- acetylation
- one acetyl group at least is attached to a molecule; posttranslational modification of proteins, generally at the N-terminus
- activation
- used only in semantic reactions; 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.
- 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)
- decarboxylation
- degradation
- breakdown of a molecule (leaving behind protein remnants; mediated by enzymes, proteasome)
- dephosphorylation
- catalyzed separation of a phosphate group from a molecule (mediated by a phosphatase)
- destabilization
- additional association of a protein decreases the stability/affinity of an existing complex
- dissociation
- 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
- hydrolysis
- catalyzed splitting of a chemical bond with the consumption of water
- hydroxylation
- indirect
- is used when there are (most likely) other signaling molecules between the
reaction’s signal donor and acceptor; used in semantic reactions
- inhibition
- means that the reactions going out from the target molecule would
- stop after this reaction or would
- follow if this reaction would not signal;
- is used in semantic reactions
- isomerization
- directed conformational change between cis- and trans-conformation of a peptide chain
- interaction
- binary relation which states nothing about directionality between two molecules with yet undefined mechanism; both molecules are entered in the 'molecules upstream' list
- oligomerization
- assembly of a complex; resumes the terms homo- and heteromerization and di-/trimerization as well
- 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 [1]
- 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
- stabilization
- additional association of a protein enhances the stability of an already existing complex
- transactivation
- general term for gene activation, involves transcription
- reactions in which the term is used are semantic (activation) and direct
- 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.
- 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
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