protein fragment
IRI: https://spec.industrialontologies.org/ontology/construct/ProteinFragment
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 fragment
Definition
peptide or protein that was a proper part of a protein molecule and resulted from cleavage of one or more peptide bonds within that protein
Explanatory Notes
1) The phrase ‘was a proper part of a protein’ indicates that the fragment existed as part of a larger protein molecule before cleavage. After the bond-breaking event, it may persist as an independent molecular entity. 2) Protein fragments may be generated by spontaneous, chemically induced, environmentally induced, mechanically associated, or enzyme-mediated peptide-bond cleavage. Examples include hydrolysis under stress conditions, fragmentation during storage or processing, and proteolytic cleavage.
Examples
- Fab fragment generated by cleavage of an antibody; Fc fragment generated by cleavage of an antibody; Peptide fragment generated during proteolytic digestion for peptide mapping; Clipped monoclonal antibody fragment detected during product characterization; Protein fragment formed during storage-related degradation; Host cell protein fragment detected as a process-related impurity
Adapted From
- https://www.bioprocessintl.com/formulation/stability-considerations-for-biopharmaceuticals-overview-of-protein-and-peptide-degradation-pathways and https://pmc.ncbi.nlm.nih.gov/articles/PMC5392216/ and https://www.ema.europa.eu/en/documents/scientific-guideline/guideline-development-production-characterisation-and-specification-monoclonal-antibodies-and-related-products-revision-1_en.pdf
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
ProteinFragment(x) → Peptide(x) ∨ Protein(x)
Semi-Formal Natural Language Axioms
if x is a ‘protein fragment’ then x is a ‘peptide’ or ‘protein’
Description Logic
SubClassOf: constr:OrganicMolecularEntity
SubClassOf: constr:Peptide or constr:Protein