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2015 | 62 | 1 | 41-55
Article title

Identification of proteins associated with amyloidosis by polarity index method

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There is a natural protein form, insoluble and resistant to proteolysis, adopted by many proteins independently of their amino acid sequences via specific misfolding-aggregation process. This dynamic process occurs in parallel with or as an alternative to physiologic folding, generating toxic protein aggregates that are deposited and accumulated in various organs and tissues. These proteinaceous deposits typically represent bundles of β-sheet-enriched fibrillar species known as the amyloid fibrils that are responsible for serious pathological conditions, including but not limited to neurodegenerative diseases, grouped under the term amyloidoses. The proteins that might adopt this fibrillar conformation are some globular proteins and natively unfolded (or intrinsically disordered) proteins. Our work shows that intrinsically disordered and intrinsically ordered proteins can be reliably identified, discriminated, and differentiated by analyzing their polarity profiles generated using a computational tool known as the polarity index method (Polanco & Samaniego, 2009; Polanco et al., 2012; 2013; 2013a; 2014; 2014a; 2014b; 2014c; 2014d). We also show that proteins expressed in neurons can be differentiated from proteins in these two groups based on their polarity profiles, and also that this computational tool can be used to identify proteins associated with amyloidoses. The efficiency of the proposed method is high (i.e. 70%) as evidenced by the analysis of peptides and proteins in the APD2 database (2012), AVPpred database (2013), and CPPsite database (2013), the set of selective antibacterial peptides from del Rio et al. (2001), the sets of natively unfolded and natively folded proteins from Oldfield et al. (2005), the set of human revised proteins expressed in neurons, and non-human revised proteins expressed in neurons, from the Uniprot database (2014), and also the set of amyloidogenic proteins from the AmyPDB database (2014).
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  • Facultad de Ciencias de la Salud, Universidad Anáhuac, Anáhuac, México
  • Facultad de Ciencias de la Salud, Universidad Anáhuac, Anáhuac, México
  • Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, USA
  • Facultad de Ciencias de la Salud, Universidad Anáhuac, Anáhuac, México
  • Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos México
  • Facultad de Ciencias de la Salud, Universidad Anáhuac, Anáhuac, México
  • Facultad de Ciencias de la Salud, Universidad Anáhuac, Anáhuac, México
  • Departamento de Ciencias Computacionales, Instituto Nacional de Astrofísica, Óptica y Electrónica, Puebla, México
  • Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, México
  • Departamento de Ciencias Computacionales, Instituto Nacional de Astrofísica, Óptica y Electrónica, Puebla, México
  • Departamento de Ciencias Computacionales, Instituto Nacional de Astrofísica, Óptica y Electrónica, Puebla, México
  • Abrahamson M, Grubb A, Olafsson I, Lundwall A (1987) Molecular cloning and sequence analysis of cDNA coding for the precursor of the human cysteine proteinase inhibitor cystatin C. FEBS Lett 216: 229-233.
  • Ackerman SJ, Corrette SE, Rosenberg HF, Bennett JC, Mastrianni DM, Nicholson-Weller A, Weller PF, Chin DT, Tenen DG (1993) Molecular cloning and characterization of human eosinophil Charcot-Leyden crystal protein (lysophospholipase). Similarities to IgE binding proteins and the S-type animal lectin superfamily. J Immunol 150: 456-468.
  • Aiba H, Mori K, Tanaka M, Ooi T, Roy A, Danchin A (1984) The complete nucleotide sequence of the adenylate cyclase gene of Escherichia coli. Nucleic Acids Res. 12: 9427-9440.
  • Albrecht JC, Nicholas J, Biller D, Cameron KR, Biesinger B, Newman C, Wittmann S, Craxton MA, Coleman H, Fleckenstein B, Honess RW (1992) Primary structure of the herpesvirus saimiri genome. J Virol 66: 5047-5058.
  • Andreola A, Bellotti V, Giorgetti S, Mangione P, Obici L, Stoppini M, Torres J, Monzani E, Merlini G, Sunde M (2006) Conformational switching and fibrillogenesis in the amyloidogenic fragment of apolipoprotein A-I. J Biol Chem 278: 2444-24451.
  • Arya SK, Gallo RC (1986) Three novel genes of human T-lymphotropic virus type III: inmune reactivity of their products with sera from acquired immune deficiency syndrome patients. Proc Natl Acad Sci USA 83: 2209-2213.
  • Auron PE, Webb AC, Rosenwasser LJ, Mucci SF, Rich A, Wolff SM, Dinarello CA (1984) Nucleotide sequence of human monocyte interleukin 1 precursor cDNA. Proc Natl Acad Sci USA 81: 7907-7911.
  • Biesiadka J, Sikorski MM, Bujacz G, Jaskolski M (1999) Crystallization and preliminary x-ray structure determination of Lupinus luteus PR10 protein. Acta Crystallogr D Biol Crystallogr 55: 1925-1927.
  • Bredt DS, Hwang PM, Glatt CE, Lowenstein C, Reed RR, Snyder SH (1991) Cloned and expressed nitric oxide synthase structurally resembles cytochrome P-450 reductase. Nature 351: 714-718.
  • Buckanovich RJ, Posner JB, Darnell RB (1993) Nova, the paraneoplastic Ri antigen, is homologous to an RNA-binding protein, is specifically expressed in the developing motor system. Neuron 11: 657-672.
  • Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM (1995) High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J Mol Biol 253: 333-346.
  • Burton ZF, Gross CA, Watanabe KK, Burgess RR (1983) The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21, DNA primase in E. coli K12. Cell 32: 335-349.
  • Bussey H, Storms RK, Ahmed A, Albermann K, Allen E, Ansorge W, Araujo R, Aparicio A, Barrell BG, Badcock K, Benes V, Botstein D, Bowman S, Brueckner M, Carpenter J, Cherry JM, Chung E, Churcher CM, Coster F, Davis K, Davis RW, Dietrich FS, Delius H, DiPaolo T, Dubois E, Duesterhoeft A, Duncan M, Floeth M, Fortin N, Friesen JD, Fritz C, Goffeau A, Hall J, Hebling U, Heumann K, Hilbert H, Hillier LW, Hunicke-Smith S, Hyman RW, Johnston M, Kalman S, Kleine K, Komp C, Kurdi O, Lashkari D, Lew H, Lin A, Lin D, Louis EJ, Marathe R, Messenguy F, Mewes HW, Mirtipati S, Moestl D, Mueller-Auer S, Namath A, Nentwich U, Oefner P, Pearson D, Petel FX, Pohl TM, Purnelle B, Rajandream MA, Rechmann S, Rieger M, Riles L, Roberts D, Schaefer M, Scharfe M, Scherens B, Schramm S, Schroeder M, Sdicu AM, Tettelin H, Urrestarazu LA, Ushinsky S, Vierendeels F, Vissers S, Voss H, Walsh SV, Wambutt R, Wang Y, Wedler E, Wedler H, Winnett E, Zhong WW, Zollner A, Vo DH, Hani J (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature 387: 103-105.
  • Chardin P, Paris S, Antonny B, Robineau S, Beraud-Dufour S, Jackson CL, Chabre M (1996) A human exchange factor for ARF contains Sec7-, pleckstrin-homology domains. Nature 384: 481-484.
  • Charles IG, Dougan G, Pickard D, Chatfield S, Smith M, Novotny P, Morrissey P, Fairweather NF (1989) Molecular cloning and characterization of protective outer membrane protein P.69 from Bordetella pertussis. Proc Natl Acad Sci USA 86: 3554-3558.
  • Chen Y, Riley DJ, Chen PL, Lee WH (1997) HEC, a novel nuclear protein rich in leucine heptad repeats specifically involved in mitosis.Mol Cell Biol 17: 6049-6056.
  • Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson CM (1999) Designing conditions for in vitro formation of amyloid protofilaments, fibrils. Proc Natl Acad Sci USA 96: 3590-3594.
  • Chou MY, Li SC, Li YT (1996) Cloning and expression of sialidase L, a NeuAcalpha2-->3Gal-specific sialidase from the leech, Macrobdella decora. J Biol Chem 271: 19219-19224.
  • Christensen HE, Ramachandran S, Tan CT, Surana U, Dong CH, Chua NH (1996) Arabidopsis profilins are functionally similar to yeast profilins: identification of a vascular bundle-specific profilin, a pollen-specific profilin. Plant J 10: 269-279.
  • Cole ST, Danos O (1987) Nucleotide sequence and comparative analysis of the human papillomavirus type 18 genome. Phylogeny of papillomaviruses, repeated structure of the E6, E7 gene products. J Mol Biol 193: 599-608.
  • Colombo G, Fanti P, Yao C, Malluche HH (1993) Isolation and complete amino acid sequence of osteocalcin from canine bone. J Bone Miner Res 8: 733-743.
  • Cook J, Holder (1994) Substructure Discovery Using Minimum Description Length, Background Knowledge. J Artif Intell Res 1: 231-255.
  • Cooke NE, Coit D, Shine J, Baxter JD, Martial JA (1981) Human prolactin. cDNA structural analysis, evolutionary comparisons. J Biol Chem 256: 4007-4016.
  • Couto JR, Taylor MR, Godwin SG, Ceriani RL, Peterson JA (1996) Cloning and sequence analysis of human breast epithelial antigen BA46 reveals an RGD cell adhesion sequence presented on an epidermal growth factor-like domain. DNA Cell Biol 15: 281-286.
  • Cram D S, Loh SM, Cheah KC, Skurray RA (1991) Sequence and conservation of genes at the distal end of transfer region on plasmids F, R6-5. Gene 104: 85-90.
  • Davies GJ, Dauter M, Brzozowski AM, Bjørnvad ME, Andersen KV, Schülein M (1998) Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A, its cellobiose complex at 2.0 A resolution. Biochemistry 37: 1926-1932.
  • De Reuse H, Danchin A (1988) The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription. J Bacteriol 170: 3827-3837.
  • del Rio G, Castro-Obregon S, Rao R, Ellerby HM, Bredesen DE (2001) APAP, a sequence-pattern recognition approach identifies substance P as a potential apoptotic peptide. FEBS Lett 494: 213-219.
  • Devlin, TM (1992) The Textbook of Biochemistry - 3rd Edition, Wiley-Liss Inc, NY, accessed May 16, 2014
  • Domenjoud L, Fronia C, Uhde F, Engel W (1988) Sequence of human protamine 2 cDNA. Nucleic Acids Res 16: 7733.
  • Drocourt D, Calmels T, Reynes JP, Baron M, Tiraby G (1990) Cassettes of the Streptoalloteichus hindustanus ble gene for transformation of lower, higher eukaryotes to phleomycin resistance. Nucleic Acids Res 18: 4009.
  • Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang C, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic Z (2001) Intrinsically disordered protein. J Mol Graph Model 19: 26-59.
  • Dunker AK, Obradovic Z, Romero P, Garner EC, Brown CJ (2000) Intrinsic protein disorder in complete genomes. Genome Inform Ser Workshop Genome Inform 11: 161-171.
  • Eckner R, Birnstiel ML (1989) Cloning of cDNAs coding for human HMG I, HMG Y proteins: both are capable of binding to the octamer sequence motif. Nucleic Acids Res 17: 5947-5959.
  • Eirin-Lopez JM, Fernanda RM, Gonzalez-Tizon AM, Martinez A, Sanchez L, Mendez J (2004) Molecular evolutionary characterization of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of five histone genes containing an H1 subtype with 'orphon' features. J Mol Evol 58: 131-144.
  • Eschenfeldt WH, Berger SL (1986) The human prothymosin alpha gene is polymorphic, induced upon growth stimulation: evidence using a cloned cDNA. Proc Natl Acad Sci USA 83: 9403-9407.
  • Eylar EH, Brostoff S, Hashim G, Caccam J, Burnett P (1971) Basic A1 protein of the myelin membrane. The complete amino acid sequence. J Biol Chem 246: 5770-5784.
  • Fahnestock SR, Alexander P, Nagle J, Filpula D (1986) Gene for an immunoglobulin-binding protein from a group G streptococcus. J Bacteriol 167: 870-880.
  • Fink AL (2005) Natively unfolded proteins. Curr Opin Struct Biol 15: 35-41.
  • Fujiwara T, Ito K, Nakayashiki T, Nakamura Y (1999) Amber mutations in ribosome recycling factors of Escherichia coli, Thermus thermophilus: evidence for C-terminal modulator element. FEBS Lett 447: 297-302.
  • Funayama N, Nagafuchi A, Sato N, Tsukita S, Tsukita S (1991) Radixin is a novel member of the band 4.1 family. J Cell Biol 115: 1039-1048.
  • Gaillard JL, Berche P, Frehel C, Gouin E, Cossart P (1991) Entry of L. monocytogenes into cells is mediated by internalin, a repeat protein reminiscent of surface antigens from gram-positive cocci. Cell 65: 1127-1141.
  • Galaktionov K, Beach D (1991) Specific activation of cdc25 tyrosine phosphatases by B-type cyclins: evidence for multiple roles of mitotic cyclins. Cell 67: 1181-1194.
  • Garcia-Villegas MR, De La Vega FM, Galindo JM, Segura M, Buckingham RH, Guarneros G (1991) Peptidyl-tRNA hydrolase is involved in lambda inhibition of host protein synthesis. EMBO J 10: 3549-3555.
  • Gautam A, Singh H, Tyagi A, Chaudhary K, Kumar R, Kapoor P, Raghava GP (2012) CPPsite: a curated database of cell penetrating peptides. Database (Oxford) 2012: bas015, accessed May 20, 2013.
  • Gerber-Huber S, Nardelli D, Haefliger JA, Cooper DN, Givel F, Germond JE, Engel J, Green NM, Wahli W (1987) Precursor-product relationship between vitellogenin, the yolk proteins as derived from the complete sequence of a Xenopus vitellogenin gene. Nucleic Acids Res 15: 4737-4760.
  • Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk, SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J (2004) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res 14: 2121-2127.
  • Ghosh S, Gifford AM, Riviere LR, Tempst P, Nolan GP, Baltimore D (1990) Cloning of the p50 DNA binding subunit of NF-kappa B: homology to rel, dorsal. Cell 62: 1019-1029.
  • Gibbs S, Lohman F, Teubel W, van de Putte P, Backendorf C (1990) Characterization of the human spr2 promoter: induction after UV irradiation or TPA treatment, regulation during differentiation of cultured primary keratinocytes. Nucleic Acids Res 18: 4401-4407.
  • Gibbs S, Lohman F, Teubel W, van de Putte P, Backendorf C (1990) Characterization of the human spr2 promoter: induction after UV irradiation or TPA treatment, regulation during differentiation of cultured primary keratinocytes. Nucleic Acids Res 18: 4401-4407.
  • Gill DR, Hatfull GF, Salmond GP (1986) A new cell division operon in Escherichia coli. Mol Gen Genet 205: 134-145.
  • Gilmour J, Liang N, Lowenstein JM (1997) Isolation, cloning and characterization of a low-molecular-mass purine nucleoside-, nucleotide-binding protein. Biochem J 326: 471-477.
  • Goedert M, Wischik CM, Crowther RA, Walker JE, Klug A. (1988) Cloning and sequencing of the cDNA encoding a core protein of the paired helical filament of Alzheimer disease: identification as the microtubule-associated protein tau. Proc Natl Acad Sci USA 85: 4051-4055.
  • Goedert M, Wischik CM, Crowther RA, Walker JE, Klug A. (1988) Cloning and sequencing of the cDNA encoding a core protein of the paired helical filament of Alzheimer disease: identification as the microtubule-associated protein tau. Proc Natl Acad Sci USA 85: 4051-4055.
  • Güssow D, Rein R, Ginjaar I, Hochstenbach F, Seemann G, Kottman A, Ploegh HL (1987) The human beta 2-microglobulin gene. Primary structure, definition of the transcriptional unit. J Immunol 139: 3132-3128.
  • Hall KU, Collins SP, Gamm DM, Massa E, DePaoli-Roach AA, Uhler MD (1999) Phosphorylation-dependent inhibition of protein phosphatase-1 by G-substrate. A Purkinje cell substrate of the cyclic GMP-dependent protein kinase. J Biol Chem 274: 3485-3495.
  • Kang J, Lemaire HG, Unterbeck A, Salbaum JM, Masters CL, Grzeschik KH, Multhaup G, Beyreuther K, Müller-Hill B (1987) The precursor of Alzheimer's disease amyloid A4 protein resembles a cell-surface receptor. Nature 325: 733-736.
  • Kawashima S, Kanehisa M (2000) AAindex: amino acid index database. Nucleic Acids Res 28 374.
  • Koolman J, Rohm KH (1996) Colour Atlas of Biochemistry, Thieme, Stuttgart, 1996, accessed May 16, 2014
  • Kwiatkowski DJ, Stossel TP, Orkin SH, Mole JE, Colten HR, Yin HL (1986) Plasma and cytoplasmic gelsolins are encoded by a single gene, contain a duplicated actin-binding domain. Nature 323: 455-458.
  • Hansen JC, Lu X, Ross ED, Woody RW (2006) Intrinsic protein disorder, amino acid composition, histone terminal domains. J Biol Chem 281: 1853-1856.
  • Harper JW, Adami GR, Wei N, Keyomarsi K, Elledge SJ (1993) The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases. Cell 75: 805-816.
  • Hay RE, Woods WD, Church RL, Petrash JM (1987) cDNA clones encoding bovine gamma-crystallins. Biochem Biophys Res Commun 146: 332-338.
  • Hemmingsen SM, Woolford C, van der Vies SM, Tilly K, Dennis DT, Georgopoulos CP, Hendrix RW, Ellis RJ (1988) Homologous plant and bacterial proteins chaperone oligomeric protein assembly.Nature 333: 330-334.
  • Hew CL, Wang NC, Joshi S, Fletcher GL, Scott GK, Hayes PH, Buettner B, Davies PL (1988) Multiple genes provide the basis for antifreeze protein diversity, dosage in the ocean pout, Macrozoarces americanus. J Biol Chem 263: 12049-12055.
  • Hu RJ, Watanabe M, Bennett V (1992) Characterization of human brain cDNA encoding the general isoforma of beta-spectrin. J Biol Chem 267: 18715-18722.
  • Iacangelo AL, Grimes M, Eiden LE (1991) The bovine chromogranin A gene: structural basis for hormone regulation, generation of biologically active peptides. Mol Endocrinol 5: 1651-1660.
  • Inokuchi K, Mutoh N, Matsuyama S, Mizushima S (1982) Primary structure of the ompF gene that codes for a major outer membrane protein of Escherichia coli K-12. Nucleic Acids Res 10: 6957-6968.
  • Inouye M, Imada M, Tsugita A (1970) The amino acid sequence of T4 phage lysozyme. IV. Dilute acid hydrolysis, the order of tryptic peptides. J Biol Chem 245: 3479-3484.
  • Izadpanah A, Gallo RL. (2005) Antimicrobial peptides. J Am Acad Dermatol 52: 381-390; quiz 391-392.
  • Janssen DB, Pries F, van der Ploeg J, Kazemier B, Terpstra P, Witholt B (1989) Cloning of 1,2-dichloroethane degradation genes of Xanthobacter autotrophicus GJ10, expression, sequencing of the dhlA gene. J Bacteriol 171: 6791-6799.
  • Jauris-Heipke S, Fuchs R, Motz M, Preac-Mursic V, Schwab E, Soutschek E, Will G, Wilske B (1993) Genetic heterogenity of the genes coding for the outer surface protein C (OspC), the flagellin of Borrelia burgdorferi. Med Microbiol Immunol 182: 37-50.
  • Jerse AE, Yu J, Tall BD, Kaper JB (1990) A genetic locus of enteropathogenic Escherichia coli necessary for the production of attaching, effacing lesions on tissue culture cells. Proc Natl Acad Sci USA 87: 7839-7843.
  • Ji H, Liu YE, Jia T, Wang M, Liu J, Xiao G, Joseph BK, Rosen C, Shi YE (1977) Identification of a breast cancer-specific gene, BCSG1, by direct differential cDNA sequencing. Cancer Res 57: 759-764. .
  • Jung A, Sippel AE, Grez M, Schutz G (1980) Exons encode functional and structural units of chicken lysozyme. Proc Natl Acad Sci USA 77: 5759-5763.
  • Karlsen S, Hough E, Olsen RL (1998) Structure and proposed amino-acid sequence of a pepsin from atlantic cod (Gadus morhua). Acta Crystallogr D Biol Crystallogr 54: 32-46.
  • Kiefer MC, Bauer DM, Barr PJ (1989) The cDNA and derived amino acid sequence for human osteopontin. Nucleic Acids Res 17: 3306.
  • Koch C, Moll T, Neuberg M, Ahorn H, Nasmyth K (1993) A role for the transcription factors Mbp1, Swi4 in progression from G1 to S phase. Science 261: 1551-1557.
  • Koenig M, Monaco AP, Kunkel LM (1988) The complete sequence of dystrophin predicts a rod-shaped cytoskeletal protein. Cell 53: 219-228.
  • Konecki DS, Benedum UM, Gerdes HH, Huttner WB (1987) The primary structure of human chromogranin A, pancreastatin. J Biol Chem 262: 17026-17030.
  • Kretzschmar HA, Stowring LE, Westaway D, Stubblebine WH, Prusiner SB, Dearmond SJ (1986) Molecular cloning of a human prion protein cDNA. DNA 5: 315-324.
  • Kukluk J, You C, Holder L, Cook D (2007) Learning node replacement graph grammars in metabolic pathways. International conference on bioinformatics. Computational Biology (BIOCOMP-07).
  • Lee JS, An G, Friesen JD, Isono K (1981) Cloning and the nucleotide sequence of the genes for Escherichia coli ribosomal proteins L28 (rpmB), L33 (rpmG). Mol Gen Genet 184: 218-223.
  • Lee WH, Shew JY, Hong FD, Sery TW, Donoso LA, Young LJ, Bookstein R, Lee EY (1987) The retinoblastoma susceptibility gene encodes a nuclear phosphoprotein associated with DNA binding activity. Nature 329: 642-645.
  • Leffers H, Nielsen MS, Andersen AH, Honore B, Madsen P, Vandekerckhove J, Celis JE (1993) Identification of two human Rho GDP dissociation inhibitor proteins whose overexpression leads to disruption of the actin cytoskeleton. Exp Cell Res 209: 165-174.
  • Li S, Finley J, Liu ZJ, Qiu SH, Chen H, Luan CH, Carson M, Tsao J, Johnson D, Lin G, Zhao J, Thomas W, Nagy LA, Sha B, DeLucas LJ, Wang BC, Luo M (2002) Crystal structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain. J Biol Chem 277: 48596-48601.
  • Loeb JD, Davis LI, Fink GR (1993) NUP2, a novel yeast nucleoporin, has functional overlap with other proteins of the nuclear pore complex. Mol Biol Cell 4: 209-222.
  • Luiten RG, Putterman DG, Schoenmakers JG, Konings RN, Day LA (1985) Nucleotide sequence of the genome of Pf3, an IncP-1 plasmid-specific filamentous bacteriophage of Pseudomonas aeruginosa. J Virol 56: 268-276.
  • Luke MM, Sutton A, Arndt KT (1991) Characterization of SIS1, a Saccharomyces cerevisiae homologue of bacterial dnaJ proteins. J Cell Biol 114: 623-638.
  • Maeda K, Kneale GG, Tsugita A, Short NJ, Perham RN, Hill DF, Petersen GB (1982) The DNA-binding protein of Pf1 filamentous bacteriophage: amino-acid sequence, structure of the gene. EMBO J 1: 255-261.
  • Maeder DL, Weiss RB, Dunn DM, Cherry JL, Gonzalez JM, DiRuggiero J, Robb FT (1999) Divergence of the hyperthermophilic archaea Pyrococcus furiosus, P. horikoshii inferred from complete genomic sequences. Genetics 152: 1299-1305.
  • Magrane M, the UniProt consortium (2011) UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011: bar009 accessed Oct 21, 2013.
  • Martin-Verstraete I, Debarbouille M, Klier A, Rapoport G (1990) Levanase operon of Bacillus subtilis includes a fructose-specific phosphotransferase system regulating the expression of the operon. J Mol Biol 214: 657-671.
  • McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliott G, Kohlberg S, Strong C, Du F, Carter J, Kremizki C, Layman D, Leonard S, Sun H, Fulton L, Nash W, Miner T, Minx P, Delehaunty K, Fronick C, Magrini V, Nhan M, Warren W, Florea L, Spieth J, Wilson RK (2004) Comparison of genome degradation in Paratyphi A, Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet 36: 1268-1274.
  • McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16: 404-405.
  • McHugh KM, Lessard JL (1988) The nucleotide sequence of a rat vascular smooth muscle alpha-actincDNA. Nucleic Acids Res 16: 4167.
  • McLaren L, Boyle S, Mason JO, Bard JB (2000) Expression and genomic characterization of protein phosphatase inhibitor-1: a novel marker for mesothelium in the Mouse. Mech Dev 96: 237-241.
  • McLaren L, Boyle S, Mason JO, Bard JB (2000) Expression and genomic characterization of protein phosphatase inhibitor-1: a novel marker for mesothelium in the Mouse. Mech Dev 96: 237-241.
  • Mengaud J, Braun-Breton C, Cossart P (1991) Identification of phosphatidylinositol-specific phospholipase C activity in Listeria monocytogenes: a novel type of virulence factor? Mol Microbiol 5: 367-372.
  • Mita S, Maeda S, Shimada K, Araki S (1984) Cloning and sequence analysis of cDNA for human prealbumin. Biochem Biophys Res Commun 124: 558-64.
  • Mosqueira FG, Negron A, Ramos S, Polanco C (2012) Biased versus unbiased randomness in homo-polymers, copolymers of amino acids in the prebiotic world. Acta Biochim Pol 59: 543-547.
  • Mosselman S, Höppener JW, Lips CJ, Jansz HS (1989) The complete islet amyloid polypeptide precursor is encoded by two exons. FEBS Lett 247: 154-158.
  • Nagase T, Ishikawa K, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O (1998) Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. DNA Res 5: 31-39.
  • Nakashima T, Higa H, Matsubara H, Benson AM, Yasunobu KT (1966) The amino acid sequence of bovine heart cytochrome c. J Biol Chem 241: 1166-1177.
  • Nanmori T, Nagai M, Shimizu Y, Shinke R, Mikami B (1993) Cloning of the beta-amylase gene from Bacillus cereus, characteristics of the primary structure of the enzyme. Appl Environ Microbiol 59: 623-627.
  • Ogata M, Sawada M, Fujino Y, Hamaoka T (1995) cDNA cloning and characterization of a novel receptor-type protein tyrosine phosphatase expressed predominantly in the brain. J Biol Chem 270: 2337-2343.
  • Ogawa T, Ishii C, Kagawa D, Muramoto K, Kamiya H (1999) Accelerated evolution in the protein-coding region of galectin cDNAs, congerin I, congerin II, from skin mucus of conger eel (Conger myriaster). Biosci Biotechnol Biochem 63: 1203-1208.
  • Oikawa S, Imai M, Ueno A, Tanaka S, Noguchi T, Nakazato H, Kangawa K, Fukuda A, Matsuo H (1984) Cloning and sequence analysis of cDNA encoding a precursor for human atrial natriuretic polypeptide. Nature 309: 724-726.
  • Oki M, Nishimoto T (1998) A protein required for nuclear-protein import, Mog1p, directly interacts with GTP-Gsp1p, the Saccharomyces cerevisiae ran homologue. Proc Natl Acad Sci USA 95: 15388-15393.
  • Okuda T, Hirai H, Valentine VA, Shurtleff SA, Kidd VJ, Lahti JM, Sherr CJ, Downing JR (1995) Molecular cloning, expression pattern,, chromosomal localization of human CDKN2D/INK4d, an inhibitor of cyclin D-dependent kinases. Genomics 29: 623-630.
  • Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, Dunker AK (2005) Comparing and combining predictors of mostly disordered proteins. Biochemistry 44: 1989-2000.
  • Oliva R, Dixon GH (1989) Chicken protamine genes are intronless. The complete genomic sequence, organization of the two loci. J Biol Chem 264: 12472-12481.
  • Olsen SR, Uhler MD (1991) Inhibition of protein kinase-A by overexpression of the cloned human protein kinase inhibitor. Mol Endocrinol 5: 1246-1256.
  • Oshima T, Aiba H, Baba T, Fujita K, Hayashi K, Honjo A, Ikemoto K, Inada T, Itoh T, Kajihara M, Kanai K, Kashimoto K, Kimura S, Kitagawa M, Makino K, Masuda S, Miki T, Mizobuchi K, Mori H, Motomura K, Nakamura Y, Nashimoto H, Nishio Y, Saito N, Sampei G, Seki Y, Tagami H, Takemoto K, Wada C, Yamamoto Y, Yano M, Horiuchi T (1996) A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map. DNA Res 3: 137-155.
  • Page AP, MacNiven K, Hengartner MO (1996) Cloning and biochemical characterization of the cyclophilin homologues from the free-living nematode Caenorhabditis elegans. Biochem J 317: 179-185.
  • Palm W, Hilschmann N (1975) [The primary structure of a crystalline monoclonal immunoglobulin kappa-type L-chain, subgroup I (Bence-Jones protein Rei.); isolation and characterization of the tryptic peptides; the complete amino acid sequence of the protein; a contribution to the elucidation of the three-dimensional structure of antibodies, in particular their combining site (author's transl).] Hoppe-Seyler's Z Physiol Chem 356: 167-191.
  • Palomeque-Messia P, Englebert S, Leyh-Bouille M, Nguyen-Disteche M, Duez C, Houba S, Dideberg O, Van Beeumen J, Ghuysen JM (1991) Amino acid sequence of the penicillin-binding protein/DD-peptidase of Streptomyces K15. Predicted secondary structures of the low Mr penicillin-binding proteins of class A. Biochem J 279: 223-230.
  • Patti JM, Jonsson H, Guss B, Switalski LM, Wiberg K, Lindberg M, Hook M (1992) Molecular characterization and expression of a gene encoding a Staphylococcus aureus collagen adhesin. J Biol Chem 267: 4766-4772.
  • Pause A, Belsham GJ, Gingras AC, Donzé O, Lin TA, Lawrence JC Jr, Sonenberg N (1994) Insulin-dependent stimulation of protein synthesis by phosphorylation of a regulator of 5'-cap function. Nature 371: 762-767.
  • Pawlicki S, Le Béchec A, Delamarche C (2008) AMYPdb: a database dedicated to amyloid precursor proteins. BMC Bioinformatics 9: 273, accessed Mar 10, 2014.
  • Pederson DM, Welsh LC, Marvin DA, Sampson M, Perham RN, Yu M, Slater MR (2001) The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus. J Mol Biol 309: 401-421.
  • Pelletier I, Pfeifer O, Altenbuchner J, van Pee KH (1994) Cloning of a second non-haem bromoperoxidase gene from Streptomyces aureofaciens ATCC 10762: sequence analysis, expression in Streptomyces lividans, enzyme purification. Microbiology (Reading, Engl) 140: 509-516.
  • Pentecost BT, Wright JM, Dixon GH (1985) Isolation and sequence of cDNA clones coding for a member of the family of high mobility group proteins (HMG-T) in trout, analysis of HMG-T-mRNA's in trout tissues. Nucleic Acids Res 13: 4871-4888.
  • Pepys MB (2006) Amyloidosis. Annu Rev Med 57: 223-241.
  • Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature 409: 529-533.
  • Piatkowski D, Schneider K, Salamini F, Bartels D (1990) Characterization of five abscisic acid-responsive cdna clones isolated from the desiccation-tolerant plant craterostigma plantagineum, their relationship to other water-stress genes. Plant Physiol 94: 1682-1688.
  • Plunkett G 3rd, Burland V, Daniels DL, Blattner FR (1993) Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res 21: 3391-3398.
  • Polanco C, Buhse T, Samaniego JL, Castañón-González JA (2013) Detection of selective antibacterial peptides by the Polarity Profile method. Acta Biochim Pol 60: 183-189.
  • Polanco C, Castañón-González JA, Samaniego JL [Letter to the Editor] Arabi YM, Arifi AA, Balkhy HH, Najm H, Aldawood AS, Ghabashi A, Hawa H, Alothman A, Khaldi A, Raiy B (2014) Clinical course and outcomes of critically ill patients with middle east respiratory syndrome coronavirus infection. Ann Intern Med DOI: 10.7326/M13-2486.
  • Polanco C, Castañón-González JA, Uversky VM [Letter to the Editor] Buhimschi IA, Nayeri UA, Zhao G, Shook LL, Pensalfini A, Funai EF, Bernstein IM, Glabe CG, Buhimschi CS (2014b) Protein misfolding, congophilia, oligomerization,, defective amyloid processing in preeclampsia. Sci Transl Med 6: 245ra92. DOI: 10.1126/scitranslmed. 3008808.
  • Polanco C, Castañón-González JA, Uversky VM, Samaniego JL, Buhse T (Letter to the Editor) G Vogel G (2014d) Delays hinder Ebola genomics. Science 346: 684-685 DOI: 10.1126/science.346.6210.684.
  • Polanco C, Samaniego JL (2009) Detection of selective cationic amphipatic antibacterial peptides by Hidden Markov models. Acta Biochim Pol 56: 167-176.
  • Polanco C, Samaniego JL, Buhse T, Mosqueira FG, Negron-Mendoza A, Ramos-Bernal S, Castanon-Gonzalez JA (2012) Characterization of Selective Antibacterial Pept by Polarity Index. Int J Pept 2012: 585027 DOI: 10.1155/2012/585027.
  • Polanco C, Samaniego JL, Castañón-González JA, Buhse T (2014) Polar profile of antiviral peptides from AVPpred Database. Cell Biochem Biophys 70: 1469-1477. DOI: 10.1007/s12013-014-0084-4.
  • Polanco C, Buhse T, Samaniego JL, Castañón González JA, Arias Estrada M (2013a) Computational model of abiogenic amino acid polymerization to form dipeptides. Acta Biochim Pol 61: 253-258.
  • Polanco C, Samaniego JL, Castañón-González JA, Buhse T, Sordo ML (2013b) Characterization of a possible uptake mechanism of selective antibacterial peptides. Acta Biochim Pol 60: 629-633.
  • Polanco C, Samaniego-Mendoza JL, Buhse T, Castañón-González JA, Leopold-Sordo M (2014a) Polar Characterization of Antifungal Peptides from APD2 Database. Cell Biochem Biophys 70: 1479-1488 DOI: 10.1007/s12013-014-0085-3.
  • Polanco C., Samaniego-Mendoza JL, Castañón-González JA, Buhse T [Letter to the Editor] Howard SJ, Hopwood S, Davies SC (2014c) Antimicrobial Resistance: A Global Challenge. Sci Transl Med DOI: 10.1126/scitranslmed.3009315.
  • Przylas I, Tomoo K, Terada Y, Takaha T, Fujii K, Saenger W, Strater N (2000) Crystal structure of amylomaltase from thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans. J Mol Biol 296: 873-886.
  • Rawas A, Muirhead H, Williams J (1996) Structure of diferric duck ovotransferrin at 2.35 A resolution. Acta Crystallogr D Biol Crystallogr 52: 631-640.
  • Real E, Rain JC, Battaglia V, Jallet C, Perrin P, Tordo N, Chrisment P, D'Alayer J, Legrain P, Jacob Y. (2004) Antiviral drug discovery strategy using combinatorial libraries of structurally constrained peptides. J Virol 78: 7410-7417.
  • Reczek D, Berryman M, Bretscher A (1997) Identification of EBP50: A PDZ-containing phosphoprotein that associates with members of the ezrin-radixin-moesin family. J Cell Biol 139: 169-179.
  • Redfern OC, Harrison A, Dallman T, Pearl FM, Orengo CA (2007) CATHEDRAL: a fast and effective algorithm to predict folds, domain boundaries from multidomain protein structures. PLoS Comput Biol 3: e232.
  • Reid GA (1988) Sequence polymorphisms in the yeast gene encoding aspartyl tRNA synthase. Nucleic Acids Res 16: 1212.
  • Remacha M, Saenz-Robles MT, Vilella MD, Ballesta JP (1988) Independent genes coding for three acidic proteins of the large ribosomal subunit from Saccharomyces cerevisiae. J Biol Chem 263: 9094-9101.
  • Robbins PW, Trimble RB, Wirth DF, Hering C, Maley F, Maley GF, Das R, Gibson BW, Royal N, Biemann K (1984) Primary structure of the Streptomyces enzyme endo-beta-N-acetylglucosaminidase H. J Biol Chem 259: 7577-7583.
  • Robinson MS (1989) Cloning of cDNAs encoding two related 100-kD coated vesicle proteins (alpha-adaptins). J Cell Biol 108: 833-842.
  • Robinson MS (1990) Cloning and expression of gamma-adaptin, a component of clathrin-coated vesicles associated with the Golgi apparatus. J Cell Biol 111: 2319-2326.
  • Rogers MJ, Ohgi T, Plumbridge J, Soll D (1988) Nucleotide sequences of the Escherichia coli nagE, nagB genes: the structural genes for the N-acetylglucosamine transport protein of the bacterial phosphoenolpyruvate: sugar phosphotransferase system, for glucosamine-6-phosphate deaminase. Gene 62: 197-207.
  • Sakakibara M, Mukai T, Hori K (1985) Nucleotide sequence of a cDNA clone for human aldolase: a messenger RNA in the liver. Biochem Biophys Res Commun 131: 413-420.
  • Saporito SM, Smith-White BJ, Cunningham RP (1988) Nucleotide sequence of the xth gene of Escherichia coli K-12. J Bacteriol 170: 4542-4547.
  • Sauer RT, Krovatin W, Poteete AR, Berget PB (1982) Phage P22 tail protein: gene, amino acid sequence. Biochemistry 21: 5811-5815.
  • Scharf M, Engels J, Tripier D (1989) Primary structures of new 'iso-hirudins'. FEBS Lett 255: 105-110.
  • Schauer AT, Carver DL, Bigelow B, Baron LS, Friedman DI (1987) lambda N antitermination system: functional analysis of phage interactions with the host NusA proteína. J Mol Biol 194: 679-690.
  • Schluter G, Celik A, Obata R, Schlicker M, Hofferbert S, Schlung A, Adham IM, Engel W (1996) Sequence analysis of the conserved protamine gene cluster shows that it contains a fourth expressed gene. Mol Reprod Dev 43: 1-6.
  • Schnier J, Kitakawa M, Isono K (1986) The nucleotide sequence of an Escherichia coli chromosomal region containing the genes for ribosomal proteins S6, S18, L9, an open reading frame. Mol Gen Genet 204: 126-32.
  • Schor SL, Schor AM (2001) Phenotypic and genetic alterations in mammary stroma: implications for tumour progression. Breast Cancer Res. 3: 373-379.
  • Seedorf K, Krammer G, Durst M, Suhai S, Rowekamp WG (1985) Human papillomavirus type 16 DNA sequence. Virology 145: 181-185.
  • Seufert W, Jentsch S (1990) Ubiquitin-conjugating enzymes UBC4 and UBC5 mediate selective degradation of short-lived, abnormal proteins. EMBO J 9: 543-550.
  • Shimizu-Matsumoto A, Itoh K, Inazawa J, Nishida K, Matsumoto Y, Kinoshita S, Matsubara K, Okubo K (1996) Isolation and chromosomal localization of the human cone cGMP phosphodiesterase gamma cDNA (PDE6H). Genomics 32: 121-124.
  • Siegel S (1970) Estadistica no Paramétrica. Trillas pp 69-74.
  • Sillitoe I, Dibley M, Bray J, Addou S, Orengo C (2005) Assessing strategies for improved superfamily recognition. Protein Sci 14: 1800-1810.
  • Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res 41 (Database issue): D490-8. doi: 10.1093/nar/gks1211.
  • Shortle D (1983) A genetic system for analysis of staphylococcal nuclease. Gene 22: 181-189.
  • Shoulders CC, Kornblihtt AR, Munro BS, Baralle FE (1983) Gene structure of human apolipoprotein A1. Nucleic Acids Res 11: 2827-2837.
  • Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D (2011) Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature 475: 96-100.
  • Sipe JD, Colten HR, Goldberger G, Edge MD, Tack BF, Cohen AS, Whitehead AS (1985) Human serum amyloid A (SAA): biosynthesis, postsynthetic processing of preSAA, structural variants defined by complementary DNA. Biochemistry 24: 2931-2936.
  • Smith DB, Davern KM, Board PG, Tiu WU, Garcia EG, Mitchell GF (1989) Mr 26,000 antigen of Schistosoma japonicum recognized by resistant WEHI 129/J mice is a parasite glutathione S-transferase. Proc Natl Acad Sci USA 83: 8703-8707.
  • Srivastava A, Lusby EW, Berns KI (1983) Nucleotide sequence and organization of the adeno-associated virus 2 genome. J Virol 45: 555-564.
  • Stahl HD, Kemp DJ, Crewther PE, Scanlon DB, Woodrow G, Brown GV, Bianco AE, Anders RF, Coppel RL (1985) Sequence of a cDNA encoding a small polymorphic histidine-, alanine-rich protein from Plasmodium falciparum. Nucleic Acids Res 13: 7837-7846.
  • Stewart AF, Willis IM, Mackinlay AG (1984) Nucleotide sequences of bovine alpha S1-, kappa-casein cDNAs. Nucleic Acids Res 12: 3895-3907.
  • Suva LJ, Winslow GA, Wettenhall RE, Hammonds RG, Moseley JM, Diefenbach-Jagger H, Rodda CP, Kemp BE, Rodriguez H, Chen EY, Hudson PJ, Martin TJ, Wood WI (1987) A parathyroid hormone-related protein implicated in malignant hypercalcemia: cloning, expresión. Science 237: 893-896.
  • Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, Kuhara S, Horikoshi K (2000) Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans, genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res 28: 4317-4331.
  • Takamizawa A, Mori C, Fuke I, Manabe S, Murakami S, Fujita J, Onishi E, Andoh T, Yoshida I, Okayama H (1991) Structure and organization of the hepatitis C virus genome isolated from human carriers. J Virol 65: 1105-1113.
  • Talarico TL, Ray PH, Dev IK, Merrill BM, Dallas WS (1992) Cloning, sequence analysis, and overexpression of Escherichia coli folK, the gene coding for 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase. J Bacteriol 174: 5971-5977.
  • Tamiya T, Lamouroux A, Julien JF, Grima B, Mallet J, Fromageot P, Menez A (1985) Cloning and sequence analysis of the cDNA encoding a snake neurotoxin precursor. Biochimie 67: 185-189.
  • Tanaka Y, Tsujimura A, Fujita N, Isono S, Isono K (1989) Cloning and analysis of an Escherichia coli operon containing the rpmF gene for ribosomal protein L32, the gene for a 30-kilodalton protein. J Bacteriol 171: 5707-5712.
  • Teesalu T, Sugahara KN, Ruoslahti E (2013) Tumor-penetrating peptides. Front Oncol 3: 216.
  • Thakur N, Qureshi A, Kumar M (2012) AVPpred: collection and prediction of highly effective antiviral peptides. Nucleic Acids Res 40: W199-W204. accessed March 10, 2013.
  • Thompson LH, Brookman KW, Jones NJ, Allen SA, Carrano AV (1990) Molecular cloning of the human XRCC1 gene, which corrects defective DNA strand break repair, sister chromatid Exchange. Mol Cell Biol 10: 6160-6171.
  • Timberlake KC (1992) Chemistry. 5th edn, Haper-Collins Publishers Inc, NY, accessed May 16, 2014
  • Tomaschewski J, Gram H, Crabb JW, Ruger W (1985) T4-induced alpha- and beta-glucosyltransferase: cloning of the genes, a comparison of their products based on sequencing data. Nucleic Acids Res. 13: 7551-7568.
  • Tompa P (2002) Intrinsically unstructured proteins. Trends Biochem Sci 27: 527-533. .
  • Uversky VN (2009) Intrinsic disorder in proteins associated with neurodegenerative diseases. Frontiers in Bioscience 14: 5188-5238.
  • Uversky VN (2010a) Mysterious oligomerization of the amyloidogenic proteins. FEBS Journal 277: 2940-2953.
  • Uversky VN (2002) What does it mean to be natively unfolded? Eur J Biochem 269: 2-12.
  • Uversky VN (2010b) The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome. J Biomed Biotechnol 2010: 568068.
  • Uversky VN, Dunker AK (2010) Understanding protein non-folding. Biochim Biophys Acta 1804: 1231-1264.
  • Uversky VN (2013) Intrinsic disorder-based protein interactions, their modulators. Curr Pharm Des 19: 4191-4213.
  • Uversky VN, Fink AL (2004) Conformational constraints for amyloid fibrillation: the importance of being unfolded. Biochim Biophys Acta 1698: 131-153.
  • Uversky VN, Gillespie JR, Fink AL (2000) Why are 'natively unfolded' proteins unstructured under physiologic conditions? Proteins 41: 415-427.
  • Uversky VN, Oldfield CJ, Dunker AK (2008) Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 37: 215-246.
  • Uversky VN, Oldfield CJ, Dunker AK (2008a) Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 37: 215-246.
  • Vallins WJ, Brand NJ, Dabhade N, Butler-Browne G, Yacoub MH, Barton PJ (1990) Molecular cloning of human cardiac troponin I using polymerase chain reaction. FEBS Lett 270: 57-61.
  • Vaughan JM, Rivier J, Spiess J, Peng C, Chang JP, Peter RE, Vale W (1992) Isolation and characterization of hypothalamic growth-hormone releasing factor from common carp, Cyprinus carpio. Neuroendocrinology 56: 539-549.
  • Vidal R, Frangione B, Rostagno A, Mead S, Révész T, Plant G, Ghiso J (1999) A stop-codon mutation in the BRI gene associated with familial British dementia. Nature 399: 776-781.
  • Wallon G, Kryger G, Lovett ST, Oshima T, Ringe D, Petsko GA (1997) Crystal structures of Escherichia coli, Salmonella typhimurium 3-isopropylmalate dehydrogenase, comparison with their thermophilic counterpart from Thermus thermophilus. J Mol Biol 266: 1016-1031.
  • Wang G, Li X, Wang Z (2009) APD2: the updated antimicrobial peptide database, its application in peptide design. Nucleic Acids Res 37: D933-D937.
  • Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645.
  • Warmke JW, Ganetzky B (1994) A family of potassium channel genes related to eag in Drosophila, mammals. Proc Natl Acad Sci USA 91: 3438-3442.
  • Wasenius VM, Saraste M, Salven P, Eramaa M, Holm L, Lehto VP (1989) Primary structure of the brain alpha-spectrin. J Cell Biol 108: 79-93.
  • Watanabe K, Kitamura K, Iha H, Suzuki Y (1990) Primary structure of the oligo-1,6-glucosidase of Bacillus cereus ATCC7064 deduced from the nucleotide sequence of the cloned gene. Eur J Biochem 192: 609-620.
  • Watson DC, Wong NC, Dixon GH (1979) The complete amino-acid sequence of a trout-testis non-histone protein, H6, localized in a subset of nucleosomes, its similarity to calf-thymus non-histone proteins HMG-14, HMG-17. Eur J Biochem 95: 193-202.
  • Weber FE, Dyer JH, Lopez Garcia F, Werder M, Szyperski T, Wuthrich K, Hauser H (1998) In pre-sterol carrier protein 2 (SCP2) in solution the leader peptide 1-20 is flexibly disordered,, residues 21-143 adopt the same globular fold as in mature SCP2. Cell Mol Life Sci 54: 751-759.
  • Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293: 321-331.
  • Xing Y, Higuchi K. (2002) Amyloid fibril proteins. Mech Ageing Dev 123: 1625-1636.
  • Xue B, Dunker AK, Uversky VN (2012) Orderly order in protein intrinsic disorder distribution: Disorder in 3500 proteomes from viruses, the three domains of life. J Biomol Struct Dyn 30: 137-149.
  • Xue B, Williams RW, Oldfield CJ, Dunker AK, Uversky VN (2010a) Archaic chaos: Intrinsically disordered proteins in Archaea. BMC Systems Biology 4 (Suppl 1) S1.
  • Xue B, Williams RW, Oldfield CJ, Goh GK, Dunker AK, Uversky VN (2010) Viral disorder or disordered viruses: Do viral proteins possess unique features? Protein Peptide Lett 17: 932-951.
  • Yang C, Zhu Y, Magee DM, Cox RA (1996) Molecular cloning and characterization of the Coccidioides immitis complement fixation/chitinase antigen. Infect Immun 64: 1992-1997.
  • Yang RC, MacKenzie CR, Narang SA (1988) Nucleotide sequence of a Bacillus circulans xylanase gene. Nucleic Acids Res 16: 7187.
  • You C, Holder L, Cook D (2006) Application of Graph-based Data Mining to Metabolic Pathways. Workshop on Data Mining in Bioinformatics, IEEE International Conference on Data Mining.
  • Zakut-Houri R, Bienz-Tadmor B, Givol D, Oren M (1985) Human p53 cellular tumor antigen: cDNA sequence, expression in COS cells. EMBO J 4: 1251-1255.
  • Zannis VI, McPherson J, Goldberger G, Karathanasis SK, Breslow JL (1984) Synthesis, intracellular processing, and signal peptide of human apolipoprotein E. J Biol Chem 259: 5495-5499.
  • Zhang W, Brooun A, McCandless J, Banda P, Alam M (1996) Signal transduction in the archaeon Halobacterium salinarium is processed through three subfamilies of 13 soluble, membrane-bound transducer proteins. Proc Natl Acad Sci USA 93: 4649-4654.
  • Zhu PP, Reizer J, Peterkofsky A (1994) Unique dicistronic operon (ptsI-crr) in Mycoplasma capricolum encoding enzyme I, the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system: cloning, sequencing, promoter analysis, and protein characterization. Protein Sci 3: 2115-2128.
  • Zurawski G, Zurawski SM (1985) Structure of the Escherichia coli S10 ribosomal protein operon. Nucleic Acids Res 13: 4521-4526.
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