메뉴 건너뛰기




Volumn 2, Issue , 2008, Pages

The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN;

EID: 58149097413     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-100     Document Type: Article
Times cited : (52)

References (67)
  • 1
    • 0023061429 scopus 로고
    • Complexes of sequential metabolic enzymes
    • 2441660
    • Srere PA Complexes of sequential metabolic enzymes Annu Rev Biochem 1987, 56:89-124 2441660
    • (1987) Annu Rev Biochem , vol.56 , pp. 89-124
    • Srere, P.A.1
  • 2
    • 0027366579 scopus 로고
    • The Cell Bag of Enzymes or Network of Channels
    • 206744 8407814
    • Mathews CK The Cell Bag of Enzymes or Network of Channels J Bacteriol 1993, 175(20):6377-6381 206744 8407814
    • (1993) J Bacteriol , vol.175 , Issue.20 , pp. 6377-6381
    • Mathews, C.K.1
  • 3
    • 0344631518 scopus 로고    scopus 로고
    • Substrate channeling
    • 10527733
    • Spivey HO Ovadi J Substrate channeling Methods 1999, 19(2):306-321 10527733
    • (1999) Methods , vol.19 , Issue.2 , pp. 306-321
    • Spivey, H.O.1    Ovadi, J.2
  • 4
    • 0033991699 scopus 로고    scopus 로고
    • Macromolecular compartmentation and channeling
    • 10553282
    • Ovadi J Srere PA Macromolecular compartmentation and channeling Int Rev Cytol 2000, 192:255-280 10553282
    • (2000) Int Rev Cytol , vol.192 , pp. 255-280
    • Ovadi, J.1    Srere, P.A.2
  • 5
    • 0034161474 scopus 로고    scopus 로고
    • Macromolecular interactions: Tracing the roots
    • 10694888
    • Srere PA Macromolecular interactions: Tracing the roots Trends Biochem Sci 2000, 25(3):150-153 10694888
    • (2000) Trends Biochem Sci , vol.25 , Issue.3 , pp. 150-153
    • Srere, P.A.1
  • 7
    • 0019631384 scopus 로고
    • A generalized theory of the transition time for sequential enzyme reactions
    • 1163345 7337699
    • Easterby JS A generalized theory of the transition time for sequential enzyme reactions Biochem J 1981, 199(1):155-161 1163345 7337699
    • (1981) Biochem J , vol.199 , Issue.1 , pp. 155-161
    • Easterby, J.S.1
  • 8
    • 0026436963 scopus 로고
    • Enzyme organization and the direction of metabolic flow: Physicochemical considerations
    • 1499341
    • Westerhoff HV Welch GR Enzyme organization and the direction of metabolic flow: Physicochemical considerations Curr Top Cell Regul 1992, 33:361-390 1499341
    • (1992) Curr Top Cell Regul , vol.33 , pp. 361-390
    • Westerhoff, H.V.1    Welch, G.R.2
  • 9
    • 0028898649 scopus 로고
    • Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetase
    • 7532005
    • Rudolph J Stubbe J Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetase Biochemistry 1995, 34(7):2241-2250 7532005
    • (1995) Biochemistry , vol.34 , Issue.7 , pp. 2241-2250
    • Rudolph, J.1    Stubbe, J.2
  • 11
    • 0028674909 scopus 로고
    • Binding of malate dehydrogenase and NADH channelling to complex I
    • 7734152
    • Ovadi J Huang Y Spivey HO Binding of malate dehydrogenase and NADH channelling to complex I J Mol Recognit 1994, 7(4):265-272 7734152
    • (1994) J Mol Recognit , vol.7 , Issue.4 , pp. 265-272
    • Ovadi, J.1    Huang, Y.2    Spivey, H.O.3
  • 12
    • 0001398340 scopus 로고
    • Alternative view of enzyme reactions
    • 397529 3857576
    • Dewar MJ Storch DM Alternative view of enzyme reactions Proc Natl Acad Sci USA 1985, 82(8):2225-2229 397529 3857576
    • (1985) Proc Natl Acad Sci USA , vol.82 , Issue.8 , pp. 2225-2229
    • Dewar, M.J.1    Storch, D.M.2
  • 13
  • 14
    • 0024322685 scopus 로고
    • Channeling of glycolytic intermediates by temporary, stationary bi-enzyme complexes is probable in vivo
    • 2696177
    • Batke J Channeling of glycolytic intermediates by temporary, stationary bi-enzyme complexes is probable in vivo Trends Biochem Sci 1989, 14(12):481-482 2696177
    • (1989) Trends Biochem Sci , vol.14 , Issue.12 , pp. 481-482
    • Batke, J.1
  • 15
    • 0023708854 scopus 로고
    • Control of metabolism by dynamic macromolecular interactions
    • 3293924
    • Keleti T Ovadi J Control of metabolism by dynamic macromolecular interactions Curr Top Cell Regul 1988, 29:1-33 3293924
    • (1988) Curr Top Cell Regul , vol.29 , pp. 1-33
    • Keleti, T.1    Ovadi, J.2
  • 16
    • 0017800423 scopus 로고
    • Kinetic evidence for interaction between aldolase and D-glyceraldehyde-3-phosphate dehydrogenase
    • 205415
    • Ovadi J Keleti T Kinetic evidence for interaction between aldolase and D-glyceraldehyde-3-phosphate dehydrogenase Eur J Biochem 1978, 85(1):157-161 205415
    • (1978) Eur J Biochem , vol.85 , Issue.1 , pp. 157-161
    • Ovadi, J.1    Keleti, T.2
  • 17
    • 0023244119 scopus 로고
    • A simple approach to detect active-site-directed enzyme-enzyme interactions. The aldolase/glycerol-phosphate-dehydrogenase enzyme system
    • 3569280
    • Vertessy B Ovadi J A simple approach to detect active-site-directed enzyme-enzyme interactions. The aldolase/ glycerol-phosphate-dehydrogenase enzyme system Eur J Biochem 1987, 164(3):655-659 3569280
    • (1987) Eur J Biochem , vol.164 , Issue.3 , pp. 655-659
    • Vertessy, B.1    Ovadi, J.2
  • 18
    • 0027511971 scopus 로고
    • Channelling can affect concentrations of metabolic intermediates at constant net flux: Artefact or reality?
    • 8477736
    • Cornish-Bowden A Cardenas ML Channelling can affect concentrations of metabolic intermediates at constant net flux: Artefact or reality? Eur J Biochem 1993, 213(1):87-92 8477736
    • (1993) Eur J Biochem , vol.213 , Issue.1 , pp. 87-92
    • Cornish-Bowden, A.1    Cardenas, M.L.2
  • 19
    • 0025862030 scopus 로고
    • No convincing evidence is available for metabolite channelling between enzymes forming dynamic complexes
    • 1753770
    • Pettersson G No convincing evidence is available for metabolite channelling between enzymes forming dynamic complexes J Theor Biol 1991, 152(1):65-69 1753770
    • (1991) J Theor Biol , vol.152 , Issue.1 , pp. 65-69
    • Pettersson, G.1
  • 20
    • 0026089342 scopus 로고
    • Substrate channeling in glycolysis: A phantom phenomenon
    • 50838 1988948
    • Wu XM Gutfreund H Lakatos S Chock PB Substrate channeling in glycolysis: a phantom phenomenon Proc Natl Acad Sci USA 1991, 88(2):497-501 50838 1988948
    • (1991) Proc Natl Acad Sci USA , vol.88 , Issue.2 , pp. 497-501
    • Wu, X.M.1    Gutfreund, H.2    Lakatos, S.3    Chock, P.B.4
  • 21
    • 1642576078 scopus 로고    scopus 로고
    • Reconstitution of the entry point of plant phenylpropanoid metabolism in yeast (Saccharomyces cerevisiae): Implications for control of metabolic flux into the phenylpropanoid pathway
    • 14607837
    • Ro DK Douglas CJ Reconstitution of the entry point of plant phenylpropanoid metabolism in yeast (Saccharomyces cerevisiae): implications for control of metabolic flux into the phenylpropanoid pathway J Biol Chem 2004, 279(4):2600-2607 14607837
    • (2004) J Biol Chem , vol.279 , Issue.4 , pp. 2600-2607
    • Ro, D.K.1    Douglas, C.J.2
  • 22
    • 3142600919 scopus 로고    scopus 로고
    • Discrete event, multi-level simulation of metabolite channeling
    • 15245802
    • Degenring D Rohl M Uhrmacher AM Discrete event, multi-level simulation of metabolite channeling Biosystems 2004, 75(1-3):29-41 15245802
    • (2004) Biosystems , vol.75 , Issue.1-3 , pp. 29-41
    • Degenring, D.1    Rohl, M.2    Uhrmacher, A.M.3
  • 23
    • 0033943727 scopus 로고    scopus 로고
    • Engineering a living cell to desired metabolite concentrations and fluxes: Pathways with multifunctional enzymes
    • 10935931
    • Kholodenko BN Westerhoff HV Schwaber J Cascante M Engineering a living cell to desired metabolite concentrations and fluxes: Pathways with multifunctional enzymes Metab Eng 2000, 2(1):1-13 10935931
    • (2000) Metab Eng , vol.2 , Issue.1 , pp. 1-13
    • Kholodenko, B.N.1    Westerhoff, H.V.2    Schwaber, J.3    Cascante, M.4
  • 24
    • 48549083577 scopus 로고    scopus 로고
    • Computational analysis of protein-protein interactions in metabolic networks of Escherichia coli and yeast
    • 18546484
    • Huthmacher C Gille C Holzhutter HG Computational analysis of protein-protein interactions in metabolic networks of Escherichia coli and yeast Genome Inform 2007, 18:162-172 18546484
    • (2007) Genome Inform , vol.18 , pp. 162-172
    • Huthmacher, C.1    Gille, C.2    Holzhutter, H.G.3
  • 25
    • 43449119501 scopus 로고    scopus 로고
    • A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling
    • 17988690
    • Huthmacher C Gille C Holzhutter HG A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling J Theor Biol 2008, 252(3):456-464 17988690
    • (2008) J Theor Biol , vol.252 , Issue.3 , pp. 456-464
    • Huthmacher, C.1    Gille, C.2    Holzhutter, H.G.3
  • 26
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • 10521342
    • Barabasi AL Albert R Emergence of scaling in random networks Science 1999, 286(5439):509-512 10521342
    • (1999) Science , vol.286 , Issue.5439 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 28
    • 27944493925 scopus 로고    scopus 로고
    • Scale-free networks in cell biology
    • 16254242
    • Albert R Scale-free networks in cell biology J Cell Sci 2005, 118(Pt 21):4947-4957 16254242
    • (2005) J Cell Sci , vol.118 , Issue.PART 21 , pp. 4947-4957
    • Albert, R.1
  • 29
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • 11034217
    • Jeong H Tombor B Albert R Oltvai ZN Barabasi AL The large-scale organization of metabolic networks Nature 2000, 407(6804):651-654 11034217
    • (2000) Nature , vol.407 , Issue.6804 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 30
    • 0035823264 scopus 로고    scopus 로고
    • The small world inside large metabolic networks
    • 1088812 11522199
    • Wagner A Fell DA The small world inside large metabolic networks Proc Biol Sci 2001, 268(1478):1803-1810 1088812 11522199
    • (2001) Proc Biol Sci , vol.268 , Issue.1478 , pp. 1803-1810
    • Wagner, A.1    Fell, D.A.2
  • 31
    • 34249736324 scopus 로고    scopus 로고
    • Biological impacts and context of network theory
    • 17449819
    • Almaas E Biological impacts and context of network theory J Exp Biol 2007, 210(Pt 9):1548-1558 17449819
    • (2007) J Exp Biol , vol.210 , Issue.PART 9 , pp. 1548-1558
    • Almaas, E.1
  • 32
    • 0035733690 scopus 로고    scopus 로고
    • Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
    • 11694880
    • Ge H Liu Z Church GM Vidal M Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae Nat Genet 2001, 29(4):482-486 11694880
    • (2001) Nat Genet , vol.29 , Issue.4 , pp. 482-486
    • Ge, H.1    Liu, Z.2    Church, G.M.3    Vidal, M.4
  • 33
    • 0036279153 scopus 로고    scopus 로고
    • Protein interaction verification and functional annotation by integrated analysis of genome-scale data
    • 12049748
    • Kemmeren P van Berkum NL Vilo J Bijma T Donders R Brazma A Holstege FC Protein interaction verification and functional annotation by integrated analysis of genome-scale data Mol Cell 2002, 9(5):1133-1143 12049748
    • (2002) Mol Cell , vol.9 , Issue.5 , pp. 1133-1143
    • Kemmeren, P.1    van Berkum, N.L.2    Vilo, J.3    Bijma, T.4    Donders, R.5    Brazma, A.6    Holstege, F.C.7
  • 34
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • 12118076
    • Deane CM Salwinski L Xenarios I Eisenberg D Protein interactions: Two methods for assessment of the reliability of high throughput observations Mol Cell Proteomics 2002, 1(5):349-356 12118076
    • (2002) Mol Cell Proteomics , vol.1 , Issue.5 , pp. 349-356
    • Deane, C.M.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 35
    • 0037447257 scopus 로고    scopus 로고
    • Assessing experimentally derived interactions in a small world
    • 404686 12676999
    • Goldberg DS Roth FP Assessing experimentally derived interactions in a small world Proc Natl Acad Sci USA 2003, 100(8):4372-4376 404686 12676999
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.8 , pp. 4372-4376
    • Goldberg, D.S.1    Roth, F.P.2
  • 36
    • 22844450110 scopus 로고    scopus 로고
    • Systematic interpretation of genetic interactions using protein networks
    • 15877074
    • Kelley R Ideker T Systematic interpretation of genetic interactions using protein networks Nat Biotechnol 2005, 23(5):561-566 15877074
    • (2005) Nat Biotechnol , vol.23 , Issue.5 , pp. 561-566
    • Kelley, R.1    Ideker, T.2
  • 38
    • 42149116826 scopus 로고    scopus 로고
    • A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
    • 2387231 18414481
    • Ramani AK Li Z Hart GT Carlson MW Boutz DR Marcotte EM A map of human protein interactions derived from co-expression of human mRNAs and their orthologs Mol Syst Biol 2008, 4:180 2387231 18414481
    • (2008) Mol Syst Biol , vol.4 , pp. 180
    • Ramani, A.K.1    Li, Z.2    Hart, G.T.3    Carlson, M.W.4    Boutz, D.R.5    Marcotte, E.M.6
  • 39
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • 15567862
    • Lee I Date SV Adai AT Marcotte EM A probabilistic functional network of yeast genes Science 2004, 306(5701):1555-1558 15567862
    • (2004) Science , vol.306 , Issue.5701 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 40
    • 27344459447 scopus 로고    scopus 로고
    • Minimum spanning trees on weighted scale-free networks
    • Macdonald P Almaas E Barabasi A Minimum spanning trees on weighted scale-free networks Europhys Lett 2005, 72:308-314
    • (2005) Europhys Lett , vol.72 , pp. 308-314
    • Macdonald, P.1    Almaas, E.2    Barabasi, A.3
  • 44
    • 15444372528 scopus 로고    scopus 로고
    • Subnets of scale-free networks are not scale-free: Sampling properties of networks
    • 555505 15767579
    • Stumpf MP Wiuf C May RM Subnets of scale-free networks are not scale-free: Sampling properties of networks Proc Natl Acad Sci USA 2005, 102(12):4221-4224 555505 15767579
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.12 , pp. 4221-4224
    • Stumpf, M.P.1    Wiuf, C.2    May, R.M.3
  • 45
    • 1242319556 scopus 로고    scopus 로고
    • The metabolic world of Escherichia coli is not small
    • 341771 14757824
    • Arita M The metabolic world of Escherichia coli is not small Proc Natl Acad Sci USA 2004, 101(6):1543-1547 341771 14757824
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.6 , pp. 1543-1547
    • Arita, M.1
  • 46
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • 420374 12566402
    • Forster J Famili I Fu P Palsson BO Nielsen J Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network Genome Res 2003, 13(2):244-253 420374 12566402
    • (2003) Genome Res , vol.13 , Issue.2 , pp. 244-253
    • Forster, J.1    Famili, I.2    Fu, P.3    Palsson, B.O.4    Nielsen, J.5
  • 47
    • 25444467580 scopus 로고    scopus 로고
    • Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
    • 1175969 15960801
    • Blank LM Kuepfer L Sauer U Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast Genome Biol 2005, 6(6):R49 1175969 15960801
    • (2005) Genome Biol , vol.6 , Issue.6
    • Blank, L.M.1    Kuepfer, L.2    Sauer, U.3
  • 50
    • 0038718854 scopus 로고    scopus 로고
    • The structure and function of complex networks
    • Newman ME The structure and function of complex networks SIAM REVIEW 2003, 45:167-256
    • (2003) SIAM REVIEW , vol.45 , pp. 167-256
    • Newman, M.E.1
  • 51
    • 0242692460 scopus 로고    scopus 로고
    • Duplication models for biological networks
    • 14633392
    • Chung F Lu L Dewey TG Galas DJ Duplication models for biological networks J Comput Biol 2003, 10(5);677-687 14633392
    • (2003) J Comput Biol , vol.10 , Issue.5 , pp. 677-687
    • Chung, F.1    Lu, L.2    Dewey, T.G.3    Galas, D.J.4
  • 53
    • 11444249446 scopus 로고    scopus 로고
    • Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions
    • 15600352
    • Kotera M Okuno Y Hattori M Goto S Kanehisa M Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions J Am Chem Soc 2004, 126(50):16487-16498 15600352
    • (2004) J Am Chem Soc , vol.126 , Issue.50 , pp. 16487-16498
    • Kotera, M.1    Okuno, Y.2    Hattori, M.3    Goto, S.4    Kanehisa, M.5
  • 54
    • 0036856356 scopus 로고    scopus 로고
    • A duplication growth model of gene expression networks
    • 12424120
    • Bhan A Galas DJ Dewey TG A duplication growth model of gene expression networks Bioinformatics 2002, 18(11):1486-1493 12424120
    • (2002) Bioinformatics , vol.18 , Issue.11 , pp. 1486-1493
    • Bhan, A.1    Galas, D.J.2    Dewey, T.G.3
  • 55
    • 24944442468 scopus 로고    scopus 로고
    • Effect of sampling on topology predictions of protein-protein interaction networks
    • 16003372
    • Han JD Dupuy D Bertin N Cusick ME Vidal M Effect of sampling on topology predictions of protein-protein interaction networks Nat Biotechnol 2005, 23(7):839-844 16003372
    • (2005) Nat Biotechnol , vol.23 , Issue.7 , pp. 839-844
    • Han, J.D.1    Dupuy, D.2    Bertin, N.3    Cusick, M.E.4    Vidal, M.5
  • 56
    • 0037432528 scopus 로고    scopus 로고
    • How Reliable are Experimental Protein-Protein Interaction Data?
    • 12662919
    • Sprinzak E Sattath S Margalit H How Reliable are Experimental Protein-Protein Interaction Data? Journal of Molecular Biology 2003, 327(5):919-923 12662919
    • (2003) Journal of Molecular Biology , vol.327 , Issue.5 , pp. 919-923
    • Sprinzak, E.1    Sattath, S.2    Margalit, H.3
  • 57
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • 12000970
    • von Mering C Krause R Snel B Cornell M Oliver SG Fields S Bork P Comparative assessment of large-scale data sets of protein-protein interactions Nature 2002, 417(6887):399-403 12000970
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 63
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • 9623998
    • Watts DJ Strogatz SH Collective dynamics of 'small-world' networks Nature 1998, 393(6684):440-442 9623998
    • (1998) Nature , vol.393 , Issue.6684 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 64
    • 25944437904 scopus 로고    scopus 로고
    • Dynamical and correlation properties of the internet
    • 11736611
    • Pastor-Satorras R Vazquez A Vespignani A Dynamical and correlation properties of the internet Phys Rev Lett 2001, 87(25);258701 11736611
    • (2001) Phys Rev Lett , vol.87 , Issue.25 , pp. 258701
    • Pastor-Satorras, R.1    Vazquez, A.2    Vespignani, A.3
  • 65
    • 18744389789 scopus 로고    scopus 로고
    • Assortative mixing in networks
    • 12443515
    • Newman ME Assortative mixing in networks Phys Rev Lett 2002, 89(20):208701 12443515
    • (2002) Phys Rev Lett , vol.89 , Issue.20 , pp. 208701
    • Newman, M.E.1
  • 66
  • 67
    • 0042635247 scopus 로고    scopus 로고
    • Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality
    • 11461356
    • Newman ME Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality Phys Rev E Stat Nonlin Soft Matter Phys 2001, 64(1 Pt 2):016132 11461356
    • (2001) Phys Rev E Stat Nonlin Soft Matter Phys , vol.64 , Issue.1 PART 2 , pp. 016132
    • Newman, M.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.