Marty's testable ID hypothesis

[Mercer (John Mercer)]

@Marty

There you go again, just repeating your misunderstanding ad nauseum, hoping that will make it true.

How interesting that you omitted your embedded hypothesis itself: quaternary structure turns on catalytic activity.

That’s how designed, split proteins work. It’s not how natural ones do, as a rule.

@Marty

Looks to me like you’re the one making invalid assumptions – about what I think.

No, you told me what you think:

@Marty

For a protein complex, you need the complement at a “right” location so that the resulting quaternary structure has meaningful catalytic activity.

My point isn’t about right or wrong locations of binding sites. I am pointing out something much more fundamental and revealing: your claim about how quaternary structure regulates function:

Can you name a single case in biology in which the catalytic activity requires quaternary structure, as it does for all of these human-designed complexes?

@Mercer

The original example of a conditional split protein complementation system was reported by Johnsson & Varshavsky (50), who demonstrated that ubiquitin fragments only reassembled into an active protease tag when fused to two interacting proteins (a leucine zipper homodimer). This pivotal split ubiquitin system laid the foundation for all future protein-fragment complementation assays (PCAs) that link the function of a split reporter protein to a specific protein–protein interaction (PPI) (Figure 1). Conceptually, any protein whose activity results in a clear and measurable readout can act as the reporter in a PCA. To date, many proteins, such as ubiquitin (50), β-galactosidase (118), dihydrofolate reductase (104), β-lactamase (36), firefly luciferase (81), TEV protease (152), thymidine kinase (84), Cas9 (160), horseradish peroxidase (83), RNA polymerase (106), and aminoacyl tRNA synthetase (134), have been engineered as split PCA reporters to detect both transient and irreversible PPIs. The types of readouts for these assays include fluorescence, bioluminescence, cell survival, gene transcription, protein translation, positron emission, genome editing, and electron microscopy. Since this review focuses on split fluorescent proteins (FPs) and their numerous and often overlooked applications, we refer the interested reader to earlier, thorough reviews for more details about the properties and scope of split nonfluorescent proteins (85, 89, 90, 127, 153, 154).

@Marty

If you ever want to know what I actually think, feel free to ask.

Why do you think that protein complexes in vivo are regulated like intelligently designed (by humans) split proteins?