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protein catabolic process

vr.tr.protein-catabolic-process · thing-q14876077

Let an agent explain protein breakdown pathways, find Gene Ontology annotations, and relate protein degradation to physiology and disease with sources.

Thing Registry Activities and processes ACT.PRC
Bundle → Layer → Finding → QuestionsClassifiersWhat it isWhy it existsDistinguishing featuresWhat robots and AI may and may not doMoral aspectsOwnersLinks to other meta-modelsIdentity and identifiersDirect propertiesRecognitionCapabilities and actionsHazards and failure modesStandards and interfacesContext of useSources

Bundle → Layer → Finding → Questions Filled

4 bundles · 8 layers · 8 findings · 16 questions

Pathway Which route.

Route

Proteasome or lysosome.

Route

Pathway and machinery.

  1. Which pathway degrades the protein? provenance
  2. What evidence shows it? provenance

Signal

Degrons and tags.

Signal

Tag.

  1. Which signal targets it, such as ubiquitin chains? provenance
  2. Which enzymes add it? provenance
Annotation Databases.

GO terms

Ontology.

GO term

ID and evidence.

  1. Which GO terms apply? provenance
  2. With which evidence codes? provenance

Protein records

UniProt.

Record

Organism, the substrate protein degraded, and proteins that take part in degradation, kept distinct.

  1. Which protein is degraded? provenance
  2. Which record describes it? provenance
Physiology Roles.

Regulation

Turnover.

Turnover

Half-life.

  1. What is the protein's half-life? measurement
  2. In which cells? provenance

Disease

Failure.

Disease link

Condition and evidence.

  1. Which diseases involve failed degradation? provenance
  2. What evidence? provenance
Methods Measurement.

Assays

Turnover assays.

Assay

Method.

  1. How was degradation measured? provenance
  2. With which controls? provenance

Drugs

Pharmacology.

Drug

Agent and target.

  1. Which drugs act on these pathways? provenance
  2. At which step? provenance

Classifiers Filled

Family
Thing Registry
Category
Activities and processes
Entry kind
thing
Plane
ACT
Domain
ACT.PRC
Other names and narrower kinds
epidermal growth factor catabolic process, low-density lipoprotein particle receptor catabolic process, glycoprotein catabolic process, hemoglobin catabolic process, lipoprotein catabolic process, proteasomal protein catabolic process, insulin catabolic process, mitochondrial protein catabolic process, protein catabolic process in the vacuole, histone catabolic process, rhodopsin catabolic process, PSII associated light-harvesting complex II catabolic process

What it is Filled

The chemical reactions and pathways resulting in the breakdown of a protein by destruction of its native, active configuration, with or without hydrolysis of peptide bonds (Gene Ontology GO:0030163); in eukaryotes mainly through the ubiquitin-proteasome system and lysosomal or vacuolar pathways, and in bacteria through ATP-dependent proteases.

Why it exists Filled

Let an agent explain protein breakdown pathways, find Gene Ontology annotations, and relate protein degradation to physiology and disease with sources.

Distinguishing features Filled

  • The ubiquitin-proteasome system degrades most short-lived proteins.
  • Autophagy delivers proteins and organelles to lysosomes.
  • Denaturation without hydrolysis also counts as catabolism in the GO definition.

What robots and AI may and may not do Filled

Must not

  • give medical advice

May

  • explain processes and point to databases

Moral aspects Filled

  • accuracy

Who is affected

  • researchers
  • students

Owners Filled

Steward

nobody; a biological process

Master systems

  • Gene Ontology

Links to other meta-models Filled

parent

  • Q14864262 - registry parent class
  • Q22274829 - registry parent class
  • Q22276126 - registry parent class

related

  • catabolic process - metabolism
  • proteasome - machinery
  • lysosome - organelle
  • Gene Ontology - annotation

What else AI and robots need to interact with it Filled

Identity and identifiers required Filled

  • Vercy registry: vr.tr.protein-catabolic-process
  • Wikidata: Q14876077 (https://www.wikidata.org/wiki/Q14876077)
  • Gene Ontology: GO:0030163 protein catabolic process

Direct properties not applicable Not applicable

Not applicable

A process has no physical properties; half-lives are recorded under physiology.

Recognition optional Filled

  • Not visible; measured by protein turnover experiments

Capabilities and actions required Filled

  • explain main degradation pathways
  • give Gene Ontology terms
  • relate degradation to disease and drugs with sources
  • describe experimental methods

Hazards and failure modes required Filled

  • Protein aggregation diseases when degradation fails

Standards and interfaces required Filled

  • Gene Ontology definitions

Context of use required Filled

  • Removing damaged or unneeded proteins, regulating protein levels and recycling amino acids.
  • ubiquitin-dependent and ubiquitin-independent proteasomal degradation
  • ER-associated degradation (ERAD)
  • lysosomal, vacuolar and autophagic degradation
  • organellar and bacterial protease degradation
  • non-proteolytic denaturation

Sources Filled

  1. Q14876077 - identity of the registry item, labels and sitelinks
  2. Proteolysis - protein breakdown
  3. GO:0030163 - protein catabolic process - Identifier, definition including loss of native configuration without peptide-bond hydrolysis, and parent terms.
  4. Protein Degradation - Eukaryotic degradation pathways, ubiquitin targeting, lysosomes, autophagy and protein turnover.
  5. Regulated Proteolysis in Bacteria - Bacterial protein degradation through ATP-dependent proteases including Lon, ClpXP and FtsH.
  6. Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants - Plant degradation pathways, substrate signals, autophagy and organellar proteases.
  7. Introduction to GO annotations - Meaning of biological process annotations, gene product participation, references and evidence codes.

Open questions

  • The registry merges many substrate-specific catabolic processes; they should be separate entries.

Machine files

Card as JSON Specification Card backlog vercy.card/1

Provenance

thing registry research (pass 2) · unreviewed

Built from: models/things/publications/thing-q14876077/spec.json