메뉴 건너뛰기




Volumn 30, Issue 1, 1998, Pages 49-60

Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides

Author keywords

Kohonen network; Mitochondrial intermediate peptidase (MIP); Mitochondrial processing peptidase (MPP); Mitochondrial targeting; Neural network; Protein import; Sequence motif

Indexed keywords

ARGININE; METALLOPROTEINASE; PROTEINASE;

EID: 0031964126     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980101)30:1<49::AID-PROT5>3.0.CO;2-F     Document Type: Article
Times cited : (92)

References (58)
  • 1
    • 0024146932 scopus 로고
    • Biogenesis of mitochondria: Assembly of the mitochondrial membrane system
    • Attardi, G., Schatz, G. Biogenesis of mitochondria: Assembly of the mitochondrial membrane system. Annu. Rev. Cell. Biol. 4:289-333, 1988.
    • (1988) Annu. Rev. Cell. Biol. , vol.4 , pp. 289-333
    • Attardi, G.1    Schatz, G.2
  • 2
    • 0025091956 scopus 로고
    • Protein sorting to mitochondria: Evolutionary conservations of folding and assembly
    • Hartl, F.-U., Neupert, W. Protein sorting to mitochondria: Evolutionary conservations of folding and assembly. Science 247:930-938, 1990.
    • (1990) Science , vol.247 , pp. 930-938
    • Hartl, F.-U.1    Neupert, W.2
  • 3
    • 0026323440 scopus 로고
    • Import of proteins into mitochondria
    • Glick, B., Schatz, G. Import of proteins into mitochondria. Annu. Rev. Genet. 25:21-44, 1991.
    • (1991) Annu. Rev. Genet. , vol.25 , pp. 21-44
    • Glick, B.1    Schatz, G.2
  • 4
    • 0028834046 scopus 로고
    • Can Hsp70 proteins act as force-generating motors?
    • Glick, B.S. Can Hsp70 proteins act as force-generating motors? Cell 80:11-14, 1995.
    • (1995) Cell , vol.80 , pp. 11-14
    • Glick, B.S.1
  • 5
    • 0025114862 scopus 로고
    • How do polypeptides cross the mitochondrial membranes?
    • Neupert, W., Hartl, F.-U., Craig, E.A., Pfanner, N. How do polypeptides cross the mitochondrial membranes? Cell 63:447-450, 1990.
    • (1990) Cell , vol.63 , pp. 447-450
    • Neupert, W.1    Hartl, F.-U.2    Craig, E.A.3    Pfanner, N.4
  • 6
    • 0029240213 scopus 로고
    • Protein sorting: Pulling in the proteins
    • Pfanner, N., Meijer, M. Protein sorting: Pulling in the proteins. Curr. Biol. 5:132-135, 1995.
    • (1995) Curr. Biol. , vol.5 , pp. 132-135
    • Pfanner, N.1    Meijer, M.2
  • 7
    • 0027399210 scopus 로고
    • The protein import machinery of mitochondria
    • Schatz, G. The protein import machinery of mitochondria. Protein Sci. 2:141-146, 1993.
    • (1993) Protein Sci. , vol.2 , pp. 141-146
    • Schatz, G.1
  • 8
    • 85134867979 scopus 로고
    • Design of protein targeting signals and membrane protein engineering
    • Wrede, P., Schneider, G. (eds.). Berlin: Walter de Gruyter Verlag
    • von Heijne, G. Design of protein targeting signals and membrane protein engineering. In: "Concepts in Protein Engineering and Design." Wrede, P., Schneider, G. (eds.). Berlin: Walter de Gruyter Verlag, 1994:263-279.
    • (1994) Concepts in Protein Engineering and Design , pp. 263-279
    • Von Heijne, G.1
  • 10
    • 0026440343 scopus 로고
    • Mitochondrial processing proteinase: A general processing proteinase of spinach leaf mitochondria is a membrane-bound enzyme
    • Eriksson, A.C., Glaser, E. Mitochondrial processing proteinase: A general processing proteinase of spinach leaf mitochondria is a membrane-bound enzyme. Biochim. Biophys. Acta 1140:208-214, 1992.
    • (1992) Biochim. Biophys. Acta , vol.1140 , pp. 208-214
    • Eriksson, A.C.1    Glaser, E.2
  • 11
    • 0026709336 scopus 로고
    • The general mitochondrial processing peptidase from potato is an integral part of the cytochrome bc1 complex of the respiratory chain
    • Braun, H.P., Emmermann, M., Kruft, V., Schmitz, U.K. The general mitochondrial processing peptidase from potato is an integral part of the cytochrome bc1 complex of the respiratory chain. EMBO J. 11:3219-3227, 1992.
    • (1992) EMBO J. , vol.11 , pp. 3219-3227
    • Braun, H.P.1    Emmermann, M.2    Kruft, V.3    Schmitz, U.K.4
  • 12
    • 0000749103 scopus 로고
    • A general processing proteinase of spinach leaf mitochondria is associated with the bc1 complex of the respiratory chain
    • Brennicke, A., Kuck, U. (eds.). Weinheim: VCH Verlagsgesellschaft
    • Eriksson, A.C., Sjöling, S., Glaser, E. A general processing proteinase of spinach leaf mitochondria is associated with the bc1 complex of the respiratory chain. In: "Plant Mitochondria." Brennicke, A., Kuck, U. (eds.). Weinheim: VCH Verlagsgesellschaft, 1993:233-241.
    • (1993) Plant Mitochondria , pp. 233-241
    • Eriksson, A.C.1    Sjöling, S.2    Glaser, E.3
  • 13
    • 0028075242 scopus 로고
    • The ubiquinol cytochrome c oxidoreduxtase of spinach leaf mitochondria is involved in both respiration and protein processing
    • Eriksson, A.C., Sjöling, S., Glaser, E. The ubiquinol cytochrome c oxidoreduxtase of spinach leaf mitochondria is involved in both respiration and protein processing. Biochim. Biophys. Acta 1186:221-231, 1994.
    • (1994) Biochim. Biophys. Acta , vol.1186 , pp. 221-231
    • Eriksson, A.C.1    Sjöling, S.2    Glaser, E.3
  • 14
    • 0011251247 scopus 로고
    • The mitochondrial intermediate peptidase
    • von Heijne, G. (ed.). Austin: RG Landes
    • Isaya, G., Kalousek, F. The mitochondrial intermediate peptidase. In: "Signal Peptidases." von Heijne, G. (ed.). Austin: RG Landes, 1994:87-103.
    • (1994) Signal Peptidases , pp. 87-103
    • Isaya, G.1    Kalousek, F.2
  • 15
    • 0012293890 scopus 로고
    • Two mitochondrial matrix proteases act sequentially in the processing of mammalian matrix enzymes
    • Kalousek, F., Hendrick, J.P., Rosenberg, L.E. Two mitochondrial matrix proteases act sequentially in the processing of mammalian matrix enzymes. Proc. Natl. Acad. Sci. U.S.A. 85:7536-7540, 1988.
    • (1988) Proc. Natl. Acad. Sci. U.S.A. , vol.85 , pp. 7536-7540
    • Kalousek, F.1    Hendrick, J.P.2    Rosenberg, L.E.3
  • 16
    • 0027992732 scopus 로고
    • Structural requirement for recognition of the precursor proteins by the mitochondrial processing peptidase
    • Ou, W., Kumamoto, T., Mihara, K., Kitada, S., Niidome, T., Ito, A., Omura, T. Structural requirement for recognition of the precursor proteins by the mitochondrial processing peptidase. J. Biol. Chem. 269:24673-24678, 1994.
    • (1994) J. Biol. Chem. , vol.269 , pp. 24673-24678
    • Ou, W.1    Kumamoto, T.2    Mihara, K.3    Kitada, S.4    Niidome, T.5    Ito, A.6    Omura, T.7
  • 17
    • 0027295559 scopus 로고
    • Import, processing, and two-dimensional NMR structure of a linker-deleted signal peptide of rat liver mitochondrial aldehyde dehydrogenase
    • Thornton, K., Wang, Y., Weiner, H., Gorenstein, D.G. Import, processing, and two-dimensional NMR structure of a linker-deleted signal peptide of rat liver mitochondrial aldehyde dehydrogenase. J. Biol. Chem. 268:19906-19914, 1993.
    • (1993) J. Biol. Chem. , vol.268 , pp. 19906-19914
    • Thornton, K.1    Wang, Y.2    Weiner, H.3    Gorenstein, D.G.4
  • 18
  • 19
    • 0028600070 scopus 로고
    • 1β presequence is important for recognition by the mitochondrial processing peptidase
    • 1β presequence is important for recognition by the mitochondrial processing peptidase. J. Biol. Chem. 269:32059-32062, 1994.
    • (1994) J. Biol. Chem. , vol.269 , pp. 32059-32062
    • Sjöling, S.1    Eriksson, A.2    Glaser, E.3
  • 20
    • 0028787643 scopus 로고
    • Conversion of a nonprocessed mitochondrial precursor protein into one that is processed by the mitochondrial processing peptidase
    • Waltner, M., Weiner, H. Conversion of a nonprocessed mitochondrial precursor protein into one that is processed by the mitochondrial processing peptidase. J. Biol. Chem. 270:26311-26317, 1995.
    • (1995) J. Biol. Chem. , vol.270 , pp. 26311-26317
    • Waltner, M.1    Weiner, H.2
  • 21
    • 0026672260 scopus 로고
    • Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks
    • Hirst, J.D., Sternberg, M.J.E. Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochemistry 31:7211-7218, 1991.
    • (1991) Biochemistry , vol.31 , pp. 7211-7218
    • Hirst, J.D.1    Sternberg, M.J.E.2
  • 22
    • 0028568175 scopus 로고
    • Artificial neural networks and simulated molecular evolution are potential tools for sequence-oriented protein design
    • Schneider, G., Schuchhardt, J., Wrede, P. Artificial neural networks and simulated molecular evolution are potential tools for sequence-oriented protein design. Comput. Appl. Biosci. 10:635-645, 1994.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 635-645
    • Schneider, G.1    Schuchhardt, J.2    Wrede, P.3
  • 23
    • 0029355441 scopus 로고
    • Development of simple fitness landscapes for peptides by artificial neural filter systems
    • Schneider, G., Schuchhardt, J., Wrede, P. Development of simple fitness landscapes for peptides by artificial neural filter systems. Biol. Cybernet. 73:245-254, 1995.
    • (1995) Biol. Cybernet. , vol.73 , pp. 245-254
    • Schneider, G.1    Schuchhardt, J.2    Wrede, P.3
  • 25
    • 0030049440 scopus 로고    scopus 로고
    • Binding of mitochondrial presequences to yeast cytosolic heat shock protein 70 depends on the amphiphilicity of the presequence
    • Endo, T., Mitsui, S., Nakai, M., Roise, D. Binding of mitochondrial presequences to yeast cytosolic heat shock protein 70 depends on the amphiphilicity of the presequence. J. Biol. Chem. 271:4161-4167, 1996.
    • (1996) J. Biol. Chem. , vol.271 , pp. 4161-4167
    • Endo, T.1    Mitsui, S.2    Nakai, M.3    Roise, D.4
  • 26
    • 0028068519 scopus 로고
    • Structure of the signal sequences for two mitochondrial matrix proteins that are not proteolytically processed upon import
    • Hammen, P.K., Gorenstein, D.G., Weiner, H. Structure of the signal sequences for two mitochondrial matrix proteins that are not proteolytically processed upon import. Biochemistry 33:8610-8617, 1994.
    • (1994) Biochemistry , vol.33 , pp. 8610-8617
    • Hammen, P.K.1    Gorenstein, D.G.2    Weiner, H.3
  • 27
    • 0029955775 scopus 로고    scopus 로고
    • Processing comparison between the membrane-bound spinach leaf mitochondrial processing peptidase: MPP. integrated into the cytochrome bc1 complex and the soluble rat liver matrix MPP
    • Sjöling, S., Waltner, M., Kalousek, F., Glaser, E., Weiner, H. Processing comparison between the membrane-bound spinach leaf mitochondrial processing peptidase: MPP. integrated into the cytochrome bc1 complex and the soluble rat liver matrix MPP. Eur. J. Biochem. 242:114-121, 1996.
    • (1996) Eur. J. Biochem. , vol.242 , pp. 114-121
    • Sjöling, S.1    Waltner, M.2    Kalousek, F.3    Glaser, E.4    Weiner, H.5
  • 28
    • 0022731676 scopus 로고
    • Mitochondrial targeting sequences may form amphiphilic helices
    • von Heijne, G. Mitochondrial targeting sequences may form amphiphilic helices. EMBO J. 5:1335-1342, 1986.
    • (1986) EMBO J. , vol.5 , pp. 1335-1342
    • Von Heijne, G.1
  • 29
    • 0028050261 scopus 로고
    • OWL: A non-redundant composite protein sequence database
    • Bleasby, A.J., Akrigg, D., Attwood, T.K. OWL: A non-redundant composite protein sequence database. Nucleic Acids Res. 22:3574-3577, 1994.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 3574-3577
    • Bleasby, A.J.1    Akrigg, D.2    Attwood, T.K.3
  • 30
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W.R., Lipman, D.L. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85:2444-2448, 1988.
    • (1988) Proc. Natl. Acad. Sci. U.S.A. , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.L.2
  • 31
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander, C., Schneider, R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68, 1991.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 32
    • 0026562263 scopus 로고
    • The SWISS-PROT protein sequence data bank
    • Bairoch, A., Boeckmann, B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 20:2019-2022, 1992.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 2019-2022
    • Bairoch, A.1    Boeckmann, B.2
  • 34
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • Kohonen, T. Self-organized formation of topologically correct feature maps. Biol. Cybern. 43:59-69, 1982.
    • (1982) Biol. Cybern. , vol.43 , pp. 59-69
    • Kohonen, T.1
  • 36
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman, D.A., Steitz, T.A., Goldman, A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem. 15:321-353, 1986.
    • (1986) Annu. Rev. Biophys. Biophys. Chem. , vol.15 , pp. 321-353
    • Engelman, D.A.1    Steitz, T.A.2    Goldman, A.3
  • 37
    • 0028773889 scopus 로고
    • Volume changes on protein folding
    • Harpaz, Y., Gerstein, M., Chothia, C. Volume changes on protein folding. Structure 2:641-649, 1994.
    • (1994) Structure , vol.2 , pp. 641-649
    • Harpaz, Y.1    Gerstein, M.2    Chothia, C.3
  • 41
    • 0027233815 scopus 로고
    • Development of artificial neural networks for pattern recognition in protein sequences
    • Schneider, G., Wrede, P. Development of artificial neural networks for pattern recognition in protein sequences. J. Mol. Evol. 36:586-595, 1993.
    • (1993) J. Mol. Evol. , vol.36 , pp. 586-595
    • Schneider, G.1    Wrede, P.2
  • 42
    • 0342513293 scopus 로고    scopus 로고
    • Evolutionary optimization in multimodal search space
    • Schneider, G., Schuchhardt, J., Wrede, P. Evolutionary optimization in multimodal search space. Biol. Cybern. 74:203-207, 1996.
    • (1996) Biol. Cybern. , vol.74 , pp. 203-207
    • Schneider, G.1    Schuchhardt, J.2    Wrede, P.3
  • 43
    • 0028801881 scopus 로고
    • Peptide design in machina: Development of artificial mitochondrial protein precursor cleavage sites by simulated molecular evolution
    • Schneider, G., Schuchhardt, J., Wrede, P. Peptide design in machina: Development of artificial mitochondrial protein precursor cleavage sites by simulated molecular evolution. Biophys. J. 68:434-447, 1995.
    • (1995) Biophys. J. , vol.68 , pp. 434-447
    • Schneider, G.1    Schuchhardt, J.2    Wrede, P.3
  • 44
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews, B.W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta. 405:442-451, 1975.
    • (1975) Biochim. Biophys. Acta. , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 45
    • 0027234320 scopus 로고
    • Analysis of cleavage site patterns in protein precursor sequences with a Perceptron-type neural network
    • Schneider, G., Röhlk, S., Wrede, P. Analysis of cleavage site patterns in protein precursor sequences with a Perceptron-type neural network. Biochem. Biophys. Res. Commun. 194:951-959, 1993.
    • (1993) Biochem. Biophys. Res. Commun. , vol.194 , pp. 951-959
    • Schneider, G.1    Röhlk, S.2    Wrede, P.3
  • 46
    • 0023920458 scopus 로고
    • Mitochondrial presequences
    • Roise, D., Schatz, G. Mitochondrial presequences. J. Biol. Chem. 263:4509-4511, 1988.
    • (1988) J. Biol. Chem. , vol.263 , pp. 4509-4511
    • Roise, D.1    Schatz, G.2
  • 47
    • 0024542834 scopus 로고
    • Domain structure of mitochondrial and chloroplast targeting peptides
    • von Heijne, G., Steppuhn, J., Herrman, R.G. Domain structure of mitochondrial and chloroplast targeting peptides. Eur. J. Biochem. 180:535-545, 1989.
    • (1989) Eur. J. Biochem. , vol.180 , pp. 535-545
    • Von Heijne, G.1    Steppuhn, J.2    Herrman, R.G.3
  • 48
    • 0025053384 scopus 로고
    • Cleavage site motifs in mitochondrial targeting peptides
    • Gavel, Y., von Heijne, G. Cleavage site motifs in mitochondrial targeting peptides. Protein. Eng. 4:33-37, 1990.
    • (1990) Protein. Eng. , vol.4 , pp. 33-37
    • Gavel, Y.1    Von Heijne, G.2
  • 49
    • 0027291015 scopus 로고
    • Prediction of protein structure at better than 70% accuracy
    • Rost, B., Sander, C. Prediction of protein structure at better than 70% accuracy. J. Mol. Biol. 232:584-599, 1993.
    • (1993) J. Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 50
    • 0028300741 scopus 로고
    • Combining evolutionary information and neural networks to predict protein secondary structure
    • Rost, B., Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72, 1994.
    • (1994) Proteins , vol.19 , pp. 55-72
    • Rost, B.1    Sander, C.2
  • 51
    • 0028447768 scopus 로고
    • Elucidating the folding problem of helical peptides using empirical parameters
    • Munoz, V., Serrano, L. Elucidating the folding problem of helical peptides using empirical parameters. Nature Struct. Biol. 1:399-409, 1994.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 399-409
    • Munoz, V.1    Serrano, L.2
  • 52
    • 0029155035 scopus 로고
    • Helix Design, prediction and stability
    • Munoz, V., Serrano, L. Helix Design, prediction and stability. Curr. Opin. Biotech. 6:382-386, 1995.
    • (1995) Curr. Opin. Biotech. , vol.6 , pp. 382-386
    • Munoz, V.1    Serrano, L.2
  • 53
    • 0024688488 scopus 로고
    • Survey of amino-terminal proteolytic cleavage sites in mitochondrial precursor proteins: Leader peptides cleaved by two matrix proteases share a three-amino acid motif
    • Hendrick, J.P., Hodges, P.E., Rosenberg, L.E. Survey of amino-terminal proteolytic cleavage sites in mitochondrial precursor proteins: Leader peptides cleaved by two matrix proteases share a three-amino acid motif. Proc. Natl. Acad. Sci. U.S.A. 86:4056-4060, 1989.
    • (1989) Proc. Natl. Acad. Sci. U.S.A. , vol.86 , pp. 4056-4060
    • Hendrick, J.P.1    Hodges, P.E.2    Rosenberg, L.E.3
  • 54
    • 0027967490 scopus 로고
    • Arginine residues in the extension peptide are required for cleavage of a precursor by mitochondrial processing peptidase
    • Niidome, T., Kitada, S., Shimokata, K., Ogishima, T., Ito, A. Arginine residues in the extension peptide are required for cleavage of a precursor by mitochondrial processing peptidase. J. Biol. Chem. 269:24719-24722, 1994.
    • (1994) J. Biol. Chem. , vol.269 , pp. 24719-24722
    • Niidome, T.1    Kitada, S.2    Shimokata, K.3    Ogishima, T.4    Ito, A.5
  • 55
    • 0029608884 scopus 로고
    • Analysis of elements in the substrate required for processing by mitochondrial processing peptidase
    • Ogishima, T., Niidome, T., Shimokata, K., Kitada, S., Ito, A. Analysis of elements in the substrate required for processing by mitochondrial processing peptidase. J. Biol. Chem. 270:30322-30326, 1995.
    • (1995) J. Biol. Chem. , vol.270 , pp. 30322-30326
    • Ogishima, T.1    Niidome, T.2    Shimokata, K.3    Kitada, S.4    Ito, A.5
  • 56
    • 0027941422 scopus 로고
    • Characterization of the mitochondrial processing protease of Neurospora crassa
    • Arretz, M., Schneider, H., Guiard, B., Brunner, M., Neupert, W. Characterization of the mitochondrial processing protease of Neurospora crassa. J. Biol. Chem. 269:4959-4967, 1994.
    • (1994) J. Biol. Chem. , vol.269 , pp. 4959-4967
    • Arretz, M.1    Schneider, H.2    Guiard, B.3    Brunner, M.4    Neupert, W.5
  • 57
    • 0024518002 scopus 로고
    • Sequence and structural requirements of a mitochondrial protein import signal defined by saturation cassette mutagenesis
    • Bedwell, D.M., Strobel, S.A., Yun, K., Jongeward, G.D., Emr, S.D. Sequence and structural requirements of a mitochondrial protein import signal defined by saturation cassette mutagenesis. Mol. Cell. Biol. 9:1014-1025, 1989.
    • (1989) Mol. Cell. Biol. , vol.9 , pp. 1014-1025
    • Bedwell, D.M.1    Strobel, S.A.2    Yun, K.3    Jongeward, G.D.4    Emr, S.D.5
  • 58
    • 0031022743 scopus 로고    scopus 로고
    • Improvement of protein secondary structure prediction using binary word encoding
    • Kawabata, T., Doi, J. Improvement of protein secondary structure prediction using binary word encoding. Proteins 27:36-46, 1997.
    • (1997) Proteins , vol.27 , pp. 36-46
    • Kawabata, T.1    Doi, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.