By Claus-Wilhelm von der Lieth, Thomas Luetteke, Martin Frank
This e-book is the 1st to be devoted to the bioinformatics of carbohydrates and glycoproteins. It offers an advent to this rising box of technology either for the experimentalist operating in glycobiology and glycomics, and in addition for the pc scientist searching for history info for the advance of hugely subtle algorithmic approaches. The ebook offers an outline of the cutting-edge within the box, with reports on databases, and the instruments in use for research, interpretation, and prediction of the buildings of complicated carbohydrates, and demonstrates the price of bioinformatics for glycobiology.
the provision of finished databases and corresponding bioinformatics instruments, to entry and examine the big quantities of experimental facts with regards to the constitution of carbohydrates, might be a prerequisite for the luck of the large-scale glycomics tasks that objective to decipher new, up to now unknown, organic services of glycans. Efficient bioinformatics descriptions and instruments can significantly increase the potency of glycomics learn, by way of facts caliber, research and experimental charges.
for a whole realizing of the molecular procedures during which carbohydrates are concerned, comparable to protein–carbohydrate interactions and the influence of glycosylation on protein functionality, wisdom of the 3D constitution of the carbohydrate, the protein–carbohydrate advanced, or the glycoprotein is frequently quintessential. This ebook presents a radical advent into tools used for conformational research of carbohydrates.
Key positive aspects:
- Describes bioinformatic techniques to deal with carbohydrate-active enzymes and glycosylation.
- Provides an outline on bioinformatics instruments that facilitate research of carbohydrate constructions.
- Gives advent into molecular modelling of carbohydrate 3D constitution and carbohydrates inside the Protein Databank.
- Assumes just a uncomplicated wisdom of biology and bioinformatics.
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Extra info for Bioinformatics for Glycobiology and Glycomics: An Introduction
3). 3). In the composite stem name, the portion relating to the group of carbon atoms furthest from C1 (which may contain less than four atoms) is given first. 3 Frequent Substituents. g. 4). 2 (a) The pyranose ring forms of d-galactose. The two anomeric configurations (hemiacetals) and the open form are depicted. Isolated monosaccharides typically show an equilibrium mixture of different cyclic forms in aqueous solution (furanose rings may also be formed through 1,4-cyclization). (b) A monosaccharide bound to a non-monosaccharide molecule (aglycone).
D) Ketoses, monosaccharides with non-terminal carbonyl functions, are systematically named with the suffix -ulo. The chiral C-atoms (gray boxes) define the stereochemical identifier, here the stem type arabinose. The resulting ketose is fructose, a component of the commonly known table sugar. 3 Stem types for monosaccharides with up to four stereogenic centers. The d- or l- series is not indicated in this table. IUPAC 3-letter code Gro Ery Tre Ara Rib Lyx Xyl All Alt Gal Glc Gul Ido Man Tal IUPAC name Class Class name (abbreviated) Number of C-atoms Glyceraldehyde Erythrose Threose Arabinose Ribose Lyxose Xylose Allose Altrose Galactose Glucose Gulose Idose Mannose Talose Triose Tetrose Tetrose Pentose Pentose Pentose Pentose Hexose Hexose Hexose Hexose Hexose Hexose Hexose Hexose TRI TET TET PEN PEN PEN PEN HEX HEX HEX HEX HEX HEX HEX HEX 3 4 4 5 5 5 5 6 6 6 6 6 6 6 6 most commonly found substitutions is the acetylamino group NHC(O)CH3 , abbreviated NAc, typically at C2 in hexoses.
8. Petrescu A-J, Milac A-L, Petrescu SM, Dwek RA, Wormald MR: Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure and folding. Glycobiology 2004, 14:103–114. 9. Rudd PM, Wormald MR, Stanfield RL, Huang M, Mattsson N, Speir JA, DiGennaro JA, Fetrow JS, Dwek RA, Wilson IA: Roles for glycosylation of cell surface receptors involved in cellular immune recognition. J Mol Biol 1999, 293:351–366. 10. Helenius A, Aebi M: Roles of N-linked glycans in the endoplasmic reticulum.