List of effect terms

acetylation one acetyl group at least is attached to a molecule; posttranslational modification of proteins, generally at the N-terminus amidation addition of an amide group from a glycine to a protein amino acid [1] activation increase of protein activity; it means that the reactions going out from the target molecule would follow after this reaction assembly congregation of molecules in a certain subcellular location (e.g. membranous lipid rafts); term does not emphasize direct interaction binding any kind of chemical/physical bond (covalent bond, hydrogen bond, ion complex, Van-der-Waals) that is established between reaction partners - if not defined more stringently as condensation, acetylation etc. carboxylation addition of a carboxy group to a protein amino acid [1] cleavage peptide bond between amino acids is cleaved by an endoprotease competition two or more molecules competing for a reaction partner/ signal condensation chemical reaction forming a new chemical bond while setting free molecular water conjugation coupling of a molecule with at least one ubiquitin-like molecule (e.g. Nedd8/Rub1) deacetylation removement of an acetyl group deamidation removement of an amide group decarboxylation removement of a carboxy group decrease of abundance decrease of cleavage decrease of folding decrease of phosphorylation indirect effect, can occur via dephosphorylation or via inhibition of phosphorylation decrease of processing decrease of secretion decrease of transport decrease of ubiquitination deconjugation deglycosylation removement of a glycosyl group degradation breakdown of a molecule (leaving behind protein remnants; mediated by enzymes, proteasome) dehydroxylation removement of a hydroxy group demethylation removement of a methyl group demyristoylation removement of a myristoyl moiety denitration denitrosylation removement of a nitrosyl group depalmitoylation removement of a palmitoyl moiety dephosphorylation catalyzed separation of a phosphate group from a molecule (mediated by a phosphatase) desulfation removement of a sulfate group destabilization additional association of a protein decreases the stability/affinity of an existing complex dissociation breakup of a complex DNA binding binding of proteins (transcription factors) to DNA exchange catalyzed replacement of a group by another (e.g. exchange of G-protein associated GDP with GTP by a GEF) expression transfer of information encoded in the DNA (nucleotide sequence) into the protein (amino acid sequence); reactions with effect expression include several steps: transcription, splicing, capping, and translation. glycosylation transfer of one or more glycosyl groups to a molecule, resulting in a glycoprotein; posttranslational modification N-glycosylation O-glycosylation hydrolysis catalyzed splitting of a chemical bond with the consumption of water hydroxylation addition of a hydroxy group to a protein amino acid [1] increase of abundance increase of folding increase of secretion increase of transport inhibition decrease of protein activity means that the reactions going out from the target molecule would stop after this reaction or would follow if this reaction would not signal; interaction binary relation which states nothing about directionality between two molecules with yet undefined mechanism; both molecules are entered in the 'molecules upstream' list isomerization directed conformational change between cis- and trans-conformation of a peptide chain methylation posttranslational modification, covalent transfer of a methyl group to a substrate myristoylation covalent or non-covalent attachment of a myristoyl moiety to a protein amino acid [1] nitration nitrosylation covalent transfer of NO to a substrate; S-nitrosylation (transfer of NO to Cys-residues) of a protein controls its activity similar to O-phosphorylation oligomerization assembly of a complex; resumes the terms homo- and heteromerization and di-/trimerization as well palmitoylation covalent or non-covalent attachment of a palmitoyl moiety to a protein amino acid [1] phosphorylation catalyzed binding of a phosphate group to a molecule (for example mediated by protein kinases) prenylation class of lipid modification involving covalent addition of either farnesyl (15-carbon) or geranylgeranyl (20-carbon) isoprenoids to conserved cysteine residues at or near the C-terminus of proteins [2] processing is used as a term for the catalyzed maturation of proteins (usually associated with proteolytic cutting of the signal peptide or more) redox reaction a reaction in which one or more electrons are transferred regulation of abundance abundance of a protein is regulated in an undefined way regulation of acetylation acetylation status of a protein is regulated in an undefined way regulation of activity activity of a protein is regulated in an undefined way regulation of amidation amidation status of a protein is regulated in an undefined way regulation of carboxylation carboxylation status of a protein is regulated in an undefined way regulation of cleavage cleavage of a protein is regulated in an undefined way regulation of degradation degradation of a protein is regulated in an undefined way regulation of folding folding of a protein is regulated in an undefined way regulation of glycosylation glycosylation status of a protein is regulated in an undefined way regulation of localization localization of a protein is regulated in an undefined way regulation of methylation methylation status of a protein is regulated in an undefined way regulation of N-glycosylation N-glycosylation status of a protein is regulated in an undefined way regulation of nitration nitration status of a protein is regulated in an undefined way regulation of oxidation oxidation status of a protein is regulated in an undefined way regulation of phosphorylation phosphorylation status of a protein is regulated in an undefined way regulation of secretion secretion of a protein is regulated in an undefined way regulation of stability stability of a protein is regulated in an undefined way regulation of sulfation sulfation status of a protein is regulated in an undefined way regulation of transport transport of a protein is regulated in an undefined way regulation of ubiquitination ubiquitination status of a protein is regulated in an undefined way stabilization additional association of a protein enhances the stability of an already existing complex sulfation addition of a sulfate group as an ester to a protein amino acid [1] transactivation general term for gene activation, involves transcription translocation indicates the regulated transfer of a signaling molecule to another subcellular location (often from cytosol to nucleus) transregulation direct transcriptional regulation by binding of a transcription factor to its cognate site within the gene regulatory region; the term transregulation does not differentiate between activation or inhibition. transrepression repression of a gene by a transcription factor ubiquitination coupling of a molecule with ubiquitin unknown indicates that it is not known, if the signal acceptor in the semantic reaction is activated or inhibited

[1] Definition taken from GO; Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29.

[2] Zhang F. L., Casey P. J.; Protein prenylation: molecular mechanisms and functional consequences. (1996), Annu. Rev. Biochem. 65, 241-269.