Bioinformatics for glycomics: Status, methods, requirements and perspectives

Abstract

The term 'glycomics' describes the scientific attempt to identify and study all the glycan molecules - the glycome - synthesised by an organism. The aim is to create a cell-by-cell catalogue of glycosyltransferase expression and detected glycan structures. The current status of databases and bioinformatics tools, which are still in their infancy, is reviewed. The structures of glycans as secondary gene products cannot be easily predicted from the DNA sequence. Glycan sequences cannot be described by a simple linear one-letter code as each pair of monosaccharides can be linked in several ways and branched structures can be formed. Few of the bioinformatics algorithms developed for genomics/proteomics can be directly adapted for glycomics. The development of algorithms, which allow a rapid, automatic interpretation of mass spectra to identify glycan structures is currently the most active field of research. The lack of generally accepted ways to normalise glycan structures and exchange glycan formats hampers an efficient cross-linking and the automatic exchange of distributed data. The upcoming glycomics should accept that unrestricted dissemination of scientific data accelerates scientific findings and initiates a number of new initiatives to explore the data.

Activation of Murine CD4+ and CD8+ T Lymphocytes Leads to Dramatic Remodeling ofN-Linked Glycans

“…Perhaps even more important, literally hundreds of minor glycans can be detected by MS analysis, but the subsequent annotation and verification of structure is prohibitive. However, progress for developing automatic methods of annotation with sophisticated algorithms is being made (65)(66)(67), and technology advances in sample preparation and analysis will rapidly evolve.…”

Web Resources for the Glycoscientist

“…Data from the PDB, for example, were used to create the GDB:Structures database (11) and the DOUGAL database on glycoprotein structures (12). O-glycosidically modified proteins are collected in O-Glyc-Base (13), whereas antigens from E. coli O-glycans can be found in ECODAB (14). Sugabase (15) provides NMR data that are available for CarbBank structures.…”

“…Statistical analysis of glycosylation sites in the PDB and SwissProt http://www.glycosciences.de/tools/glyseq/ [61] 46 GlyVicinity Statistical analysis of protein-carbohydrate interactions data from the PDB http://www.glycosciences.de/tools/ glyvicinity/ [61] 3D structure/conformation tools 47 Sweet-II Generation of carbohydrate 3D structure models http://www.glycosciences.de/modeling/ sweet2/ [62] 48 Glycam Biomolecule Builder Generation of carbohydrate 3D structure models http://www.glycam.com/CCRC/biombuilder/ biomb_index.jsp [63] 49 pdb2linucs Detection of carbohydrate moieties in PDB structures http://www.glycosciences.de/tools/ pdb2 linucs/ [23] 50 pdb-care Validation of carbohydrate 3D structures http://www.glycosciences.de/tools/pdb-care/ [64] 51 CARP Carbohydrate Ramachandran Plot http://www.glycosciences.de/tools/carp/ [61] 52 GlyTorsion Statistical analysis of torsion angles derived from the PDB http://www.glycosciences.de/tools/ glytorsion/ [61] 53 GlyProt In silico glycosylation of proteins http://www.glycosciences.de/modeling/ glyprot/ [65] 54 Dynamic Molecules Online molecular dynamics (MD) simulations http://www.md-simulations.de [66] Notation and graphical representation of carbohydrates 55 IUPAC Official IUPAC recommendations for carbohydrate notation http://www.chem.qmul.ac.uk/iupac/2carb/ [67] 56 LINUCS Linear notation for carbohydrate structures http://www.glycosciences.de/tools/linucs/ [68] 57 LiGraph Graphical representation of carbohydrate structures http://www.glycosciences.de/tools/LiGraph/ [14] 58 KEGG CSM Composite Structure Map, graphical query tool for KEGG databases http://www.genome.jp/kegg-bin/draw_csm [69] 59 Glycan Builder Graphical input of carbohydrate structures http://www.eurocarbdb.org/applications/ structure-tools/ [70] www.chembiochem.org ously query the BCSDB and the GLYCO-SCIENCES.de databases [18] and to crosslink structures of the CFG and the GLY-COSCIENCES.de databases. Therefore, users who are exploring an entry in one of these two databases, for which there is also information in the other database, can easily access all of the data in both resources.…”

“…For these reasons, glycobioinformatics is still in its infancy and lagging behind bioinformatics applications for genomics or proteomics. [14] Nevertheless, there is a variety of tools and databases currently available to glycoscientists.…”

Is it possible to consider «kinetomics» and «argyromics» as novel trends of functional morphology and systems biology of parasitic and nonparasitic protozoa? a brief analytical review

“…equivalent to chemical genetics (Carlson, 2012;Jung, 2014); interferomics -a science about interfering RNAs (Reddy, 2013); lipidomics -a science about lipids and cellular fats (Lagarde, 2003;Kagan, 2004;Wenk, 2005); eicosanomics -a science about eicosanoids (Balazy, 2004); glycomics -a science about sugars (Kheronsky, 2003;Lubner, 2003;von der Lieth, 2004;Mrksich, 2004); ionomics -a science about ions in living cells (Salt, 2008;Baxter, 2009;Baxter, 2010;Danku, 2013); metalloproteomics -a science about metalloproteins (Shi, 2008;Barnett, 2012;Fu, 2014;Roberts, 2014) and similar metallomics as a science about the metal functions in living cells (Szpunar, 2004; Lopez-Barea, 2006; Szpunar, 2006;Mounicou, 2009); proteomics -a science about proteins (Geisow, 1998;Persidis, 1998;Müllner, 1998); kinomics -a science about enzymeskinases (Johnson, 2005;Gomase, 2008;Vieth, 2005); phytochemomics -a science about phytochemical bioactive agents (Amigo-Benavent, 2014). Many principles of similar sciences can be automatically extended to the case of protistology -as complex principles for comparative colocalization morphology of the Protozoa species.…”