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Volumn 211, Issue 1, 2008, Pages 89-104

Prediction of N-linked glycan branching patterns using artificial neural networks

Author keywords

Artificial intelligence; CHO cells; Complex type; Endoplasmic reticulum; Glycan branching patterns; Glycosylation; Golgi apparatus; High mannose; N Linked; Neural network

Indexed keywords

CELLS; GROWTH KINETICS; NITROGEN COMPOUNDS; PATTERN RECOGNITION; PROTEINS; TISSUE;

EID: 37349076888     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2007.10.005     Document Type: Article
Times cited : (10)

References (51)
  • 1
    • 0019377631 scopus 로고
    • Synthesis and processing of asparagine-linked oligosaccharides
    • Hubbard S.C., and Ivatt R.J. Synthesis and processing of asparagine-linked oligosaccharides. Annu. Rev. Biochem. 50 (1981) 555
    • (1981) Annu. Rev. Biochem. , vol.50 , pp. 555
    • Hubbard, S.C.1    Ivatt, R.J.2
  • 2
    • 0021891884 scopus 로고
    • Assembly of asparagine-linked oligosaccharides
    • Kornfeld R., and Kornfeld S. Assembly of asparagine-linked oligosaccharides. Annu. Rev. Biochem. 54 (1985) 631
    • (1985) Annu. Rev. Biochem. , vol.54 , pp. 631
    • Kornfeld, R.1    Kornfeld, S.2
  • 3
    • 0023617056 scopus 로고
    • Subcellular organization of glycosylation in mammalian cells
    • Roth J. Subcellular organization of glycosylation in mammalian cells. Biochim. Biophys. Acta 906 (1987) 405
    • (1987) Biochim. Biophys. Acta , vol.906 , pp. 405
    • Roth, J.1
  • 4
    • 2442719330 scopus 로고    scopus 로고
    • Oligosaccharides implicated in recognition are predicted to have relatively ordered structures
    • Almond A., Petersen B.O., and Duus J.O. Oligosaccharides implicated in recognition are predicted to have relatively ordered structures. Biochemistry 43 (2004) 5853
    • (2004) Biochemistry , vol.43 , pp. 5853
    • Almond, A.1    Petersen, B.O.2    Duus, J.O.3
  • 6
    • 0025981417 scopus 로고
    • Glycosylation of recombinant protein therapeutics: control and functional implications
    • Cumming D.A. Glycosylation of recombinant protein therapeutics: control and functional implications. Glycobiology 1 (1991) 115
    • (1991) Glycobiology , vol.1 , pp. 115
    • Cumming, D.A.1
  • 7
    • 0023338172 scopus 로고
    • Tissue-specific N-glycosylation, site-specific oligosaccharide patterns and lentil lectin recognition of rat Thy-1
    • Parekh R.B., Tse A.G., Dwek R.A., Williams A.F., and Rademacher T.W. Tissue-specific N-glycosylation, site-specific oligosaccharide patterns and lentil lectin recognition of rat Thy-1. EMBO J 6 (1987) 1233
    • (1987) EMBO J , vol.6 , pp. 1233
    • Parekh, R.B.1    Tse, A.G.2    Dwek, R.A.3    Williams, A.F.4    Rademacher, T.W.5
  • 8
    • 0026516422 scopus 로고
    • Glycosylation engineering
    • Stanley P. Glycosylation engineering. Glycobiology 2 (1992) 99
    • (1992) Glycobiology , vol.2 , pp. 99
    • Stanley, P.1
  • 10
    • 0028172714 scopus 로고
    • Mammalian alpha-mannosidases-multiple forms but a common purpose?
    • Daniel P.F., Winchester B., and Warren C.D. Mammalian alpha-mannosidases-multiple forms but a common purpose?. Glycobiology 4 (1994) 551
    • (1994) Glycobiology , vol.4 , pp. 551
    • Daniel, P.F.1    Winchester, B.2    Warren, C.D.3
  • 11
    • 0017087138 scopus 로고
    • Purification and characterization of the alpha-D-mannosidase of rat liver cytosol
    • Shoup V.A., and Touster O. Purification and characterization of the alpha-D-mannosidase of rat liver cytosol. J. Biol. Chem. 251 (1976) 3845
    • (1976) J. Biol. Chem. , vol.251 , pp. 3845
    • Shoup, V.A.1    Touster, O.2
  • 12
    • 0036019907 scopus 로고    scopus 로고
    • Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds
    • Spiro R.G. Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12 (2002) 43R
    • (2002) Glycobiology , vol.12
    • Spiro, R.G.1
  • 14
    • 0034610095 scopus 로고    scopus 로고
    • Multiple cell culture factors can affect the glycosylation of Asn-184 in CHO-produced tissue-type plasminogen activator
    • Andersen D.C., Bridges T., Gawlitzek M., and Hoy C. Multiple cell culture factors can affect the glycosylation of Asn-184 in CHO-produced tissue-type plasminogen activator. Biotechnol. Bioeng. 70 (2000) 25
    • (2000) Biotechnol. Bioeng. , vol.70 , pp. 25
    • Andersen, D.C.1    Bridges, T.2    Gawlitzek, M.3    Hoy, C.4
  • 15
    • 11944272604 scopus 로고
    • Environmental effects on protein glycosylation
    • Goochee C.F., and Monica T. Environmental effects on protein glycosylation. Biotechnology (N.Y.) 8 (1990) 421
    • (1990) Biotechnology (N.Y.) , vol.8 , pp. 421
    • Goochee, C.F.1    Monica, T.2
  • 16
    • 0348044474 scopus 로고    scopus 로고
    • Neural-network-based identification of tissue-type plasminogen activator protein production and glycosylation in CHO cell culture under shear environment
    • Senger R.S., and Karim M.N. Neural-network-based identification of tissue-type plasminogen activator protein production and glycosylation in CHO cell culture under shear environment. Biotechnol. Prog. 19 (2003) 1828
    • (2003) Biotechnol. Prog. , vol.19 , pp. 1828
    • Senger, R.S.1    Karim, M.N.2
  • 17
    • 0042510505 scopus 로고    scopus 로고
    • Effect of shear stress on intrinsic CHO culture state and glycosylation of recombinant tissue-type plasminogen activator protein
    • Senger R.S., and Karim M.N. Effect of shear stress on intrinsic CHO culture state and glycosylation of recombinant tissue-type plasminogen activator protein. Biotechnol. Prog. 19 (2003) 1199
    • (2003) Biotechnol. Prog. , vol.19 , pp. 1199
    • Senger, R.S.1    Karim, M.N.2
  • 18
    • 28844433564 scopus 로고    scopus 로고
    • Variable site-occupancy classification of N-linked glycosylation using artificial neural networks
    • Senger R.S., and Karim M.N. Variable site-occupancy classification of N-linked glycosylation using artificial neural networks. Biotechnol. Prog. 21 (2005) 1653
    • (2005) Biotechnol. Prog. , vol.21 , pp. 1653
    • Senger, R.S.1    Karim, M.N.2
  • 19
    • 0036186554 scopus 로고    scopus 로고
    • The importance of trimming reactions on asparagine-linked oligosaccharides for protein quality control
    • Roth J., Zuber C., Guhl B., Fan J.Y., and Ziak M. The importance of trimming reactions on asparagine-linked oligosaccharides for protein quality control. Histochem. Cell Biol. 117 (2002) 159
    • (2002) Histochem. Cell Biol. , vol.117 , pp. 159
    • Roth, J.1    Zuber, C.2    Guhl, B.3    Fan, J.Y.4    Ziak, M.5
  • 20
    • 11944269748 scopus 로고
    • Alterations in the domain structure of tissue-type plasminogen activator change the nature of asparagine glycosylation
    • Wilhelm J., Lee S.G., Kalyan N.K., Cheng S.M., Wiener F., Pierzchala W., and Hung P.P. Alterations in the domain structure of tissue-type plasminogen activator change the nature of asparagine glycosylation. Biotechnology (N.Y.) 8 (1990) 321
    • (1990) Biotechnology (N.Y.) , vol.8 , pp. 321
    • Wilhelm, J.1    Lee, S.G.2    Kalyan, N.K.3    Cheng, S.M.4    Wiener, F.5    Pierzchala, W.6    Hung, P.P.7
  • 21
    • 0020491430 scopus 로고
    • Heterogeneity of asparagine-linked oligosaccharides of five glycosylation sites on immunoglobulin M heavy chain from mineral oil plasmacytoma 104E
    • Anderson D.R., and Grimes W.J. Heterogeneity of asparagine-linked oligosaccharides of five glycosylation sites on immunoglobulin M heavy chain from mineral oil plasmacytoma 104E. J. Biol. Chem. 257 (1982) 14858
    • (1982) J. Biol. Chem. , vol.257 , pp. 14858
    • Anderson, D.R.1    Grimes, W.J.2
  • 22
    • 0026080930 scopus 로고
    • Oligosaccharide structures present on asparagine-289 of recombinant human plasminogen expressed in a Chinese hamster ovary cell line
    • Davidson D.J., and Castellino F.J. Oligosaccharide structures present on asparagine-289 of recombinant human plasminogen expressed in a Chinese hamster ovary cell line. Biochemistry 30 (1991) 625
    • (1991) Biochemistry , vol.30 , pp. 625
    • Davidson, D.J.1    Castellino, F.J.2
  • 23
    • 0025261190 scopus 로고
    • The polypeptide of immunoglobulin G influences its galactosylation in vivo
    • Lee S.O., Connolly J.M., Ramirez-Soto D., and Poretz R.D. The polypeptide of immunoglobulin G influences its galactosylation in vivo. J. Biol. Chem. 265 (1990) 5833
    • (1990) J. Biol. Chem. , vol.265 , pp. 5833
    • Lee, S.O.1    Connolly, J.M.2    Ramirez-Soto, D.3    Poretz, R.D.4
  • 24
    • 0021956734 scopus 로고
    • Oligosaccharide microheterogeneity of the murine major histocompatibility antigens. Reproducible site-specific patterns of sialylation and branching in asparagine-linked oligosaccharides
    • Swiedler S.J., Freed J.H., Tarentino A.L., Plummer Jr. T.H., and Hart G.W. Oligosaccharide microheterogeneity of the murine major histocompatibility antigens. Reproducible site-specific patterns of sialylation and branching in asparagine-linked oligosaccharides. J. Biol. Chem. 260 (1985) 4046
    • (1985) J. Biol. Chem. , vol.260 , pp. 4046
    • Swiedler, S.J.1    Freed, J.H.2    Tarentino, A.L.3    Plummer Jr., T.H.4    Hart, G.W.5
  • 25
    • 0023661070 scopus 로고
    • Virtual and solution conformations of oligosaccharides
    • Cumming D.A., and Carver J.P. Virtual and solution conformations of oligosaccharides. Biochemistry 26 (1987) 6664
    • (1987) Biochemistry , vol.26 , pp. 6664
    • Cumming, D.A.1    Carver, J.P.2
  • 26
    • 0024202766 scopus 로고
    • Regulation of glycosylation. The influence of protein structure on N-linked oligosaccharide processing
    • Hubbard S.C. Regulation of glycosylation. The influence of protein structure on N-linked oligosaccharide processing. J. Biol. Chem. 263 (1988) 19303
    • (1988) J. Biol. Chem. , vol.263 , pp. 19303
    • Hubbard, S.C.1
  • 27
    • 0020841015 scopus 로고
    • Unusual heterogeneity in the glycosylation of the G protein of the hazelhurst strain of vesicular stomatitis virus
    • Hunt L.A., Davidson S.K., and Golemboski D.B. Unusual heterogeneity in the glycosylation of the G protein of the hazelhurst strain of vesicular stomatitis virus. Arch. Biochem. Biophys. 226 (1983) 347
    • (1983) Arch. Biochem. Biophys. , vol.226 , pp. 347
    • Hunt, L.A.1    Davidson, S.K.2    Golemboski, D.B.3
  • 28
    • 33749493505 scopus 로고    scopus 로고
    • Phosphorylation and glycosylation interplay: protein modifications at hydroxy amino acids and prediction of signaling functions of the human beta(3) integrin family
    • Ahmad I., Hoessli D.C., Walker-Nasir E., Choudhary M.I., Rafik S.M., and Shakoori A.R. Phosphorylation and glycosylation interplay: protein modifications at hydroxy amino acids and prediction of signaling functions of the human beta(3) integrin family. J. Cell. Biochem. 99 (2006) 706
    • (2006) J. Cell. Biochem. , vol.99 , pp. 706
    • Ahmad, I.1    Hoessli, D.C.2    Walker-Nasir, E.3    Choudhary, M.I.4    Rafik, S.M.5    Shakoori, A.R.6
  • 29
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • Blom N., Sicheritz-Ponten T., Gupta R., Gammeltoft S., and Brunak S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4 (2004) 1633
    • (2004) Proteomics , vol.4 , pp. 1633
    • Blom, N.1    Sicheritz-Ponten, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, S.5
  • 30
    • 33749071408 scopus 로고    scopus 로고
    • Structural aspects of glycomes with a focus on N-glycosylation and glycoprotein folding
    • Petrescu A.J., Wormald M.R., and Dwek R.A. Structural aspects of glycomes with a focus on N-glycosylation and glycoprotein folding. Curr. Opin. Struct. Biol. 16 (2006) 600
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 600
    • Petrescu, A.J.1    Wormald, M.R.2    Dwek, R.A.3
  • 31
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • Blom N., Gammeltoft S., and Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294 (1999) 1351
    • (1999) J. Mol. Biol. , vol.294 , pp. 1351
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 32
    • 13644257223 scopus 로고    scopus 로고
    • Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
    • Julenius K., Molgaard A., Gupta R., and Brunak S. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15 (2005) 153
    • (2005) Glycobiology , vol.15 , pp. 153
    • Julenius, K.1    Molgaard, A.2    Gupta, R.3    Brunak, S.4
  • 33
    • 0025334980 scopus 로고
    • Improvements in protein secondary structure prediction by an enhanced neural network
    • Kneller D.G., Cohen F.E., and Langridge R. Improvements in protein secondary structure prediction by an enhanced neural network. J. Mol. Biol. 214 (1990) 171
    • (1990) J. Mol. Biol. , vol.214 , pp. 171
    • Kneller, D.G.1    Cohen, F.E.2    Langridge, R.3
  • 34
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost B., and Sander C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232 (1993) 584
    • (1993) J. Mol. Biol. , vol.232 , pp. 584
    • Rost, B.1    Sander, C.2
  • 35
    • 0033369033 scopus 로고    scopus 로고
    • Exploiting the past and the future in protein secondary structure prediction
    • Baldi P., Brunak S., Frasconi P., Soda G., and Pollastri G. Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15 (1999) 937
    • (1999) Bioinformatics , vol.15 , pp. 937
    • Baldi, P.1    Brunak, S.2    Frasconi, P.3    Soda, G.4    Pollastri, G.5
  • 36
    • 0035782925 scopus 로고    scopus 로고
    • Review: protein secondary structure prediction continues to rise
    • Rost B. Review: protein secondary structure prediction continues to rise. J. Struct. Biol. 134 (2001) 204
    • (2001) J. Struct. Biol. , vol.134 , pp. 204
    • Rost, B.1
  • 37
    • 0035698737 scopus 로고    scopus 로고
    • EVA: large-scale analysis of secondary structure prediction
    • Rost B., and Eyrich V.A. EVA: large-scale analysis of secondary structure prediction. Proteins Suppl. 5 (2001) 192
    • (2001) Proteins , vol.SUPPL. 5 , pp. 192
    • Rost, B.1    Eyrich, V.A.2
  • 38
    • 0041719954 scopus 로고    scopus 로고
    • Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
    • Pollastri G., and Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics 18 Suppl 1 (2002) S62
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Pollastri, G.1    Baldi, P.2
  • 39
    • 0035237804 scopus 로고    scopus 로고
    • Improved prediction of the number of residue contacts in proteins by recurrent neural networks
    • Pollastri G., Baldi P., Fariselli P., and Casadio R. Improved prediction of the number of residue contacts in proteins by recurrent neural networks. Bioinformatics 17 Suppl 1 (2001) S234
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 40
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • Pollastri G., Baldi P., Fariselli P., and Casadio R. Prediction of coordination number and relative solvent accessibility in proteins. Proteins 47 (2002) 142
    • (2002) Proteins , vol.47 , pp. 142
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 41
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • Pollastri G., Przybylski D., Rost B., and Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47 (2002) 228
    • (2002) Proteins , vol.47 , pp. 228
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 42
    • 0033566578 scopus 로고    scopus 로고
    • Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins
    • Fariselli P., Riccobelli P., and Casadio R. Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins. Proteins 36 (1999) 340
    • (1999) Proteins , vol.36 , pp. 340
    • Fariselli, P.1    Riccobelli, P.2    Casadio, R.3
  • 43
    • 0042674397 scopus 로고    scopus 로고
    • Using a neural network and spatial clustering to predict the location of active sites in enzymes
    • Gutteridge A., Bartlett G.J., and Thornton J.M. Using a neural network and spatial clustering to predict the location of active sites in enzymes. J. Mol. Biol. 330 (2003) 719
    • (2003) J. Mol. Biol. , vol.330 , pp. 719
    • Gutteridge, A.1    Bartlett, G.J.2    Thornton, J.M.3
  • 44
    • 0038356582 scopus 로고    scopus 로고
    • Predicted protein-protein interaction sites from local sequence information
    • Ofran Y., and Rost B. Predicted protein-protein interaction sites from local sequence information. FEBS Lett. 544 (2003) 236
    • (2003) FEBS Lett. , vol.544 , pp. 236
    • Ofran, Y.1    Rost, B.2
  • 45
    • 0036006486 scopus 로고    scopus 로고
    • Artificial neural network model for predicting protein subcellular location
    • Cai Y.D., Liu X.J., and Chou K.C. Artificial neural network model for predicting protein subcellular location. Comput. Chem. 26 (2002) 179
    • (2002) Comput. Chem. , vol.26 , pp. 179
    • Cai, Y.D.1    Liu, X.J.2    Chou, K.C.3
  • 46
    • 3142695658 scopus 로고    scopus 로고
    • Effects of glycosylation on peptide conformation: a synergistic experimental and computational study
    • Bosques C.J., Tschampel S.M., Woods R.J., and Imperiali B. Effects of glycosylation on peptide conformation: a synergistic experimental and computational study. J. Am. Chem. Soc. 126 (2004) 8421
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 8421
    • Bosques, C.J.1    Tschampel, S.M.2    Woods, R.J.3    Imperiali, B.4
  • 47
    • 0034663597 scopus 로고    scopus 로고
    • Application of multiple sequence alignment profiles to improve protein secondary structure prediction
    • Cuff J.A., and Barton G.J. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40 (2000) 502
    • (2000) Proteins , vol.40 , pp. 502
    • Cuff, J.A.1    Barton, G.J.2
  • 48
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292 (1999) 195
    • (1999) J. Mol. Biol. , vol.292 , pp. 195
    • Jones, D.T.1
  • 49
    • 0033106244 scopus 로고    scopus 로고
    • Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
    • Cuff J.A., and Barton G.J. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34 (1999) 508
    • (1999) Proteins , vol.34 , pp. 508
    • Cuff, J.A.1    Barton, G.J.2
  • 51
    • 0023526019 scopus 로고
    • Recombinant tissue plasminogen activator: a brief review
    • Grossbard E.B. Recombinant tissue plasminogen activator: a brief review. Pharm. Res. 4 (1987) 375
    • (1987) Pharm. Res. , vol.4 , pp. 375
    • Grossbard, E.B.1


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