title: Glycocodon theory--the first table of glycocodons.
abstract: Hydrophobic cellular membranes separate cells from an environment that is generally based on water. Therefore, it is not surprising that hydrophilic glycans and glycoproteins are exposed on the lipidic surface of membranes and that the glycocalyx has evolved in all basic cell types. During the evolution of multicellular life, the surface exposed protein-glycan interactions were taken as the origin of the language of cell-cell communication. The bioinformatics analysis presented here reveals that the amino acid triplets, the glycocodons, can be deduced for each glycan letter (monosaccharide). This theory proposes to distinguish between the "sugar code" (the sugar sequence) and the "glycocode" (evolutionary selected amino acids recognising the mono-sugar). Similarly to genetic code, original glycocodons are related to G, A, V, and D amino acids. Modern glycocodons can be deduced from GAVD-glycocodons using hydropathic similarity. In general, the amino acid triplets can be assembled from one dipeptide that is specific to a monosaccharide plus a polar amino acid. This theory may shed a different light on the reason for WWD conservation in the active sites of oligosaccharyltransferases and for GGQ in the active sites of ribosomes.
authors.affiliation: Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538 Bratislava, Slovak Republic. nahalka@savba.sk
authors.forename: Jozef
authors.initials: J
authors.lastname: Nahalka
mesh_terms: D000595:Amino Acid Sequence; D002167:Campylobacter / Q000201:enzymology; D003460:Crystallization; D037502:Galectin 3 / Q000737:chemistry; D005815:Genetic Code; D019276:Glycocalyx / Q000737:chemistry / Q000235:genetics; D006023:Glycoproteins / Q000737:chemistry / Q000378:metabolism; D006602:Hexosyltransferases / Q000737:chemistry; D006801:Humans; D037102:Lectins / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011134:Polysaccharides / Q000737:chemistry / Q000235:genetics*; D044224:Pseudomonas syringae / Q000378:metabolism; D016415:Sequence Alignment; D000097604:Ficolins
chemical_list: D037502:Galectin 3; D006023:Glycoproteins; D006602:Hexosyltransferases; D037102:Lectins; D008565:Membrane Proteins; D010455:Peptides; D011134:Polysaccharides; D000097604:Ficolins; C025620:dolichyl-diphosphooligosaccharide - protein glycotransferase