Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes

Helenius, 2004, Roles of N-linked glycans in the endoplasmic reticulum, Annu Rev Biochem, 73, 1019, 10.1146/annurev.biochem.73.011303.073752 Varki, 1993, Biological roles of oligosaccharides: all of the theories are correct, Glycobiology, 3, 97, 10.1093/glycob/3.2.97 Woods, 1994, Protein surface oligosaccharides and protein function, Nat Struct Biol, 1, 499, 10.1038/nsb0894-499 Mazumder, 2012, Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes, PLoS One, 7, e36212, 10.1371/journal.pone.0036212 Ohtsubo, 2006, Glycosylation in cellular mechanisms of health and disease, Cell, 126, 855, 10.1016/j.cell.2006.08.019 Li, 2009, Pharmacological significance of glycosylation in therapeutic proteins, Curr Opin Biotechnol, 20, 678, 10.1016/j.copbio.2009.10.009 Kawasaki, 2009, The significance of glycosylation analysis in development of biopharmaceuticals, Biol Pharm Bull, 32, 796, 10.1248/bpb.32.796 Hecht, 2009, Recent advances in carbohydrate-based vaccines, Curr Opin Chem Biol, 13, 354, 10.1016/j.cbpa.2009.05.127 Hart, 1992, Glycosylation, Curr Opin Cell Biol, 4, 1017, 10.1016/0955-0674(92)90134-X Zielinska, 2010, Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints, Cell, 141, 897, 10.1016/j.cell.2010.04.012 Zielinska, 2012, Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery, Mol Cell, 46, 542, 10.1016/j.molcel.2012.04.031 Bause, 1981, The role of the hydroxy amino acid in the triplet sequence Asn-Xaa-Thr(Ser) for the N-glycosylation step during glycoprotein biosynthesis, Biochem J, 195, 639, 10.1042/bj1950639 Wyss, 1995, Conformation and function of the N-linked glycan in the adhesion domain of human CD2, Science, 269, 1273, 10.1126/science.7544493 Bause, 1983, Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes, Biochem J, 209, 331, 10.1042/bj2090331 Junker, 1999, Representation of functional information in the SWISS-PROT data bank, Bioinformatics, 15, 1066, 10.1093/bioinformatics/15.12.1066 Beeley, 1977, Peptide chain conformation and the glycosylation of glycoproteins, Biochem Biophys Res Commun, 76, 1051, 10.1016/0006-291X(77)90962-7 Bause, 1982, Conformational aspects of N-glycosylation of proteins. Studies with linear and cyclic peptides as probes, Biochem J, 203, 761, 10.1042/bj2030761 Park, 2011, Genome-wide evolutionary conservation of N-glycosylation sites, Mol Biol Evol, 28, 2351, 10.1093/molbev/msr055 Kung, 2009, Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes, Mol Syst Biol, 5, 308, 10.1038/msb.2009.64 Sayers, 2010, Database resources of the national center for biotechnology information, Nucleic Acids Res, 38, D5, 10.1093/nar/gkp967 Mi, 2010, PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium, Nucleic Acids Res, 38, D204, 10.1093/nar/gkp1019 Joosten, 2011, A series of PDB related databases for everyday needs, Nucleic Acids Res, 39, D411, 10.1093/nar/gkq1105 Caragea, 2007, Glycosylation site prediction using ensembles of Support Vector Machine classifiers, BMC Bioinformatics, 8, 438, 10.1186/1471-2105-8-438 Hamby, 2008, Prediction of glycosylation sites using random forests, BMC Bioinformatics, 9, 500, 10.1186/1471-2105-9-500 UniProt-Consortium, 2012, Reorganizing the protein space at the universal protein resource (UniProt), Nucleic Acids Res, 40, D71, 10.1093/nar/gkr981 Rose, 2011, The RCSB protein data bank: redesigned web site and web services, Nucleic Acids Res, 39, D392, 10.1093/nar/gkq1021 Adamczak, 2004, Accurate prediction of solvent accessibility using neural networks-based regression, Proteins, 56, 753, 10.1002/prot.20176 Edgar, 2004, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, 5, 113, 10.1186/1471-2105-5-113 Small, 2004, Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences, Proteomics, 4, 1581, 10.1002/pmic.200300776 Petersen, 2009, A generic method for assignment of reliability scores applied to solvent accessibility predictions, BMC Struct Biol, 9, 51, 10.1186/1472-6807-9-51 Mi, 2009, PANTHER pathway: an ontology-based pathway database coupled with data analysis tools, Methods Mol Biol, 563, 123, 10.1007/978-1-60761-175-2_7 Cho, 2000, Transcription, genomes, function, Trends Genet, 16, 409, 10.1016/S0168-9525(00)02065-5 Sherry, 2001, DbSNP: the NCBI database of genetic variation, Nucleic Acids Res, 29, 308, 10.1093/nar/29.1.308 Huang, 2011, A comprehensive protein-centric ID mapping service for molecular data integration, Bioinformatics, 27, 1190, 10.1093/bioinformatics/btr101 Breiman, 1984