protein aggregate
IRI: https://spec.industrialontologies.org/ontology/construct/ProteinAggregate
Defined In: https://spec.industrialontologies.org/ontology/biopharma/MolecularEntity/
SubClass Of: organic molecular entity
Class Hierarchy
owl:Thing › bfo:entity › bfo:continuant › bfo:independent continuant › bfo:material entity › molecular entity › organic molecular entity › protein aggregate
Definition
organic molecular entity that consists of two or more protein molecules or protein fragments associated through non-covalent interactions, covalent bonds other than peptide bonds, or both
Explanatory Notes
1) Aggregates can form through diverse mechanisms including non-covalent self-association, misfolding, interfacial, environmental, or mechanical stresses, or via covalent links that are not peptide bonds. 2) The class includes assemblies formed from any mixture of folded, partially folded, misfolded, or unfolded proteins. 3) Aggregates may appear intracellularly or extracellularly. 4) The term is neutral with respect to function, or lack thereof, and solubility, which are modeled separately when relevant. 5) The term includes molecular-scale and supramolecular protein assemblies, including heterogeneous, non-stoichiometric, or reversibly associated high-molecular-weight species. Proteinaceous particles, inclusion bodies, bulk precipitates, and other larger material aggregates are not instances of this class.
Examples
- Soluble antibody HMW clusters observed by SEC; freeze-stress induced protein dimers tethered by disulfides;
Counter-Examples
- mAb monomer; ribosome; nucleosome
Adapted From
- https://pmc.ncbi.nlm.nih.gov/articles/PMC5392216/ and http://id.nlm.nih.gov/mesh/D066329 and http://biomodels.net/SBO/SBO_0000543 and https://www.fda.gov/media/85017/download
Primitive Class
This class is declared primitive and it does not have necessary and sufficient condiftions defined.
Primitive Rationale
There are insufficient constructs to define a set of necessary and sufficient conditions.
Formal Axioms
First-Order Logic Axioms
ProteinAggregate(x) → OrganicMolecularEntity(x) ∧ ∃y∃z((Protein(y) ∨ ProteinFragment(y)) ∧ (Protein(z) ∨ ProteinFragment(z)) ∧ y ≠ z ∧ hasProperContinuantPartAtAllTimes(x,y) ∧ hasProperContinuantPartAtAllTimes(x,z))
Semi-Formal Natural Language Axioms
if x is a ‘protein aggregate’ then x is an ‘organic molecular entity’ that ‘has proper continuant part at all times’ at least two distinct entities, each of which is a ‘protein’ or a ‘protein fragment’
Description Logic
constr:ProteinAggregate ⊑ constr:OrganicMolecularEntity
constr:ProteinAggregate ⊑ ∃ bfo:has_proper_continuant_part_at_all_times .(constr:Protein ⊔ constr:ProteinFragment)
SubClassOf: constr:OrganicMolecularEntity
SubClassOf: bfo:has_proper_continuant_part_at_all_times some (constr:Protein or constr:ProteinFragment)