| [1] | Wetterstrand KA (2011) DNA Sequencing Costs: Data from the NHGRI Large-Scale Genome Sequencing Program. National Human Genome Research Institute website. 24: Available: www.genome.gov/sequencingcosts Accessed 2012 April.
|
| [2] | Finlay WJ, Bloom L, Cunningham O (2011) Phage display: a powerful technology for the generation of high specificity affinity reagents from alternative immune sources. Methods Mol Biol 681: 87–101.
|
| [3] | Whitney M, Crisp JL, Olson ES, Aguilera TA, Gross LA, et al. (2010) Parallel in vivo and in vitro selection using phage display identifies protease-dependent tumor-targeting peptides. J Biol Chem 285: 22532–22541.
|
| [4] | Brown KC (2010) Peptidic tumor targeting agents: the road from phage display peptide selections to clinical applications. Curr Pharm Des 16: 1040–1054.
|
| [5] | Scholle MD, Kriplani U, Pabon A, Sishtla K, Glucksman MJ, et al. (2006) Mapping protease substrates by using a biotinylated phage substrate library. Chembiochem 7: 834–838.
|
| [6] | Dente L, Vetriani C, Zucconi A, Pelicci G, Lanfrancone L, et al. (1997) Modified phage peptide libraries as a tool to study specificity of phosphorylation and recognition of tyrosine containing peptides. J Mol Biol 269: 694–703.
|
| [7] | Matthews DJ, Wells JA (1993) Substrate phage: selection of protease substrates by monovalent phage display. Science 260: 1113–1117.
|
| [8] | Kurz M, Gu K, Al-Gawari A, Lohse PA (2001) cDNA - protein fusions: covalent protein - gene conjugates for the in vitro selection of peptides and proteins. Chembiochem 2: 666–672.
|
| [9] | Roberts RW, Szostak JW (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci U S A 94: 12297–12302.
|
| [10] | Ueda T, Kanamori T, Ohashi H (2010) Ribosome display with the PURE technology. Methods Mol Biol 607: 219–225.
|
| [11] | Bertschinger J, Grabulovski D, Neri D (2007) Selection of single domain binding proteins by covalent DNA display. Protein Eng Des Sel 20: 57–68.
|
| [12] | Sergeeva A, Kolonin MG, Molldrem JJ, Pasqualini R, Arap W (2006) Display technologies: application for the discovery of drug and gene delivery agents. Adv Drug Deliv Rev 58: 1622–1654.
|
| [13] | de Figueiredo P, Roberts RL, Nester EW (2004) DARTs: A DNA-based in vitro polypeptide display technology. Proteomics 4: 3128–3140.
|
| [14] | Odegrip R, Coomber D, Eldridge B, Hederer R, Kuhlman PA, et al. (2004) CIS display: In vitro selection of peptides from libraries of protein-DNA complexes. Proc Natl Acad Sci U S A 101: 2806–2810.
|
| [15] | Yonezawa M, Doi N, Kawahashi Y, Higashinakagawa T, Yanagawa H (2003) DNA display for in vitro selection of diverse peptide libraries. Nucleic Acids Res 31: e118.
|
| [16] | Hanes J, Plückthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci U S A 94: 4937–4942.
|
| [17] | Ullman CG, Frigotto L, Cooley RN (2011) In vitro methods for peptide display and their applications. Brief Funct Genomics 10: 125–134.
|
| [18] | Yamagishi Y, Shoji I, Miyagawa S, Kawakami T, Katoh T, et al. (2011) Natural Product-Like Macrocyclic N-Methyl-Peptide Inhibitors against a Ubiquitin Ligase Uncovered from a Ribosome-Expressed De Novo Library. Chem Biol 18: 1562–1570.
|
| [19] | Xu L, Aha P, Gu K, Kuimelis RG, Kurz M, et al. (2002) Directed evolution of high-affinity antibody mimics using mRNA display. Chem Biol 9: 933–942.
|
| [20] | Kong Y (2009) Calculating complexity of large randomized libraries. J Theor Biol 259: 641–645.
|
| [21] | Szardenings M (2003) Phage display of random peptide libraries: applications, limits, and potential. J Recept Signal Transduct Res 23: 307–349.
|
| [22] | Keefe AD, Szostak JW (2001) Functional proteins from a random-sequence library. Nature 410: 715–718.
|
| [23] | Shivange AV, Marienhagen J, Mundhada H, Schenk A, Schwaneberg U (2009) Advances in generating functional diversity for directed protein evolution. Curr Opin Chem Biol 13: 19–25.
|
| [24] | Takahashi TT, Roberts RW (2009) In vitro selection of protein and peptide libraries using mRNA display. Methods in molecular biology (Clifton, NJ) 535: 293.
|
| [25] | Overall CM, Blobel CP (2007) In search of partners: linking extracellular proteases to substrates. Nat Rev Mol Cell Biol 8: 245–257.
|
| [26] | Rawlings ND, Morton FR, Barrett AJ (2006) MEROPS: the peptidase database. Nucleic Acids Res 34: D270–D272.
|
| [27] | Lopez-Otin C, Overall CM (2002) Protease degradomics: a new challenge for proteomics. Nat Rev Mol Cell Biol 3: 509–519.
|
| [28] | Diks SH, Parikh K, van der Sijde M, Joore J, Ritsema T, et al. (2007) Evidence for a minimal eukaryotic phosphoproteome? PLoS One 2: e777.
|
| [29] | Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S (2002) The protein kinase complement of the human genome. Science 298: 1912–1934.
|
| [30] | Chong PK, Lee H, Kong JW, Loh MC, Wong CH, et al. (2008) Phosphoproteomics, oncogenic signaling and cancer research. Proteomics 8: 4370–4382.
|
| [31] | Johnson SA, Hunter T (2005) Kinomics: methods for deciphering the kinome. Nat Methods 2: 17–25.
|
| [32] | Manning G, Plowman GD, Hunter T, Sudarsanam S (2002) Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci 27: 514–520.
|
| [33] | Vasiljeva O, Reinheckel T, Peters C, Turk D, Turk V, et al. (2007) Emerging roles of cysteine cathepsins in disease and their potential as drug targets. Curr Pharm Des 13: 385–401.
|
| [34] | Winssinger N, Damoiseaux R, Tully DC, Geierstanger BH, Burdick K, et al. (2004) PNA-encoded protease substrate microarrays. Chem Biol 11: 1351–1360.
|
| [35] | Collins MO, Yu L, Choudhary JS (2007) Analysis of protein phosphorylation on a proteome-scale. Proteomics 7: 2751–2768.
|
| [36] | Villén J, Beausoleil SA, Gerber SA, Gygi SP (2007) Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci U S A 104: 1488–1493.
|
| [37] | Parikh K, Peppelenbosch MP (2010) Kinome profiling of clinical cancer specimens. Cancer Res 70: 2575–2578.
|
| [38] | Piersma SR, Labots M, Verheul HM, Jiménez CR (2010) Strategies for kinome profiling in cancer and potential clinical applications: chemical proteomics and array-based methods. Anal Bioanal Chem 397: 3163–3171.
|
| [39] | Paradela A, Albar JP (2008) Advances in the analysis of protein phosphorylation. J Proteome Res 7: 1809–1818.
|
| [40] | Rush J, Moritz A, Lee KA, Guo A, Goss VL, et al. (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 23: 94–101.
|
| [41] | Rothman DM, Shults MD, Imperiali B (2005) Chemical approaches for investigating phosphorylation in signal transduction networks. Trends Cell Biol 15: 502–510.
|
| [42] | Schutkowski M, Reineke U, Reimer U (2005) Peptide arrays for kinase profiling. Chembiochem 6: 513–521.
|
| [43] | Bonetta (2005) Probing the kinome. Nature Methods 2: 225–232.
|
| [44] | Choudhary C, Mann M (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 11: 427–439.
|
| [45] | Yen M, Yin J (2007) High-throughput profiling of posttranslational modification enzymes by phage display. Biotechniques 43: 31, 33, 35 passim.
|
| [46] | Larman HB, Zhao Z, Laserson U, Li MZ, Ciccia A, et al. (2011) Autoantigen discovery with a synthetic human peptidome. Nat Biotechnol 29: 535–541.
|
| [47] | Mahler M, Fritzler MJ (2010) Epitope specificity and significance in systemic autoimmune diseases. Ann N Y Acad Sci 1183: 267–287.
|
| [48] | Pogson M, Georgiou G, Iverson BL (2009) Engineering next generation proteases. Curr Opin Biotechnol 20: 390–397.
|
| [49] | Jung JP, Gasiorowski JZ, Collier JH (2010) Fibrillar peptide gels in biotechnology and biomedicine. Biopolymers 94: 49–59.
|
| [50] | Boschetti E, Righetti PG (2009) The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 9: 1492–1510.
|
| [51] | Estephan E, Larroque C, Bec N, Martineau P, Cuisinier FJ, et al. (2009) Selection and mass spectrometry characterization of peptides targeting semiconductor surfaces. Biotechnol Bioeng 104: 1121–1131.
|
| [52] | Whaley SR, English DS, Hu EL, Barbara PF, Belcher AM (2000) Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature 405: 665–668.
|
| [53] | Lee S, Xie J, Chen X (2010) Peptide-based probes for targeted molecular imaging. Biochemistry 49: 1364–1376.
|
| [54] | Salomon AR, Ficarro SB, Brill LM, Brinker A, Phung QT, et al. (2003) Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc Natl Acad Sci U S A 100: 443–448.
|
| [55] | Ryan KJ, Ray CG (2004) Sherris Medical Microbiology. McGraw Hill.
|
| [56] | Kwong AD, Kim JL, Rao G, Lipovsek D, Raybuck SA (1999) Hepatitis C virus NS3/4A protease. Antiviral Res 41: 67–84.
|
| [57] | Kwong AD, Kauffman RS, Hurter P, Mueller P (2011) Discovery and development of telaprevir: an NS3-4A protease inhibitor for treating genotype 1 chronic hepatitis C virus. Nat Biotechnol 29: 993–1003.
|
| [58] | Steuber H, Hilgenfeld R (2010) Recent advances in targeting viral proteases for the discovery of novel antivirals. Curr Top Med Chem 10: 323–345.
|
| [59] | Chen SH, Tan SL (2005) Discovery of small-molecule inhibitors of HCV NS3-4A protease as potential therapeutic agents against HCV infection. Curr Med Chem 12: 2317–2342.
|
| [60] | Lahm A, Yagnik A, Tramontano A, Koch U (2002) Hepatitis C virus proteins as targets for drug development: the role of bioinformatics and modelling. Curr Drug Targets 3: 281–296.
|
| [61] | Hahm B, Han DS, Back SH, Song OK, Cho MJ, et al. (1995) NS3-4A of hepatitis C virus is a chymotrypsin-like protease. J Virol 69: 2534–2539.
|
| [62] | Blight KJ, Kolykhalov AA, Reed KE, Agapov EV, Rice CM (1998) Molecular virology of hepatitis C virus: an update with respect to potential antiviral targets. Antivir Ther 3: 71–81.
|
| [63] | Steinkühler C, Urbani A, Tomei L, Biasiol G, Sardana M, et al. (1996) Activity of purified hepatitis C virus protease NS3 on peptide substrates. J Virol 70: 6694–6700.
|
| [64] | Bartenschlager R, Ahlborn-Laake L, Yasargil K, Mous J, Jacobsen H (1995) Substrate determinants for cleavage in cis and in trans by the hepatitis C virus NS3 proteinase. J Virol 69: 198–205.
|
| [65] | Shiryaev SA, Thomsen ER, Cieplak P, Chudin E, Cheltsov AV, et al. (2012) New details of HCV NS3/4A proteinase functionality revealed by a high-throughput cleavage assay. PLoS ONE 7(4): e35759.
|
| [66] | B？hmer FD, Uecker A (2009) A substrate peptide for the FLT3 receptor tyrosine kinase. Br J Haematol 144: 127–130.
|
| [67] | Jalal S, Arsenault R, Potter AA, Babiuk LA, Griebel PJ, et al. (2009) Genome to kinome: species-specific Peptide arrays for kinome analysis. Sci Signal 2: pl1.
|
| [68] | Amanchy R, Zhong J, Molina H, Chaerkady R, Iwahori A, et al. (2008) Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. J Proteome Res 7: 3900–3910.
|
| [69] | Shults MD, Kozlov IA, Nelson N, Kermani BG, Melnyk PC, et al. (2007) A multiplexed protein kinase assay. Chembiochem 8: 933–942.
|
| [70] | Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4: 1551–1561.
|
| [71] | Yang CY, Chang CH, Yu YL, Lin TC, Lee SA, et al. (2008) PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. Bioinformatics 24: i14–i20.
|
| [72] | Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, et al. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635–648.
|
| [73] | Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, et al. (2011) Phospho.ELM: a database of phosphorylation sites–update 2011. Nucleic Acids Res 39: D261–D267.
|
| [74] | Rychlewski L, Kschischo M, Dong L, Schutkowski M, Reimer U (2004) Target specificity analysis of the Abl kinase using peptide microarray data. J Mol Biol 336: 307–311.
|
| [75] | Songyang Z, Carraway KL, Eck MJ, Harrison SC, Feldman RA, et al. (1995) Catalytic specificity of protein-tyrosine kinases is critical for selective signalling. Nature 373: 536–539.
|
| [76] | Heibeck TH, Ding SJ, Opresko LK, Zhao R, Schepmoes AA, et al. (2009) An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells. J Proteome Res 8: 3852–3861.
|
| [77] | J？rgensen C, Sherman A, Chen GI, Pasculescu A, Poliakov A, et al. (2009) Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326: 1502–1509.
|
| [78] | Stuible M, Dubé N, Tremblay ML (2008) PTP1B regulates cortactin tyrosine phosphorylation by targeting Tyr446. J Biol Chem 283: 15740–15746.
|
| [79] | Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, et al. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325: 834–840.
|
| [80] | Uy R, Wold F (1977) Posttranslational covalent modification of proteins. Science 198: 890–896.
|
| [81] | Goto Y, Katoh T, Suga H (2011) Flexizymes for genetic code reprogramming. Nat Protoc 6: 779–790.
|
| [82] | Ohta A, Yamagishi Y, Suga H (2008) Synthesis of biopolymers using genetic code reprogramming. Curr Opin Chem Biol 12: 159–167.
|
| [83] | Frankel A, Millward SW, Roberts RW (2003) Encodamers: unnatural peptide oligomers encoded in RNA. Chem Biol 10: 1043–1050.
|
| [84] | Shiryaev SA, Kozlov IA, Ratnikov BI, Smith JW, Lebl M, et al. (2007) Cleavage preference distinguishes the two-component NS2B-NS3 serine proteinases of Dengue and West Nile viruses. Biochem J 401: 743–752.
|
| [85] | Hattori S, Iida N, Kosako H (2008) Identification of protein kinase substrates by proteomic approaches. Expert Rev Proteomics 5: 497–505.
|
| [86] | Kozlov IA, Melnyk PC, Zhao C, Hachmann JP, Shevchenko V, et al. (2006) A method for rapid protease substrate evaluation and optimization. Comb Chem High Throughput Screen 9: 481–487.
|
| [87] | Peck SC (2006) Analysis of protein phosphorylation: methods and strategies for studying kinases and substrates. Plant J 45: 512–522.
|
| [88] | George J, Teear ML, Norey CG, Burns DD (2003) Evaluation of an imaging platform during the development of a FRET protease assay. J Biomol Screen 8: 72–80.
|
| [89] | Manning BD, Cantley LC (2002) Hitting the target: emerging technologies in the search for kinase substrates. Sci STKE 2002: PE49. PE49 p.
|
| [90] | Stadler V, Felgenhauer T, Beyer M, Fernandez S, Leibe K, et al. (2008) Combinatorial synthesis of peptide arrays with a laser printer. Angew Chem Int Ed Engl 47: 7132–7135.
|
| [91] | Beyer M, Nesterov A, Block I, K？nig K, Felgenhauer T, et al. (2007) Combinatorial synthesis of peptide arrays onto a microchip. Science 318: 1888.
|
| [92] | Hilpert K, Winkler DF, Hancock RE (2007) Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat Protoc 2: 1333–1349.
|
| [93] | Breitling F, Nesterov A, Stadler V, Felgenhauer T, Bischoff FR (2009) High-density peptide arrays. Mol Biosyst 5: 224–234.
|
| [94] | LeProust EM, Peck BJ, Spirin K, McCuen HB, Moore B, et al. (2010) Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res 38: 2522–2540.
|
| [95] | Miyamoto-Sato E, Takashima H, Fuse S, Sue K, Ishizaka M, et al. (2003) Highly stable and efficient mRNA templates for mRNA-protein fusions and C-terminally labeled proteins. Nucleic Acids Res 31: e78.
|
| [96] | Pieles U, Englisch U (1989) Psoralen covalently linked to oligodeoxyribonucleotides: synthesis, sequence specific recognition of DNA and photo-cross-linking to pyrimidine residues of DNA. Nucleic Acids Res 17: 285–299.
|
| [97] | Tolbert TJ, Wong CH (2002) New methods for proteomic research: preparation of proteins with N-terminal cysteines for labeling and conjugation. Angew Chem Int Ed Engl 41: 2171–2174.
|
| [98] | Blanco-Canosa JB, Dawson PE (2008) An efficient Fmoc-SPPS approach for the generation of thioester peptide precursors for use in native chemical ligation. Angew Chem Int Ed Engl 47: 6851–6855.
|
| [99] | Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53–59.
|
| [100] | He M, Stoevesandt O, Palmer EA, Khan F, Ericsson O, et al. (2008) Printing protein arrays from DNA arrays. Nat Methods 5: 175–177.
|
| [101] | Tao SC, Zhu H (2006) Protein chip fabrication by capture of nascent polypeptides. Nat Biotechnol 24: 1253–1254.
|
| [102] | Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, et al. (2004) Self-assembling protein microarrays. Science 305: 86–90.
|
| [103] | He M, Taussig MJ (2001) Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res 29: E73–E73.
|
