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Volumn 2, Issue 6, 2005, Pages 937-947

Microarray-based functional protein profiling using peptide nucleic acid-encoded libraries

Author keywords

Activity based protein; Combinatorial chemistry; Functional profiling; Kinase; Microarray; Peptide nucleic acid; Profiling; Protease; Self assembly

Indexed keywords

NUCLEIC ACID; PEPTIDE;

EID: 28544447160     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2.6.937     Document Type: Review
Times cited : (22)

References (53)
  • 1
    • 10544256600 scopus 로고    scopus 로고
    • Expression monitoring by hybridization to high-density oligonucleotide arrays
    • Dyrskjot L, Zieger K, Kruhoffer M et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675-1680 (1996).
    • (1996) Nature Biotechnol. , vol.14 , pp. 1675-1680
    • Dyrskjot, L.1    Zieger, K.2    Kruhoffer, M.3
  • 2
    • 0029852580 scopus 로고    scopus 로고
    • Use of a cDNA microarray to analyse gene expression patterns in human cancer
    • DeRisi J, Penland L, Brown PO et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genet. 14, 457-460 (1996).
    • (1996) Nature Genet. , vol.14 , pp. 457-460
    • DeRisi, J.1    Penland, L.2    Brown, P.O.3
  • 3
    • 0034659898 scopus 로고    scopus 로고
    • Genomics, gene expression and DNA arrays
    • Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays. Nature 405, 827-836 (2000).
    • (2000) Nature , vol.405 , pp. 827-836
    • Lockhart, D.J.1    Winzeler, E.A.2
  • 4
    • 0035241690 scopus 로고    scopus 로고
    • Mass spectrometry in proteomics
    • Aebersold R, Goodlett DR. Mass spectrometry in proteomics. Chem. Rev. 101, 269-295 (2001).
    • (2001) Chem. Rev. , vol.101 , pp. 269-295
    • Aebersold, R.1    Goodlett, D.R.2
  • 5
    • 0033604499 scopus 로고    scopus 로고
    • Active site-directed protein regulation
    • Kobe B, Kemp BE. Active site-directed protein regulation. Nature 402, 373-376 (1999).
    • (1999) Nature , vol.402 , pp. 373-376
    • Kobe, B.1    Kemp, B.E.2
  • 6
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
    • (2004) Nature , vol.431 , pp. 931-945
  • 7
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P, Giot L, Cagney G et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3
  • 9
    • 0345600247 scopus 로고    scopus 로고
    • A protein interaction map of Drosophila melanogaster
    • Giot L, Bader JS, Brouwer C et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736 (2003).
    • (2003) Science , vol.302 , pp. 1727-1736
    • Giot, L.1    Bader, J.S.2    Brouwer, C.3
  • 10
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer VR, Horak CE, Scafe CS et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538 (2001).
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3
  • 11
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee TI, Rinaldi NJ, Robert F et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1    Rinaldi, N.J.2    Robert, F.3
  • 12
    • 0037123767 scopus 로고    scopus 로고
    • Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases
    • Robyr D, Suka Y, Xenarios I et al. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109, 437-446 (2002).
    • (2002) Cell , vol.109 , pp. 437-446
    • Robyr, D.1    Suka, Y.2    Xenarios, I.3
  • 13
    • 0037458030 scopus 로고    scopus 로고
    • Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry
    • Salomon AR, Ficarro SB, Brill LM et al. Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc. Natl Acad. Sci. USA 100, 443-448 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 443-448
    • Salomon, A.R.1    Ficarro, S.B.2    Brill, L.M.3
  • 14
    • 18744415995 scopus 로고    scopus 로고
    • Kinomics: Methods for deciphering the kinome
    • Johnson SA, Hunter T. Kinomics: methods for deciphering the kinome. Nature Methods 2, 17-25 (2005).
    • (2005) Nature Methods , vol.2 , pp. 17-25
    • Johnson, S.A.1    Hunter, T.2
  • 15
    • 2342460878 scopus 로고    scopus 로고
    • Membrane protease proteomics: Isotope-coded affinity tag MS identification of undescribed MT1-matrix metalloproteinase substrates
    • Tam EM, Morrison CJ, Wu YI, Stack MS, Overall CM. Membrane protease proteomics: isotope-coded affinity tag MS identification of undescribed MT1-matrix metalloproteinase substrates. Proc. Natl Acad. Sci. USA 101, 6917-6922 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6917-6922
    • Tam, E.M.1    Morrison, C.J.2    Wu, Y.I.3    Stack, M.S.4    Overall, C.M.5
  • 16
    • 0346728473 scopus 로고    scopus 로고
    • Systematic genome-wide screens of gene function
    • Carpenter AE, Sabatini DM. Systematic genome-wide screens of gene function. Nature Rev. Genet. 5, 11-22 (2004).
    • (2004) Nature Rev. Genet. , vol.5 , pp. 11-22
    • Carpenter, A.E.1    Sabatini, D.M.2
  • 17
    • 20044366920 scopus 로고    scopus 로고
    • Cell microarrays and RNA interference chip away at gene function
    • Wheeler DB, Carpenter AE, Sabatini DM. Cell microarrays and RNA interference chip away at gene function. Nature Genet. 37, S25-S30 (2005).
    • (2005) Nature Genet. , vol.37
    • Wheeler, D.B.1    Carpenter, A.E.2    Sabatini, D.M.3
  • 18
    • 11144311139 scopus 로고    scopus 로고
    • Lessons from natural molecules
    • Clardy J, Walsh C. Lessons from natural molecules. Nature 432, 829-837 (2004).
    • (2004) Nature , vol.432 , pp. 829-837
    • Clardy, J.1    Walsh, C.2
  • 19
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter JC, Adams MD, Myers EW et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, J.C.1    Adams, M.D.2    Myers, E.W.3
  • 20
    • 33845339435 scopus 로고    scopus 로고
    • Protease inhibitors in the clinic
    • Abbenante G, Fairlie DP. Protease inhibitors in the clinic. Med. Chem. 1, 71-104 (2005).
    • (2005) Med. Chem. , vol.1 , pp. 71-104
    • Abbenante, G.1    Fairlie, D.P.2
  • 21
    • 0027690228 scopus 로고
    • Biotinylated isocoumarins, new inhibitors and reagents for detection, localization, and isolation of serine proteases
    • Kam CM, Abuelyaman AS, Li, Z, Hudig D, Powers JC. Biotinylated isocoumarins, new inhibitors and reagents for detection, localization, and isolation of serine proteases. Bioconjugate Chem. 4, 560-567 (1993).
    • (1993) Bioconjugate Chem. , vol.4 , pp. 560-567
    • Kam, C.M.1    Abuelyaman, A.S.2    Li, Z.3    Hudig, D.4    Powers, J.C.5
  • 22
  • 23
    • 0035799319 scopus 로고    scopus 로고
    • Profiling serine hydrolase activities in complex proteomes
    • Kidd D, Liu Y, Cravatt BF. Profiling serine hydrolase activities in complex proteomes. Biochemistry 40, 4005-4015 (2001).
    • (2001) Biochemistry , vol.40 , pp. 4005-4015
    • Kidd, D.1    Liu, Y.2    Cravatt, B.F.3
  • 24
    • 0033835372 scopus 로고    scopus 로고
    • Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools
    • Greenbaum D, Medzihradszky KF, Burlingame A, Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem. Biol. 7, 569-581 (2000).
    • (2000) Chem. Biol. , vol.7 , pp. 569-581
    • Greenbaum, D.1    Medzihradszky, K.F.2    Burlingame, A.3    Bogyo, M.4
  • 25
    • 0036051482 scopus 로고    scopus 로고
    • Chemical approaches for functionally probing the proteome
    • Greenbaum D, Baruch A, Hayrapetian L et al. Chemical approaches for functionally probing the proteome. Mol. Cell. Proteomics 1, 60-68 (2002).
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 60-68
    • Greenbaum, D.1    Baruch, A.2    Hayrapetian, L.3
  • 27
    • 0036391485 scopus 로고    scopus 로고
    • Design and synthesis of class-selective activity probes for protein tyrosine phosphatases
    • Lo L-C, Pang TL, Kuo CH, Chiang YL, Wang HY, Lin JJ. Design and synthesis of class-selective activity probes for protein tyrosine phosphatases. J. Proteome Res. 1, 35-40 (2002).
    • (2002) J. Proteome Res. , vol.1 , pp. 35-40
    • Lo, L.-C.1    Pang, T.L.2    Kuo, C.H.3    Chiang, Y.L.4    Wang, H.Y.5    Lin, J.J.6
  • 28
    • 0037126198 scopus 로고    scopus 로고
    • Design and synthesis of activity probes for glycosidases
    • Tsai CS, Li YK, Lo LC. Design and synthesis of activity probes for glycosidases. Org. Lett. 4, 3607-3610 (2002).
    • (2002) Org. Lett. , vol.4 , pp. 3607-3610
    • Tsai, C.S.1    Li, Y.K.2    Lo, L.C.3
  • 29
    • 0036022519 scopus 로고    scopus 로고
    • Proteomic profiling of mechanistically distinct enzyme classes using common chemotype
    • Adam G, Sorensen EJ, Cravatt BF. Proteomic profiling of mechanistically distinct enzyme classes using common chemotype. Nature Biotechnol. 20, 805-809 (2002).
    • (2002) Nature Biotechnol. , vol.20 , pp. 805-809
    • Adam, G.1    Sorensen, E.J.2    Cravatt, B.F.3
  • 31
    • 0036678119 scopus 로고    scopus 로고
    • Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness
    • Jessani N, Liu Y, Humphrey M, Cravatt BF. Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc. Natl Acad. Sci. USA 99, 10335-10340 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 10335-10340
    • Jessani, N.1    Liu, Y.2    Humphrey, M.3    Cravatt, B.F.4
  • 32
    • 2242432614 scopus 로고    scopus 로고
    • A role for the protease falcipain 1 in host cell invasion by the human malaria parasite
    • Greenbaum DC, Baruch A, Grainger M et al. A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. Science 298, 2002-2006 (2002).
    • (2002) Science , vol.298 , pp. 2002-2006
    • Greenbaum, D.C.1    Baruch, A.2    Grainger, M.3
  • 33
    • 1942522084 scopus 로고    scopus 로고
    • Profiling enzyme activities in vivo using click chemistry methods
    • Speers AE, Cravatt BF. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11, 535-546 (2004).
    • (2004) Chem. Biol. , vol.11 , pp. 535-546
    • Speers, A.E.1    Cravatt, B.F.2
  • 34
    • 0037132625 scopus 로고    scopus 로고
    • Peptide microarrays for the determination of protease substrate specificity
    • Salisbury CM, Maly DJ, Ellman JA. Peptide microarrays for the determination of protease substrate specificity. J. Am. Chem. Sci. 124, 14868-14870 (2002).
    • (2002) J. Am. Chem. Sci. , vol.124 , pp. 14868-14870
    • Salisbury, C.M.1    Maly, D.J.2    Ellman, J.A.3
  • 35
    • 0036629182 scopus 로고    scopus 로고
    • Towards quantitative assays with peptide chips: A surface engineering approach
    • Houseman BT, Mrksich M. Towards quantitative assays with peptide chips: a surface engineering approach. Trends Biotechnol. 20, 279-281 (2002).
    • (2002) Trends Biotechnol. , vol.20 , pp. 279-281
    • Houseman, B.T.1    Mrksich, M.2
  • 37
    • 9244243049 scopus 로고    scopus 로고
    • Profiling kinase activities by using a peptide chip and mass spectrometry
    • Min DH, Su J, Mrksich M. Profiling kinase activities by using a peptide chip and mass spectrometry. Angew. Chem. Int. Ed. 43, 5973-5977 (2004).
    • (2004) Angew. Chem. Int. Ed. , vol.43 , pp. 5973-5977
    • Min, D.H.1    Su, J.2    Mrksich, M.3
  • 38
    • 4544293437 scopus 로고    scopus 로고
    • Automated synthesis: High-content peptide microarrays for deciphering kinase specificity and biology
    • Schutkowski M, Reimer U, Panse S et al. Automated synthesis: high-content peptide microarrays for deciphering kinase specificity and biology. Angew. Chem. Int. Ed. 43, 2671-2674 (2004).
    • (2004) Angew. Chem. Int. Ed. , vol.43 , pp. 2671-2674
    • Schutkowski, M.1    Reimer, U.2    Panse, S.3
  • 39
    • 0026341239 scopus 로고
    • Sequence-selective recognition of DNA by strand displacement with thyamine-substituted polyamide
    • Nielsen PE, Egholm, M, Berg RH, Buchardt O. Sequence-selective recognition of DNA by strand displacement with thyamine-substituted polyamide. Science 254, 1497-1500 (1991).
    • (1991) Science , vol.254 , pp. 1497-1500
    • Nielsen, P.E.1    Egholm, M.2    Berg, R.H.3    Buchardt, O.4
  • 40
    • 0027364174 scopus 로고
    • PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules
    • Egolm M, Buchardt O, Christensen L et al. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365, 566-568 (1993).
    • (1993) Nature , vol.365 , pp. 566-568
    • Egolm, M.1    Buchardt, O.2    Christensen, L.3
  • 41
    • 0035801347 scopus 로고    scopus 로고
    • From split-pool libraries to spatially addressable microarrays and its application to functional proteomic profiling
    • Winssinger, N, Harris JL, Backes BJ, Schultz PG. From split-pool libraries to spatially addressable microarrays and its application to functional proteomic profiling. Angew. Chem. Int. Ed. 40, 3152-3155 (2001).
    • (2001) Angew. Chem. Int. Ed. , vol.40 , pp. 3152-3155
    • Winssinger, N.1    Harris, J.L.2    Backes, B.J.3    Schultz, P.G.4
  • 43
    • 4344690276 scopus 로고    scopus 로고
    • Synthesis of a PNA-encoded cysteine protease inhibitor library
    • Debaene, F, Mejias, L, Harris JL, Winssinger N. Synthesis of a PNA-encoded cysteine protease inhibitor library. Tetrahedron 60, 8677-8690 (2004).
    • (2004) Tetrahedron , vol.60 , pp. 8677-8690
    • Debaene, F.1    Mejias, L.2    Harris, J.L.3    Winssinger, N.4
  • 44
    • 5444262942 scopus 로고    scopus 로고
    • Activity profile of dust mite allergen extract using substrate libraries and functional proteomic microarrays
    • Harris J, Mason DE, Li J et al. Activity profile of dust mite allergen extract using substrate libraries and functional proteomic microarrays. Chem. Biol. 11, 1361-1372 (2004).
    • (2004) Chem. Biol. , vol.11 , pp. 1361-1372
    • Harris, J.1    Mason, D.E.2    Li, J.3
  • 46
    • 27944500629 scopus 로고    scopus 로고
    • PNA encoding: From solution based libraries to organized microarrays
    • Harris JL, Winssinger N. PNA encoding: from solution based libraries to organized microarrays. Chem. Eur. J. 11, 6792-6801 (2005).
    • (2005) Chem. Eur. J. , vol.11 , pp. 6792-6801
    • Harris, J.L.1    Winssinger, N.2
  • 47
    • 0036083016 scopus 로고    scopus 로고
    • New kids on the block: Emerging PNA-based DNA diagnostics
    • Demidov VV. New kids on the block: emerging PNA-based DNA diagnostics. Expert. Rev. Mol. Diagn. 2, 199-201 (2002).
    • (2002) Expert. Rev. Mol. Diagn. , vol.2 , pp. 199-201
    • Demidov, V.V.1
  • 48
    • 0028129843 scopus 로고
    • Stability of peptide nucleic acids in human serum and cellular extracts
    • Demidov VV, Potaman VN, Frank-Kamenetskii MD et al. Stability of peptide nucleic acids in human serum and cellular extracts. Biochem. Pharmacol. 48, 1310-1313 (1994).
    • (1994) Biochem. Pharmacol. , vol.48 , pp. 1310-1313
    • Demidov, V.V.1    Potaman, V.N.2    Frank-Kamenetskii, M.D.3
  • 49
    • 0032766821 scopus 로고    scopus 로고
    • Peptide nucleic acid. A molecule with two identities
    • Nielsen PE. Peptide nucleic acid. A molecule with two identities. Acc. Chem. Res. 32, 624-630 (1999).
    • (1999) Acc. Chem. Res. , vol.32 , pp. 624-630
    • Nielsen, P.E.1
  • 50
    • 0020852609 scopus 로고
    • New class of sensitive and selective fluorogenic substrates for serine proteinases. Amino acid and dipeptide derivatives of rhodamine
    • Leytus SP, Patterson WL, Mangel WF. New class of sensitive and selective fluorogenic substrates for serine proteinases. Amino acid and dipeptide derivatives of rhodamine. Biochem. J. 215, 253-260 (1983).
    • (1983) Biochem. J. , vol.215 , pp. 253-260
    • Leytus, S.P.1    Patterson, W.L.2    Mangel, W.F.3
  • 52
    • 0030962626 scopus 로고    scopus 로고
    • Asthma and indoor exposure to allergens
    • Platts-Mills TA, Carter MC. Asthma and indoor exposure to allergens. N. Engl. J. Med. 336, 1382-1384 (1997).
    • (1997) N. Engl. J. Med. , vol.336 , pp. 1382-1384
    • Platts-Mills, T.A.1    Carter, M.C.2
  • 53
    • 0033855351 scopus 로고    scopus 로고
    • The significance of enzymic and other biological activities of proteins in relation to their capacity to serve as allergens
    • Shakib F, Furmonaviciene R. The significance of enzymic and other biological activities of proteins in relation to their capacity to serve as allergens. Clin. Exp. Allergy 30, 1056-1057 (2000).
    • (2000) Clin. Exp. Allergy , vol.30 , pp. 1056-1057
    • Shakib, F.1    Furmonaviciene, R.2


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