185. Kuchler, K., Sterne, R.E. and Thomer, J. 1989. Saccharomyces cerevisiae STE6 gene product: a novel pathwzy for protein export in eukaryotic cells. Embo. J., 8:3973-84.
186. Kumar, A., Agarwal, S., Heyman, J.A., Matson, S., Heidman, M., Piccirillo, S., Umansky, L., Drawid,A., Jansen, R., Liu, Y., Cheung, K.H., Miller, P., Gerstein, M., Roeder, G.S. and Snyder, M. 2002. Subcellular localization of the yeast proteome. Genes Dev., 16: 707-19.
187. Ladomery, M. and Dellaire, G, 20021. Multifunctional zinc nger proteins in development and disease. Ann. Hum. Genet., 66:331-42.
188. Layer, P.G., Allebrandt, K., Andermann, P., Bodur, E., Boopathy, R., Bytyqi, A.H. and Paraoanu, L.E. 2005. On the multifunctionallity of cholin-esterases. Chem. Biol. Interact., 157-158:37-41.
189. Layer, P.G., weikert, T., and Alber, R. 1993. Cholinesterases regulate neurite growth of chick nerve cells in vitro by means of a non-enzymatic mechanism. Cell Tissue Res., 273:219-26.
190. Lee, S.B., Huang, K., Palmer, R., Truong, V.B., Herzlinger, D., Kolquist, K.A., Wong, J., Paulding, C., Yoon, S.K., Gerald, W., Oliner, J.D. and Haber. D. A. 1999. The Wilms tumor suppressor WTI encodes transcriptional activator of amphiregulin. Cell., 98:663-73.
191. Lee, Y.N., Nechushtan, H., Figov, N. and Razin, E. 2004. The function of lysyl-tRNA synthetase and Ap4A as signaling regulators of MITF activity in FcepsilonRI-activated mast cells. Immunity, 20:145-51.
192. Lee, Y.N. and Razin, E. 2(X)5. Nonconventional involvement of LysRS in the molecular mechanism of USF2 transcriptional activity in FcepsilonRI-activated mast cells. Mol. Cell Biol., 24;8904-12.
193. Leffert, H.L. and Sell, S. 1974. Alpha1-fetoprotein biosynthesis during the growth cycle of differentiated fetal rat hepatocytes in primary monolayer culture. J. Cell Biol., 61:823-9.
194. Leissring M.A., Farris, W., Wu, X., Christodoulou, D.C., Haigis, M.C., Guarente, L. and Seikoe, D.J. 2004. Alternative translation initiation generates a novel isoform of insulin-degrading enzyme targeted to mitochondria. Biochem. J., 383:439-46.
195. Lesk, A.M. 2001. Introduction to Protein Architecture, Oxford University, Press, Oxford New York.
196. Levay, P.F. and Viljoen, M. 1995. Lactoferrin: a general review. Haematologica., 80:252-67.
197. Levitin, F., Baruch, A., Weiss, M., Stiegman, K., Hartmann, M.L., Yoeli-Lerner, M., Ziv, R., Zrihan-Licht, S., Shina, S., Gat, A., Lifischitz, B., Simha, M., Stadler, Y., Cholostoy, A., Gil, B., Greaves, D., Keydar, I., Zaretsky, J., Smorodinsky, N. and Wreschner, D.H. 2005a. A novel protein derived from the MUC1 gene by alternative splicing and frameshifting. J. Biol. Chem., 280:10655-63.
198. Levitin, F., Stem, O., Weiss, M., Gil-Henn, C., Ziv, R., Prokocimer, Z., Smorodinsky, N.I., Rubinstein, D.B. and Wreschner, D.H. 2005b. The MUC1 SEA module is a self-cleaving domain. J. Biol. Chem., 280:33374-86.
199. Lewis, B.P., Green, R.E. and Brenner, S.E. 2003. Evidence for the widespread coupling of alternative spilicing and nonsense-mediated mRNA decay in humams. Proc. Natl. Acad. Sci. U.S A., 100:189-92.
200. Lewis, U.J., Sinha, Y.N. and. Lewis, G.P. 2000. Structure and properties of members of the hGH family: a review. Endocr. J., 47(Suppl):S1-8.
201. Li, M.S., Li, P.F., Yang, F.Y., He, S.P., Du, G.G. and Li, G. 2002. The intracellular mechanism of alpha-fetoprotein promoting the proliferation of NIH 3T3 cells. Cell Res., 121:151-6.
202. Li, Q.J., Yao, M., Wong, W., Parpura. V. and Martins-Green, M. 2004. The N. and C-terminal peptides of hIL8/CXCL8 are ligands for hCXCR1 and hCXCR2. Faseb J., 18:776-8.
203. Li, Y., Bharti, A., Chen, D., Gong, J. and Kufe, D. 1998. Interaction of glycogen synthase kinase 3beta with the DF3/MUC1 carcinoma-associated antigen and beta-catenin. Mol. Cell Biol., 18:7216-24.
204. Li, Y., Chen, W., Ren, J., Yu, W.H., Li, Q., Yoshida, K. and Kufe, D. 2003a. DF3/MUC1 signaling in multiple myeloma cells is regulated by interleukin-7. Cancer Biol. Ther., 2:187-93.
205. Li, Y., Kuwahara, H., Ren, J., Wen, G. and Kufe, D. 2001a. The c-Src tyrosine kinase regulates signaling of the human DF3/MUC1 carcinoma-associated antigen with GSK3 beta and beta-catenin. J. Biol. Chem., 276:6061-4.
206. Li, Y., Ren, J., Yu, W., Li, Q., Kuwahara, H., Yiu, L., Carraway, KL3rd and Kufe, D. 2001b. The epidermal growth factor receptor regulates interaction of the human DF3/MUC1 carcinoma antigen with c-Src and beta-catenin. J. Biol. Chem., 276:35239-42.
207. Li, Y., Yu, W. H., Ren, J., Chen, W., Huang, L., Kharbanda, S., Loda, M. and Kufe, D. 2003b. Heregulin targets gamma-catenin to the nucleolus by a mechanism dependent on the DF3/MUC1 oncoprotein. Mol. Cancer Res., 1:765-75.
208. Ligtenberg, M.J., Kruijshaar, L., Buijs, F., van Meijer, M., Litvinov, S.V. and Hilkens, J. 1992. Cell-associated episialin is a complex containing two proteins derived from a common precursor. J. Biol. Chem., 267:6171-7.
209. Linsley, P.S., Kallestad, J.C., and Horn, D, 1988. Biosynthesis of high molecular weight breast carcinoma associated mucin glycoproteins. J. Biol. Chem., 263:8390-7.
210. Liou, J., Kim, M.L., Heo, W.D., Jones, U., Myers, J.W., Ferrell, JEJr and Meyer, T. 2005. STIM is a Ca2+ sensor essential for Ca2+-store-depletion-triggered Ca2+ in ux. Curr. Biol., 15:1235-41.
211. Litvinov, S.V. and Hilkens, J. 1993. The epithelial sialomucin, episialin, is sialylated during recycling. J. Biol. Chem., 268:21364-71.
212. Loeb, D.M., Korz, D., Katnelson, M., Burwell, E.A., Friedman, A.D. and Sukumar, S. 2002. Cyclin E is a target of WT1 transcriptional repression. J. Biol. Chem., 277:19627-32.
213. Loft eld, R.B. and Vanderjagt, D. 1972. The frequency of errors in protein biosynthesis. Biochem. J., 128:1353-6.
214. Lopez-Lastra, M., Rivas, A. and Barria, M.I. 2005. Protein synthesis in eukaryotes: the growing biological relevance of cap-independent translation initiation. Biol. Res., 38:121-46.
215. Lu, P.D., Harding, H.P. and Run. D. 2004. Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response. J. Cell Biol., 167:27-33.
216. Lubas, W.A., Frank, D.W., Krause, M. and Hanover, J.A. 1997. O-Linked GlcNAc transferase is a conserved nucleocytoplasmic protein containing tetratricopeptide repeats. J. Biol. Chem., 272:9316-24.
217. Lykke-Andersen, J., Shu, M.D., and Steitz, J.A. 2001. Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science, 293: 1836-9.
218. Ma, S., Hill, K. E., Caprioli, R.M. and Burk, R.F. 2002. Mass spectrometric characterization of full-length rat selenoprotein P and three isoforms shortened at the C terminus. Evidence that three UGA codons in the mRNA open reading frame have alternative functions of specifying selenocysteine insertion or translation termination. J. Biol. Chem., 277:12749-54.
219. Mackenzie, S.A. 2005. Plant organellar protein targeting: a traf c plan still under construction. Trends Cell Biol., 15:548-54.
220. Maderazo, A.B., He, F., Mangus, D.A. and Jacobson, A. 2000. Upf1p control of nonsense mRNA translation is regulated by Nmd2p and Upf3p. Mol. Cell Biol., 20:4591-603.
221. Makarova, K.S , Aravind, L. and Koonin, E.V. 1999. A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases. Protein Sci., 8:1714-9.
222. Manch-Citron, J.N., Dey, A., Schneider, R. and Nguyen, N.Y. 1999. The translational hop junction and the 5′ transcriptional start site for the Prevotella loeschen adhesin encoded by plaA. Curr. Microbiol.. 38:22-6.
223. Mann, D.M., Romm, E. and Miglionni, M. 1994. Delineation of the glycosaminoglycan-binding site in the human in ammatory response protein lactoferrin. J. Biol. Chem., 269:23661-7.
224. Manning, G., Plowman, G.D., Hunter, T. and Sudarsanam, S. 2002a. Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci., 27:514-20.
225. Manning, G., Whyte, D.B., Martinez, R., Hunter, T. and Sudarsanam, S. 2002b. The protein kinase complement of the human genome. Science, 298:1912-34.
226. Mariller, C., Benaissa, M., Hardiville, S., Breton, M., Pradelle, G., Mazurier, J. and Pierce, A. 2007. Human delta-lactoferrin is a transcription factor that enhances Skp1 (S-phase kinase-associated protein) gene expression. Febs J., 274:2038-53.
227. Marino, M., Ascenzi, P. and Acconcia, F. 2006. S-palmitoylation modulates estrogen receptor alpha localization and functions. Steroids, 71:298-303.
228. Martinoia, E., Klein, M., Geisler, M., Bovet, L., Forestier, C., Kolukisaoglu, U., Muller-Rober, B. and Schulz, B. 2002. Multifunctionality of plant ABC transporters - more than just detoxifiers. Planta, 214:345-55.
229. Matsufuji, S., Matsufuji, T., Miyazaki, Y., Murakami, Y., Atkins, J.F., Gesteland, R.F. and Hayashi, S. 1995. Autoregulatory frameshifting in decoding mammalian omithine decarboxylase antizyme. Cell., 80:51-60.
230. McCaughan, K.K., Brown, C.M., Dalphin, M.E., Berry, M.J. and Tate, W.P. 1995. Translational termination efficiency in mammals is influenced by the base following the stop codon. Proc. Natl. Acad. Sci. U.S.A., 92: 5431-5.
231. McGrath, J.P. and Varshavsky, A. 1989. The yeast STE6 gene encodes a homologue of the mammalian multidrug resistance P-glycoprotein. Nature, 340:400-4.
232. McNally, D. and Fares, M.A. 2007. In silico identi?cation of functional divergence between the multiple groEL gene paralogs in Chlamydiae BMC Evol. Biol., 7:81.
233. Meador, W.E., Means, A.R. and Quiocho, F.A. 1992. Target enzyme recognition by calmodulin. 2.4 A structure of a calmodulin-peptide complex. Science, 257:1251-5.
234. Medina, L., Grove, K. and Haltiwanger, R.S. 1998. SV40 large T antigen is modi?ed with O-linked N-acetylglucosamine but not with other forms of glycosylation. Glycobiology, 8:383-91.
235. Medzihradszky, K.F. 2001. Characterization of site-speci?c glycosylation. In Posttranslational modi?cations of proteins (C. Kannicht, Ed.), pp. 101-102. Humana Press.
236. Milligan, G., Parenti, M. and Magee, A.I. 1995. The dynamic role of palmitoylation in signal transduction. Trends Biochem. Sci., 20:181-7.
237. Milligan, S.R., Khan, O. and Nash, M. 1998. Competitive binding of xenobiotic oestrogens to rat alpha-fetoprotein and to sex steroid binding proteins in human and rainbow trout (Oncorhynchus mykiss) plasma Gen. Comp. Endocrinol., 112:89-95.
238. Min, W. and Jones, D.H., 1994. In vitro splicing of concanavalin A is catalyzed by asparaginyl endopeptidase. Nat. Struct. Biol. 1:502-4.
239. Miranda, L.R., Duval, M., Doherty, H., Seaman, M.S., Posner, M.R. and Cavacini, L.A. 2007. The neutralization properties of a HIV-specific antibody are markedly altered by glycosylation events outside the antigen-binding domain. J. Immunol., 178:7132-8.
240. Mironov, A.A., Fickett, J.W. and Gelfand, M.S. 1999. Frequent alternative splicing of human genes. Genome. Res., 9:1288-93.
241. Missler, M., Fernandez-Chacon, R. and Sudhof, T.C. 1998. The making of neurexins. J. Neurochem., 71:1339-47.
242. Missler, M. and Sudhof, T.C. 1998. Neurexins: three genes and 1001 products. Trends Genet., 14:20-6.
243. Mizejewski, G.J. 1993. An apparent dimerization motif in the third domain of alpha-fetoprotein: molecular mimicry of the steroid/thyroid nuclear receptor superfamily. Bioessays, 15:427-32.
244. Mizejewski, G.J., Vonnegut, M. and Jacobson, H.I. 1983. Estradiol-activated alpha-fetoprotein suppresses the uterotropic response to estrogens. Proc. Natl. Acad. Sci. U.S.A., 80:2733-7.
245. Mosley, A.L., Lakshmanan, J., Aryal, B.K. and Ozcan, S. 2003. Glucose-mediated phosphorylation converts the transcription factor Rgt1 from a repressor to an activator. J. Biol. Chem., 278:10322-7.
246. Mostaqul Huq, M.D., Gupta, P. and Wei, L.N. 2008. Post-translational modi?cations of nuclear co-repressor RIP140: a therapeutic target for metabolic diseases. Curr. Med. Chem., 15:386-92.
247. Murai, N., Murakami, Y. and Matsufuji, S. 2003. Identi?cation of nuclear export signals in antizyme-1. J. Biol. Chem., 278:44791-8.
248. Murakami, Y., Matsufuji, S., Kameji, T., Hayashi, S., Igarashi, K. Tamura, T., Tanaka, K. and Ichihara, A. 1992. Ornithine decarboxylase is degraded by the 26S proteasome without ubiquitination. Nature, 360:597-9.
249. Nadolski, M.J. and Linder, M.E. 2007. Protein lipidation. Febs J., 274:5202-10.
250. Nagai, M., Becker, J.L. and Deutsch, H.F. 1982. The fatty acid levels of rat alpha-fetoprotein derived from fetuses, pregnancy and hepatoma sera. Oncodev. Biol. Med., 3:343-50.
251. Nagradova, N.K. 2004. Protein folding in the cell: on the mechanisms of its acceleration. Biochemistry (Mosc), 69:830-43.
252. Namy, O., Duchateau-Nguyen, G. and Rousset, J.P. 2002. Translational readthrough of the PDE2 stop codon modulates cAMP levels in Saccharomyces cerevisiae. Mol. Microbiol., 43:641-52.
253. Namy, O., Rousset, J.P., Napthine, S. and Brierlev, L 2004. Reprograramed genetic decoding in cellular gene expression. Mol. Cell., 13:157-68
254. Naval, J., Villacampa, M.J., Goguel, A.F. and Uriel, J. 1985. Cell-type-specefic receptors for alpha-fetoprotein in a mouse T-lymphoma cell line. Proc. Natl. Acad. Sci. U.S.A. 82:3301-5.
255. Nemansky, M., Thotakura, N.R., Lyons, C.D., Ye, S., Reinhold, B.B., Reinhold, V.N. and Blithe, D.L. 1998. Developmental changes in the glycosylation of glycoprotein hormone free alpha subunit during pregnancy. J. Biol. Chem. 273:12068-76.
256. Nishi, S., Matsue, H., Yoshida, H., Yamaoto, R. and Sakai, M. 1991. Localization of the estrogen-binding site of alpha-fetoprotein in the chimeric human-rat proteins. Proc. Natl. Acad. Sci. U.S.A., 88:3102-5.
257. Noren, C.J., Wang, J. and Perler, F.B. 2000. Dissecting the Chemistry of Protein Splicing and Its Applications. Angew Chem. Int. Ed. Engl., 39:450-66.
258. Noti, A., Le Hir, H, and Moore, M.J. 2004. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev., 18:210-22.
259. Nykjaer, A. and Willnow, T.E. 2002 The low-density lipoprotein receptor. gene family: a cellular Swiss army knife? Trends Cell Biol., 12:273-80.
260. Ohkura, K. and Hori, H. 2000. Analyses of insulin-potentiating fragments of human growth hormone by computative simulation, essential unit for insulin-involved biological responses. Bioorg Med. Chem., 8:1733-40
261. Ohno, S. 1970. Evolution by gene duplication, Springer-Verlag, Berlin.
262. Osterhout, J.L., Waheed, A.A., Hiol, A., Ward, R.J., Davey, P.C., Nini, L., Wang, J., Milligan, G., Jones, T.L. and Druey, K.M. 2003. Palmitoylation regulates regulator of G-protein signaling (RGS) 16 function 11. Palmitoylation of a cysteine residue in the RGS box is critical for RGS16 GTPase accelerating activity and regulation of Gi-coupled signalling. J. Biol. Chem., 278:19309-16.
263. Otani, A., Slike, B.M,, Dorrell, M.I., Hood, J., Kinder, K., Ewalt, K.L., Cheresh, D., Schimmel, P. and Friedlander, M. 2002. A fragment of human TrpRS as a potent antagonist of ocular angiogenesis. Proc. Natl. Acad. Sci. U.S.A., 99:178-83.
264. Packham, G., Brimmell, M. and Cleveland, J.L. 1997. Mammalian cells express two differently localized Bag-1 isoforms generated by alternative translation initiation. Biochem. J., 328 (Pt 3):807-13.
265. Paraoanu, L.E. and Layer, PG. 2004. Mouse acetylcholinesterase interacts in yeast with the extracellular matrix component laminin-1beta. FEBS Lett, 576:161-4.
266. Paulus, H. 2001. Inteins as enzymes. Bioorg Chem., 29:119-29
267. Pawson, T. and Gish, G.D. 1992. SH2 and SH3 domains: from structure to function. Cell., 71:359-62.
268. Pawson, T and Nash, P. 2003. Assembly of cell regulatory systems through protein interaction domains. Science, 300:445-52.
269. Perler, F.B. 2005. Protein splicing mechanisms and applications. IUBMB. Life, 57:469-76.
270. Perler, F.B., Davis, E.O., Dean, G.E., Gimblet F.S., Jack, W.E., Neff, N., Noren, C.J., Thorner, J. and Belfort, M. 1994. Protein splicing elements inteins and exteins - a definition of terms and recommended nomenclature. Nucleic Acids Res. 21:1125-7.
271. Persechini, A. and Kretsinger, R.H. 1988. The central helix of calmodulin functions as a exible tether. J. Biol. Chem., 263:12175-8
272. Pestova, T.V. and Hellen, C.U. 1999. Ribosome recruitment and scanning: what's new? Trends Biochem. Sci., 24:85-7.
273. Pham, C.T., MacIvor, D.M., Hug, B.A., Heusel, J.W. and Ley, T.J. 1996. Long-range disruption of gene expression by a selectable marker cassette. Proc. Natl. Acad. Sci. U.S.A., 93:13090-5.
274. Pietrokovski, S. 2001. Intein spread and extinction in evolution. Trends Genet., 17:465-72.
275. Plant, E.P., Jacobs, K.L., Harger, J.W., Meskauskas, A., Jacobs, J.L., Baxter, J.L., Petrov, A.N. and Dinman, J.D. 2003. The 9-A solution: how mRNA pseudoknots promote efficient programmed-1 ribosomal frameshifting. Rna., 9:168-74.
276. Plateau, P. and Blanquet, S. 1982. Zinc-dependent synthesis of various dinucleoside 5′, 5′-P1,P3-Tri- or 5″, 5′-P1,P4-tetraphosphates by Escherichia coli lysyl-tRNA synthetase. Biochemistry, 21:5273-9.
277. Porras, P. Padilla, C.A., Krayl, M., Voos, W. and Barcena, J.A. 2006. One single in-frame AUG codon is responsible for a diversity of subcellular localizations of glutaredoxin 2 in Saccharomyces cerevisiae. J. Biol. Chem., 281:16551-62.
278. Qiao, F. and Bowie, J.U. 2005. The many faces of SAM Sci. STKE 2005: re7.
279. Quinton, T.M., Kim, S., Dangelmaier, C., Dorsam, R. T., Jin, J., Daniel, J.L. and Kunapuli, S.P. 2002. Protein kinase C- and calcium-regulated pathways independently synergize with Gi pathways in agonist-induced brinogen receptor activation. Biochem. J., 368:535-43.
280. Rammensee, H.G. 2004. Immunology: protein surgery. Nature, 427:203-4
281. Regev-Rudzki, N., Karniely, S., Ben-Haim, N.N. and Pines, O. 2005. Yeast aconitase in two locations and two metabolic pathways: seeing small amounts is believing. Mol. Biol. Cell., 16:4163-71.
282. Regev-Rudzki, N. and Pines, O. 2007. Eclipsed distribution: a phenomenon of dual targeting of protein and its significance. Bioessays, 29:772-82.
283. Rehfeld, J.F. and Goetze, J.P. 2003. The posttranslational phase of gene expression: new possibilities in molecular diagnosis. Curr. Mol. Med., 3:25-38.
284. Ren, J., Li, Y. and Kufe, D. 2002. Protein kinase C delta regulates function of the DF3/MUC1 carcinoma antigen in beta-catenin signaling. J. Biol. Chem. 277:1716-22.
285. Resh, M.D. 1999. Fatty acylation of proteins: new insights into membrane targeting of myristoylated and palmitoylated proteins. Biochim. Biophys. Acta., 1451:1-16.
286. Revell, P.A., Grossman, W.J., Thomas, D.A., Cao, X., Behl, R., Ratner, J.A., Lu, Z.H. and Ley, T.J. 2005 Granzyme B. and the downstream granzymes C and/or F are important for cytotoxic lymphocyte functions. J. Immunol., 174:2124-31.
287. Richardson, J.S. 1981. The anatomy and taxonomy of protein structure. Adv. Protein Chem., 34:167-339
288. Roberts, A.W. 2005. G-CSF: a key regulator of neutrophil production, but that's not all! Growth Factors, 23:33-41.
289. Robinson, D.N. and Cooley, L. 1997. Examination of the function of two kelch proteins generated by stop codon suppression. Development, 124:1405-17.
290. Rochette-Egly, C. 2003. Nuclear receptors: integration of multiple signalling pathways through phosphorylation. Cell Signal. 15:355-66.
291. Rom, E. and Kahana, C. 1994. Polyamines regulate the expression of ornithine decarboxylase antizyme in vitro by inducing ribosomal frame-shifting. Proc. Natl. Acad. Sci. U.S.A., 91:3959-63.
292. Roos, J., DiGregorio, P.J., Yeromin, A.V., Ohlsen, K., Lioudyno, M., Zhang, S., Safrina, O., Kozak, J.A., Wagner, S.L. Cahalan, M.D., Velicelebi, G. and Stauderman, K.A. 2005. STIMI, an essential and conserved component of store-operated Ca2+ channel function. J. Cell Biol., 169:435-45
293. Roos, M.D., Su, K., Baker, J.R. and Kudlow, J.E. 1997. O glycosylation of an Sp1-derived peptide blocks known Sp1 protein interaction. Mol. Cell Biol., 17:5472-80.
294. Roquemore, E.P., Chevrier, M.R., Cotter, R.J. and Hart, G.W. 1996. Dynamic O-GlcNAcylation of the small heat shock protein alpha B-crystallin. Biochemistry, 35:3578-86.
295. Routier, F.H., Davies, M.J., Bergemann, K. and Hounsell, E.F. 1997. The glycosylation pattern of humanized IgGI antibody (D1.3) expressed in CHO cells. Glycoconj J., 14:201-7.
296. Ruiz-Gutierrez, V., Moreno, R., Moreda, W., Copado, M.A. and Rodriguez-Burgos, A. 2001. Detection of squalene in alpha-fetoprotein and fetal serum albumin from bovine. J. Protein Chem., 20:19-23.
297. Ruoslahti, E., Estes, T. and Seppala, M. 1979. Binding of bilirubin by bovine and human alpha-fetoprotein. Biochim. Biophys. Acta., 578:511-9.
298. Sampath, P., Mazumder, B., Seshadri, V., Gerber, C.A., Chavatte, L., Kinter, M., Ting, S.M., Dignam, J.D., Kim, S., Driscoll, D.M. and Fox, P.L. 2004. Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation. Cell, 119:195-208.
299. Santonico, E., Castagnoli, L. and Cesareni, G. 2005. Methods to reveal domain networks. Drug Discov, Today, 10:1111-7.
300. Sass, E., Blachinsky, E., Karniely, S. and Pines, O. 2001. Mitochondrial and cytosolic isoforms of yeast fumarase are derivatives of a single translation product and have identical amino termini. J. Biol. Chem., 276:46111-7.
301. Schartner, J.M., Fathman, C.G, and Seroogy, C.M. 2007. Preservation of self: an overview of E3 ubiquitin ligases and T cell tolerance. Semin. Immunol., 19:188-96.
302. Scheiffele, P., Fan, J., Choih, J., Fetter, R. and Sera? ni, T. 2000. Nieuroligin expressed in nonneuronal cells triggers presynaptic development in contacting axons. Cell, 101:657-69.
303. Schmucker, D., Clemens, J.C., Shu, H., Worby, C.A., Xiao, J., Muda, M., Dixon, J.E. and Zipursky, S.L. 2000. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell, 101:671-84.
304. Sheeley, D.M., Merrill, B.M. and Taylor, L.C. 1997. Characterization of monoclonal antibody glycosylation: comparison of expression systems and identification of terminal alpha-linked galactose. Anal Biochem., 247:102-10.
305. Shyr, C.R., Collins, L.L., Mu, X.M., Platt, K.A. and Chang, C. 2002. Spermatogenesis and testis development are normal- in mice lacking testicular orphan nuclear receptor 2. Mol. Cell. Biol. 22:4661-6.
306. Silvius, J.R. 2002. Mechanisms of Ras protein targeting in mammalian cells. J. Membr. Biol., 190:83-92.
307. Singh, P.K. and Hollingsworh, M.A. 2006. Cell surface-associated mucins in signal transduction. Trends Cell. Biol., 16:467-76.
308. Smorodinsky, N., Weiss, M., Hartmann, M.L., Baruch, A., Harness, E., Yaakobovitz, M., Keydar, I. and Wreschner, D.H. 1996. Detection of a secreted MUC1/SEC protein by MUC1 isoforin specific monoclonal antibodies. Biochem. Biophys. Res, Commun. 228: 115-21.
309. Sort, K.N., Park, J., Chung, C.K., Chung, D.K., Yu, D.Y., Lee, K.K. and Kim, J. 2002. Human lactoferrin activates transcription of IL-1beta gene in mammalian cells. Biochem. Biophys. Res. Commun., 290: 236-41.
310. Sorg, C. 1989. Macrophage-derived cell regulatory factors. Cytokines, Karger, Basel.
311. Southworth, M.W., Amaya, K., Evans, T.C., Xu, M.Q. and Perler, F.B. 1999. Purification of proteins fused to either the amino or carboxy terminus of the Mycobacterium xenopi gyrase A intein. Biotechniques, 17:1104.116:118-20.
312. Stahl, G., Ben Salem, S., Li, Z,, McCarty, G., Raman, A.,, Shah, M. and Farabaugh, P.J. 2001. Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction. Cold Spring Harb Symp. Quant. Biol., 66: 249-58.
313. Stansfield, I., Jones, K.M., Herbert, P., Lewendon, A., Shaw, W.V. and Tuite, M.F. 1998. Missense translation errors in Saccharomyces cerevisiae. J. Mol. Biol. 282:13-24.
314. Starokadomskyy, P 2007. Protein, splicing. Molecular Biology, 41:278-93.
315. Stein, I., Itin, A., Einat, P., Skaliter, R., Grossman, Z . and Keshet, E. 1998. Translation of vascular endothelial growth factor mRNA by internal ribosome entry: implications for translation under hypoxia. Mol. Cell Biol., 18:3112-9.
316. Steneberg, P. and Samakovlis, C. 2001. A novel stop codon readthrough mechanism produces functional Headcase protein in Drosophila trachea. EMBO Rep., 2:593-7.
317. Strehl, A., Munnix, I.C., Kuijpers, M.J., van der Meijden, P.E., Cosemans, J.M., Fejge, M.A., Nieswandt, B. and Heemskerk, J.W. 2007. Dual role of platelet protein kinase C in thrombus formation: stimulation of pro-aggregatory and suppression of procoagulant activity in platelets. J. Biol. Chem., 181:7046-55.
318. Stuehr, D.J., Cho, H.J., Kwon, N.S., Weise, M.F. and Nathan, C.F. 1991 Purification and characterization of the cytokine-induced macrophage nitric oxide sythase: an FAD- and FMN-containing. avoprotein. Procc Natl. Acad. Sci. U.S.A., 88:7773-7.
319. Su, Z., Wang, J., Yu, J., Huang, X. and Gu, X. 2006. Evolution of alternative splicing after gene duplication. Genome. Res., 16:182-9.
320. Sugita, S., Khvochtev, M. and Sudhof, T.C. 1999. Neurexins are functional alpha-latrotoxin receptors. Neuron, 22:489-96.
321. Sukenaga, Y., Ishida, K., Takeda, T. and Takagi, K. 1987. cDNA sequence coding for human glutathione peroxidase. Nucleic Acids Res., 15:7178
322. Sunderland, P.A., West, C.E., Wateworth, W.M. and Bray, C.M. 2006. An evolutionarily conserved translation initiation mechanism regulates nuclear or mitochondrial targeting of DNA ligase I in Arabidopsis thaliana. Plant J., 47:356-67.
323. Suzuki, T., Park, H. and Lennarz, W.J. 2002. Cytoplasmic peptide: N-glcanase (PNGase) in eukaryotic cells: occurrence, primary structure, and potential functions. Faseb J., 16:635-41.
324. Suzuki, T., Tanabe, K., Hara, I., Taniguchi, N. and Colavita, A. 2007. Dual enzymatic properties of the cytoplasmic peptide: N-glycanase in C elegans. Biochem. Biophys. Res. Commun., 358:837-41
325. Suzuki, Y., Zeng, C.Q. and Alpert, E. 1992. Isolation and partial characterization of aspecific alpha-fetoprotein receptor on human monocytes. J. Clin. Invest. 90:1530-6.
326. Suzuki, V.A. and Lonnerdal, B, 2002. Characterization of mammalian receptors fbr lactoferin. Biochem. Cell Biol., 80: 75-810.
327. Szczypka, M.S., Wemmie, J.A., Moye-Rowley, W.S. and Thiele, D.J. 1994. A yeast metal resistance protein similar to human cystic brosis transmembrane conductance regulator (CFTR.) and multidrug resistance-associated protein. J. Biol. Chem., 269:22853-7.
328. Tagashira, M., Iijima, H., Isogai, Y., Hori, M., Takamatsu, S., Fujibayashi, Y., Yoshizawa-Kumagaye, K., Isaka, S., Nakajima, K., Yamamoto, T., Teshima, T. and Toma, K. 2001. Site-dependent effect of O-glycosylation on the conformation and biological activity of calcitonin. Biochemistry, 40:11090-5.
329. Tanabe, O., Katsuoka, F., Campbell, A.D., Song, W., Yamamoto, M., Tanimoto, K. and Engel, J.D. 2002. An embryonic/fetal beta-type globin gene repressor contains a nuclear receptor TR2/TR4 heterodimer. Embo J., 21:3434-42.
330. Talarinov, Y.S., Terentiev, A.A., Moldogazieva, N.T. and Tagirova, A.K. 1991. Human alpha-fetoprotein and its purification by chromatography on immobilized estrogens. Tomour. Biol., 12:125-30.
331. Tale, W.P., Mansell, J.B., Mannering, S.A., Irvine, J.H., Major, L.L. and Wilson, D. 1999. UGA: a dual signal for 'stop'and for recoding in protein synthesis. Biochemistry (Mosc), 64:1342-53.
332. Tatebayashi, K., Tanaka, K., Yang, H.Y., Yamamoto, K., Matsushita, V., Tomida,T., Imai, M. and Saito, H. 2007. Transmembrane mucins Hkr1 and Msb2 are putative osmosensors in the SHOI branch of yeast HOG pathway. Embo J. 26:3521-33.
333. Terentiev, A.A. and Moldogazieva, N.T. 2006. Structural and functional mapping of alpha-fetoprotein. Biochemistry (Mosc). 71:120-32.
334. Theil, E.C. and Eisenstein, R.S. 2000. Combinatorial mRNA regulation: iron regulatory proteins and iso-iron-responsive elements (Iso-IREs). J. Biol. Chem., 275:40659-62.
335. Torres, C.R. and Hart, G.W. 1984. Topography and polypeptide distribution of terminal N.-acetylglucosomine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc. J. Biol. Chem., 259:3308-17.
336. Torres, J.M., Darracq, N. and Uriel, J. 1992. Membrane proteins from lymphoblastoid cells showing cross-affinity for alpha-fetoprotein and albumin. Isolation and characterization. Biochim. Biophys Acta, 1159:60-6.
337. Torres, J.M , Laborda, J., Naval, J., Darracq, N., Calvo, M., Mishal, Z. and Uriel, J. 1989. Eypression of alpha-fetoprotein receptors by human T-lymphocytes during blastic transformation. Mol. Immunol., 26:851-7.
338. Touriol, C,, Bornes, S., Bonnal, S., Audigier, S., Prats, H., Prats, A.C. and Vagner, S. 2003. Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons. Biol. Cell, 95:169-78
339. Treitel, M.A., Kcuhin, S. and Carlson, M. 1998. Snfl protein kinase regulates phosphorylation of the Mig1 repressor in Saccharomyces cerevisiae. Mol. Cell Biol., 18:6273-80.
340. Trewhella, J. 1992. The solution structures of calmodulin and its complexes with synthetic peptides based on target enzyme binding domains. Cell Calcium, 13:377-90
341. Tsarfaty, I., Hareuveni, M., Horev, J., Zaretsky, J., Weiss, M., Jeltsch, J.M., Garnier, J.M., Lathe, R., Keydar, I. and Wreschner, D.H. 1990. Isolation and characterization of an expressed hypervariable gene coding for a breast-cancer-associated antigen. Gene, 93:313-8.
342. Tsukuda, M., Asaoka, Y., Sekiguhi, K., Kikkawa, U. and Nishizuka, Y. 1988. Properties of protein kinase C subspecies in human platelets. Biochem. Biophys. Res. Commu., 155:1387-95.
343. Ubersax, J.A, and Ferrell, JEJr, 2007. Mechanisms of specificity in protein phosphorylation. Nat. Rev. Mol. Cell Biol., 8:530-41.
344. Ullrich, B., Ushkaryov, Y.A. and Sudhof, T.C. 1995. Cartography of neurexins more than 1000 isoforms generated by alternative splicing and expressed in distinct subsets of neurons. Neuron. 14:497-507.
345. Urner, F. and Sakkaa, D. 2003, Protein phosphorylation in mammalian spermatozoa. Reproduction, 125:17-26.
346. Vigneron, N., Stroobant, V., Chapiro, J., Ooms, A., Degiovanni, G., Morel, S., van der Bruggen, P., Boon, T. and Van der, Eynde, B.J. 2004. An antigenic peptide produced by peptide splicing in the proteasome. Science, 304:587-90.
347. Vincent, T.S., Fraylick, J.E., McGuffie, E.M. and Olson, J.C. 1999 ADP-ribosylation of oncogenic Ras proteins by pseudomonas aeruginosa exoenzyme S in vivo. Mol. Microbiol., 32:1054-64.
348. von der Haar, T. and Tuite, M.F. 2007. Regulated translational bypass of stop codons in yeast. Trends Microbiol., 15:78-86.
349. Wakasugi, K. and Schimmel, P. 1999. Two distinct cytokines released from a human aminoacyl-tRNA synthetase. Science, 284: 147-51.
350. Walden, W.E., Selezneva, A.I., Dupuy, J., Volbeda, A., Fontecilla-Camps, J.C., Theil, E.C. and Volz, K. 2006. Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA. Science, 314:1903-8.
351. Wang, W., Czaplinski, K., Rao, Y. and Peltz, S.W. 2001. The role of Upf proteins in modulating the translation read-through of nonsense-containing transcripts. Embo J., 20:880-90.
352. Ward, P.P, Uribe-Luna, S. and Conneely, O.M 2002. Lactoferrin and host defense. Biochem. Cell Biol., 80:95-102.
353. Weiss, M., Zaretsky, J., Zimlichman, R., Smorodinsky, N., Dion, A.S., Keydar, I. and Wreschner, D.H. 1991. Expression of a gene coding for breast tumor-associated antigen in thyroid papillary carcinoma. Cancer Lett 58:125-30.
354. Wells, L. and Hart, G.W. 2003, O-GlcNAc turns twenty: functional implications for post-translational modi cation of nuclear and cytosolic proteins with a sugar. FEBS Lett. 546: 154-8.
355. Wen, Y., Caffrey, T.C., Wheelock, M. J., Johnson, K.R. and Hollingsworth, M.A. 2003. Nuclear association of the cytoplasmic tail of MUC1 and beta-catenin. J. Mol. Chem., 278: 38029-39.
356. Wiegand, H.L., Lu, S. and Cullen, B. R. 2003. Exon junction complexes mediate the enhancing effect of splicing on mRNA expression. Proc. Natl. Acad. Sci. U.S.A., 100: 11327-32.
357. Wilchek, M. and Miron, T. 1974. Polymers coupled to agarose as stable and high capacity spacers. Methods Enzymol 34:72-6.
358. Wilkinson, M.F. 2005. A new function for nonsense-mediated mRNA-decay factors. Trends Genet. 21:143-8.
359. Williams, C.J., Wreschner, D.H., Tanaka, A., Tsarfaty, I., Keydar, I. and Dion, A.S. 1990. Multiple protein forms of the human breast tumor-associated epithelial membrane antigen (EMA) are generated by alternative splicing and induced by hormonal stimulation. Biochem Biophys. Res. Commun., 170:1331-8.
360. Williams, I., Richardson, J., Starkey, A. and Stansfeld, I. 2004. Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae. Nucleic Acids Res., 32:6605-16.
361. Williams, R.T., Manji, S.S., Parker, N.J., Hancock, M.S., Van Stekelenburg, L., Eid, J.P., Senior, P.V., Kazenwadel, J.S., Shandala, T., Saint, R., Smith, P.J. and Dziadek, M.A. 2001. Identification and characterization of the STIM (stromal interaction molecule) gene family: coding for a novel class of transmembrane proteins. Biochem. J., 357:673-85.
362. Willnow, T.E., Sheng, Z., Ishibashi, S. and Herz, J. 1994. Inhibition of hepatic chylomicron remnant uptake by gene transfer of a receptor antagonist. Science, 264:14171-4.
363. Wilson, R.B., Renault, G., Jacquet, M. and Tatchell, K. 1993. The pde2 gene of Saccharomyces cerevisiae is allelic to real and encodes a phosphodiesterase which protects the cell from extracellwar cAMP. FEBS Lett, 325: 191-5
364. Wilson, R.B. and Tatchell, K. 1988. SRA5 encodes the low-Km cyclic AMP phosphodiesterase of Saccharomyces cerevisiae. Mol. Cell Biol., 8:505-10.
365. Wood, P. 2001. Growth hormone: its measurement and the need for assay harmonization. Ann. Clin. Biochem., 38:471-82.
366. Wreschner, D.H., Hareuveni, M., Tsarfaty, I., Smorodinsky, N. Horev, J., Zaretsky, J., Kotkes, P., Weiss, M., Lathe, R., Dion, A. et al. 1990. Human epithelial tumor antigen cDNA sequences. Differential splicing may generate multiple protein forms. Eur. J. Biochem., 189:463-73.
367. Wreschner, D.H., McGuckin, M.A., Williams, S.J., Baruch, A., Yoeli, M., Ziv, R., Okun, L., Zaretsky, J., Smorodinsky, N., Keydar, I., Neophytou, P., Stacey, M., Lin, H.H, and Gordon, S. 2002. Generation of ligand-receptor alliances by SEA module-mediated cleavage of membrane-associated mucin proteins. Protein Sci., 11:698-706.
368. Wreschner, D.H., Zrihan-Licht, S., Baruch, A., Sagiv, D., Hartman, M.L., Smorodinsky, N. and Keydar, I. 1994. Does a novel form of the breast cancer marker protein, MUC1, act as a receptor molecule that modulates signal transduction? Adv Exp. Med. Biol., 353: 17-26.
369. Wriggers, W., Chakravarty, S. and Jennings, P.A. 2005. Control of protein functional dynamics by peptide linkers. Biopolymers, 80:736-46.
370. Wu, Y. and Matthews, C.R. 2002. A cis-prolyl peptide bond isomerization dominates the folding of the alpha subunit of Trp synthase, a TIM barrel protein. J. Mol. Biol., 322: 7-13.
371. Yannay-Cohen, N. and Razin, E. 2006. Translation and transcription: the dual functionality of LysRS in mast cells. Mol. Cells, 22, 127-32.
372. Yap, K.L., Kim, J., Truong, K., Sherman, M., Yuan, T. and Ikura, M. 2000. Calmodulin target database. J. Siruct. Funct. Genomics. 1:8-14.
373. Yook, S.H., Oltvai, Z.N. and Barabasi, A.L. 2004. Functional and topological characterization of protein interaction networks. Proteomics, 4:928-42.
374. Yoshinaka, Y., Katob, I., Copeland, T.D. and Oroszlan, S. 1985. Murine leukemia virus protease is encoded by the gag-pol gene and is synthesized through suppression of an amber termination codon. Proc. Natl. Acad. Sci. U.S.A. 82: 1618-22.
375. Yuch, A. and Schneider, R.J. 1996. Selective translation initiation by ribosome jumping in adenovirus-infected and heat-shocked cells. Genes Dev., 10:1557-67.
376. Zamecnik, P.C., Stephenson, M.L., Janeway, C.M. and Randerath, K. 1966. Enzymatic synthesis of diadenosine tetraphosphate and diadenosine triphosphate with a purified lysyl-sRNA synthetase. Biochem. Biophys. Res. Commun., 24:91-7.
377. Zaretsky, J.Z., Barnea, I., Aylon, Y., Gorivodsky, M., Wreschner, D.H. and Keydar, I. 2006. MUC1 gene overexpressed in breast cancer: structure and transcriptional activity of the MUC1 promoter and role of estrogen receptor alpha (ERalpha) in regulation of the MUC1 gene expression. Mol. Cancer, 5:57.
378. Zaretsky, J.Z., Sarid, R., Aylon, Y., Mittelman, L.A., Wreschner, D-H. and Keydar, I. 1999. Analysis of the promoter of the MUC1 gene over-expressed in breast cancer. FEBS Lett. 461: 189-95.
379. Zaretsky, J.Z., Weiss, M., Tsarfaty, I., Hareuveni, M., Wreschner, D.H., and Keydar, I. 1990. Expression of genes coding for pS2, c-erbB2, estrogen receptor and the H23 breast tumor-associated antigen. A comparative analysis in breast cancer. FEBS Lett, 265:46-50
380. Zhang, S.L., Yu, Y., Roos, J., Kozak, J.A., Deerinck, T.J., Ellisman, M.H., Stauderman, K.A. and Cahalan, M.D. 2005. STIM1 is a Ca2+ sensor that activates CRAC channels and migrates from the Ca2+store to the plasma membrane. Nature, 437:902-5.
381. Zipursky, S.L,, Wojtowicz, W.M. and Hattori, D. 2006. Got diversity? Wiring the y brain with Dscam. Trends Biochem. Sci., 31:581-8.
382. Zrihan-Licht, S., Vos, H.L., Baruch, A., Elroy-Stein, O., Sagiv, D., Keydar, I., Hilkens, J. and Wreschner, D.H. 1994. Characterization and molecular cloning of a novel MUC1 protein, devoid of tandem repeats, expressed in human breast cancer tissue. Eur. J. Biochem., 224:787-95.