protein
Let an agent handle proteins by identity, sequence, structure, function and organism, using standard identifiers, and nutrition as a separate sense.
Research draft, second pass
A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.
written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify
Researched by: Claude
Purpose and description
Let an agent handle proteins by identity, sequence, structure, function and organism, using standard identifiers, and nutrition as a separate sense.
A large biomolecule made of one or more chains of amino acids folded into a specific three-dimensional structure, carrying out functions such as catalysis, structure, transport and signalling.
What it is for: Proteins do most of the work in cells; in diets, protein supplies amino acids.
It can be identify it, by sequence and accession; determine its structure; study its function; produce it, recombinantly, under biosafety rules.
Distinguishing features
A polymer of amino acids with a folded structure
Function depends on structure
Encoded by genes
Dietary protein is a nutrition concept
What it looks like
Invisible to the eye; shown as structure models, sequences or bands on gels.
Physical character
length: 50-35000 amino acids - titin is the largest
mass: 5-3800 kDa
How it is recognised
UniProt accession and gene name
PDB structures
Dietary protein on labels is a nutrient, not a specific protein
Related models
is made of - monomers
is encoded by - DNA
works in - context
is a nutrient in - dietary protein
In practice
Families and kinds
enzymes
structural proteins
transport proteins
signalling proteins and receptors
antibodies
Identifiers
UniProt accession for example P69905 protein sequence and function
PDB id four characters structures
Standards and regulation
Biosafety rules for recombinant proteins
Medicines regulation for protein therapeutics
Food labelling rules on protein content
Failure modes and hazards
Allergenic proteins in food
Misfolding diseases
Confusing orthologs across species
Where this came from
wikidata · CC0 1.0
Also registered as vr.tr.protein
Drafted structure
Bundle to layer to finding to question, as the second pass will find it: 4 bundles · 8 layers · 8 findings · 16 questions.
Identity Which protein.
Accessions prevent confusion.
Accession
UniProt and gene.
Accession
Identifiers.
- What is its UniProt accession and gene name? provenance
- Which organism? definition
Sequence
Amino acid sequence.
Sequence
The sequence.
- What is its sequence and length? measurement
- Which isoform? boundary
Structure Shape.
Structure explains function.
Experimental
PDB.
Structure
Experimental structures.
- Is there an experimental structure, at what resolution? provenance
- Which method? provenance
Predicted
Models.
Prediction
Predicted models.
- Is a predicted model available, and how confident is it? measurement
- Where might it be wrong? boundary
Function What it does.
Function is what matters in biology and medicine.
Role
Molecular function.
Function
Molecular and biological role.
- What does the protein do? definition
- How is that known? provenance
Disease
Links to disease.
Disease links
Disease associations.
- Is it linked to disease? provenance
- Is it a drug target? provenance
Use Production and diet.
Proteins are made and eaten.
Production
Recombinant.
Production
How it is produced.
- How is it produced for use? definition
- Which rules apply? provenance
Diet
Nutrition and allergy.
Nutrition
Dietary aspects.
- Is it a food allergen? boundary
- How much dietary protein is recommended, by whom? provenance
What the second pass must settle
- Should proteins be instances with UniProt accessions?
- How should dietary and biochemical senses be separated?
- How should predicted structures be marked?