Chaperone tree- Edition 5a
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Function ontology Proposal
%chaperone activity(new term)
%nucleotide hydrolysis dependent chaperone activity
%chaperone _cofactor activity dependent chaperone
activity (new)
%chaperone_cofactor activity independent chaperone
activity (new)
%nucleotide hydrolysis independent chaperone activity (new)
%holding chaperone activity (new)
%protein disulfide isomerase (term exists)
%peptidylprolyl isomerase (term exists)
%binding
%protein binding
% co-chaperone activity (synonyms: chaperone cofactor
activity, chaperone activator activity, chaperone regulator
activity) (new)
Definitions:
Chaperone activity: (NEW)
Refers to the activity of assisting in covalent and non-covalent rearrangements in
order to fold a macromolecule (such as a polypeptide or nucleic acid) to its
correct 3-dimensional structure or properly assemble multi-polypeptide
complexes, including those that contain nucleic acids and carbohydrates. This
activity is independent of and not part of the activity and function of the final
assembled structure or complex.
Nucleotide hydrolysis dependent chaperone activity (new)
Refers to the activity of a class of chaperone molecules that assists in the correct
non-covalent folding of macromolecules over cycles of nucleotide hydrolysis
dependent binding and release.
Comment: Consider additional terms ATPase activity and GTPase activity terms.
chaperone_cofactor activity depedent chaperone activity (new)
Refers to the activity of a class of chaperone molecules that assist in the correct
non-covalent assembly of post-translational proteins and are dependent on
additional protein cofactors. This function happens over one or several cycles of
nucleotide hydrolysis dependent binding and release.
chaperone_cofactor activity independent chaperone activity (new)
Refers to the activity of a class of chaperone molecules that assist in the correct
non-covalent assembly of post-translational proteins and do not dependent on
additional protein cofactors. This function happens over one or several cycles of
nucleotide-dependent binding and release.
Nucleotide hydrolysis independent chaperone activity (new)
Refers to the activity of a class of chaperone molecules that assists in the correct
folding of macromolecules in the absence of nucleotide hydrolysis.
Holding chaperone activity (new)
Refers to the activity of a class of chaperone molecules that hold or sequester
macromolecules to prevent their aggregation or misfolding and is independent of
nucleotide hydrolysis. Such substrate macromolecules attain their native
conformation with the assistance of other chaperone molecules.
Co_chaperone activity
Refers to the activity of proteins that activate the chaperone molecule (ring
shaped multisubunit complexes) to sequester the misfolded substrates and
release the folded products.
The following terms have to be obsoleted.
1) Hsp 70-90 organizing protein (synonym of holding chaperone activity)mentions specific gene product in the term and this protein (HOP) transfers
substrates from Hsp70 to hsp 90.
2) co-chaperone activity (synonym of chaperone cofactor activity)
co-chaperonin activity (obsolete)
co-chaperones are proteins that bind to chaperones and the complex folds the
misfolded proteins. Co-chaperones by themselves do not have chaperone
activity. So gene products like GroES, also called co-chaperonin, should be
annotated to chaperone cofactor activity. Some of them are nucleotide exchange
factors also. Co-chaperones and co-chaperonins are used interchangeably.
3) chaperonin ATPase activity (synonym) –consider ATPase activity and the
nucleotide hydrolysis dependent chaperone activity terms.
4) glyco-protein specific chaperone activity (obsolete)- consider GO-process term
N-linked glycoprotein maturation and nucleotide hydrolysis independent
chaperone activity
5) tubulin-specific chaperone activity (obsolete) –consider protein complex
assembly/tubulin folding and one of the chaperone activity terms
6) fimbrium specific chaperone activity (obsolete)
refers to proteins that assist in the linear organization of the protein pilus which
forms the tubular structure or the organelle, fimbria (aka pilus) which helps
bacteria attach to surface. These proteins are not involved in correcting the
folding of pilus, they just help them come together.
Consider : protein binding, bridging (GO-function) and fimbrium biogenesis
process term.
7) chaperone inhibitor activity (obsolete)- Consider ATPase inhibitor activity,
regulation of protein folding (proposing new term in process ontology) and its
children terms
8) ribosomal chaperone activity- consider ribosome biogenesis and nucleotide
dependent chaperone activity
9) heat shock protein activity: synonym of nucleotide dependent chaperone
activity
10) histone chaperone activity (obsolete): Consider histone binding, chromatin
assembly/disassembly, nucleosome assembly
In the following terms chaperone has been used to mean ‘carrier/transport’
These terms have to be children/synonym of some transport term.
1) Copper chaperone activity synonym of copper ion tansporter activity, remove
from chaperone activity node
2) Metallo chaperone activity synonym of metal ion transporter activity, remove
from chaperone activity node
3) Superoxide dismutase copper chaperone activity (gene product ?obsolete?)child of copper ion transporter activity, remove from chaperone activity node.