transmembrane protein
Let an agent explain transmembrane proteins and their structure, relay classes, functions and study methods from biochemistry references, describe membrane-active toxins and peptides at the level of published biology, and distinguish transmembrane proteins from peripheral membrane proteins, lipid-anchored proteins and secreted proteins.
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 explain transmembrane proteins and their structure, relay classes, functions and study methods from biochemistry references, describe membrane-active toxins and peptides at the level of published biology, and distinguish transmembrane proteins from peripheral membrane proteins, lipid-anchored proteins and secreted proteins.
A protein that spans the whole cell membrane, with domains on both sides, forming channels, transporters, receptors and enzymes essential to cell function, and including membrane-inserting proteins listed in the registry aliases such as pore-forming toxins, snake three-finger toxins that bind receptors, defensins of insects, fungi and plants, and antimicrobial peptides such as tachyplesin and oxyopinin that disrupt membranes; the model covers structure and biology without any guidance on toxin production or use.
What it is for: Not applicable; a protein class.
It can be explain structure and classes; relay functions and methods; describe membrane-active molecules; distinguish related proteins.
Distinguishing features
Spans the bilayer
Alpha-helical or beta-barrel
Channels and receptors
Toxin and peptide relatives
What it looks like
Not a visible object; proteins spanning the lipid bilayer.
Physical character
share of human genes: about 25-30 percent - encode membrane proteins
main folds: alpha-helical bundles and beta-barrels list
drug targets: over half of drugs target membrane proteins note
How it is recognised
Protein spanning the membrane
Channels, transporters, receptors; pore-forming toxins, three-finger toxins, defensins, tachyplesin, oxyopinin
Peripheral proteins attach to the surface; lipid-anchored proteins are tethered; secreted proteins leave the cell
Related models
is a kind of - in registry terms
is embedded in - the lipid bilayer
is contrasted with - attached to the surface
is exemplified by - a major class
In practice
Families and kinds
ion channels and transporters
G protein-coupled and other receptors
membrane enzymes
beta-barrel outer membrane proteins
pore-forming toxins and membrane-active peptides such as defensins, tachyplesin and oxyopinin
three-finger toxins that target membrane receptors
Identifiers
GO GO:0016021 membrane, integral component
Standards and regulation
No regulation of the protein class; biosafety rules apply to toxin research
Failure modes and hazards
Agents providing toxin production or use guidance
Confusing transmembrane with peripheral proteins
Registry aliases naming toxins and peptides as if kinds of transmembrane protein
Also called
+279
Where this came from
wikidata · CC0 1.0
Drafted structure
Bundle to layer to finding to question, as the second pass will find it: 4 bundles · 8 layers · 8 findings · 16 questions.
Understand What a transmembrane protein is.
Science.
Definition
Definition and structure.
Definition
Definition.
- What is a transmembrane protein, and how does it differ from peripheral, lipid-anchored and secreted proteins? definition
- Is the question about structure, function, a class, or toxin use, which the model does not assist? boundary
Classes
Classes.
Classes
Classes.
- What are channels, transporters, receptors, membrane enzymes and beta-barrel proteins? definition
- Which entry fits the specific class? action
Biology Biology.
Science.
Function
Function.
Function
Function.
- How do transmembrane proteins transport ions and molecules, transmit signals and catalyse reactions? provenance
- Which references are standard? provenance
Folding
Insertion and folding.
Folding
Folding.
- How are transmembrane proteins inserted and folded in the membrane? provenance
- Which sources are cited? provenance
Active Membrane-active molecules.
Science.
Toxins
Toxins.
Toxins
Toxins.
- What are pore-forming toxins and three-finger toxins, and how do they act, at the level of published biology? provenance
- Is the presentation limited to biology without production or use detail? boundary
Peptides
Antimicrobial peptides.
Peptides
Peptides.
- What are defensins, tachyplesin and oxyopinin, and why are they studied for antimicrobials? provenance
- Which entry fits antimicrobial peptide? action
Context Methods and medicine.
Context.
Methods
Study methods.
Methods
Methods.
- How are membrane proteins studied by cryo-EM, crystallography and prediction? provenance
- Which entry fits membrane protein structure? action
Medicine
Drug targets.
Medicine
Medicine.
- Why are membrane proteins major drug targets, and what diseases involve them? provenance
- Which entry fits G protein-coupled receptor? action
What the second pass must settle
- Should pore-forming toxin and defensin be separate primary entries?
- How should biochemistry references be linked?
- The registry entry has merged aliases naming toxins and antimicrobial peptides; should they be split off?