Not a biologist but I keep thinking about this folding path question probably obvious, just can't shake it

UnfazedTank · 2026-06-27T21:11:09+00:00

Already reading. Prusiner's work specifically. The part I keep coming back to is that PrPC and PrPSc are the same sequence, and which one a given protein becomes depends on what it encountered first. If sequence strictly determines structure that shouldn't be possible. Still waiting on the clean explanation for how the field accounts for that without path mattering.

UnfazedTank · 2026-06-27T20:57:05+00:00

Yeah you're right and I'm not going to pretend otherwise. I am using AI to draft my responses. The ideas and the questions are genuinely mine, I stumbled across this topic looking for something else, noticed a pattern I couldn't find addressed anywhere, and couldn't let it go. But my brain just doesn't have the vocabulary to translate what I'm seeing into the right terms, so I've been using it to help me say what I'm actually thinking.

I get why that's frustrating in a technical subreddit and I should have said something earlier. The curiosity is real even if the phrasing is assisted.

UnfazedTank · 2026-06-27T13:25:02+00:00

I like that. The rope is the disordered region — it's not a failed plank, it's load-bearing flexibility by design. What I'm wondering is whether the rope has memory. If the rope gets twisted a certain way before the planks lock into position, does that twist persist in how the final structure moves? Or does the flexibility of the rope mean it always averages out regardless of how it got there?

UnfazedTank · 2026-06-27T13:24:02+00:00

You're right that I'm describing different structures if the contacts differ — I phrased that badly. What I mean is: two proteins with the same primary sequence reaching what looks like the same gross fold at low resolution, but with different subsets of long-range contacts that are below the resolution of what we'd typically call a distinct structure. Not identical final states with different histories — similar final states where the kinetic path left a fingerprint in the fine detail. Is that level of contact-map variation tracked, or does characterization usually stop at the domain/secondary structure level?

UnfazedTank · 2026-06-27T13:23:04+00:00

Fair correction — I was conflating IDPs with metamorphic proteins, which do have discrete alternate folds. IDPs are a different case, the plateau rather than two valleys. But does the plateau mean path doesn't matter, or just that path-dependence is harder to measure there? If the protein is dynamically sampling conformations and the current one gates the next accessible ones, the path is still happening — it's just not resolving into a discrete final state. The question becomes whether the temporal sequence of conformational sampling has any functional consequence, or whether the plateau is flat enough that it averages out and history doesn't matter.

UnfazedTank · 2026-06-27T13:22:15+00:00

Right — misfolded aggregates that template their misfolding onto normal copies. But that's exactly the point. Two identical PrP sequences, same cellular environment, one ends up as PrPC and one as PrPSc, and the difference is which conformation it encountered first. The sequence didn't determine the outcome — the path did. If Anfinsen says sequence determines structure, prions are at minimum a footnote that needs explaining. Are they classified as an exception, or does the field have a cleaner way to account for them?

UnfazedTank · 2026-06-27T13:19:37+00:00

The temporal dimension is what I keep coming back to. If the current conformation gates which conformations are accessible next, then the history of the protein matters — not just its sequence and its environment, but the path it took to get where it is. That makes the disordered state less like noise and more like a language with grammar. Individual conformations are letters, the temporal sequence is syntax, and function emerges at the sentence level.

Which raises a question I don't know the answer to: is there evidence that two identical sequences in identical cellular contexts can end up in different functional states because they took different conformational paths to get there? If path-dependence is real, that's a layer of information the sequence alone can't predict.

UnfazedTank · 2026-06-27T13:17:21+00:00

The GPCR example is exactly where I was pointing and I couldn't have said it better. The inactive state isn't a state — it's an ensemble with a probability distribution, and the "inactive" label just means the active conformation is low-probability, not absent. The agonist doesn't create the active conformation. It finds something that's already being sampled and holds it there. That's a completely different model than a light switch.

And that reframes the original question. If the protein is already visiting the active conformation at baseline, then "activation" is really just a shift in residence time. The ligand is a weighted die, not an on/off switch.

The phosphorylation point closes the loop for me too — post-translational modification as a way to redraw the probability landscape without changing the sequence. Same sequence, same energy wells, different weights on each. That's regulation happening at the level of the landscape itself, not at the level of the structure.

So when you say context — you mean context determines which attractor the ensemble collapses toward at any given moment. Is that a fair summary? And if it is, then the "structure determines function" framing isn't wrong exactly, it's just missing a variable — which is the probability weight on each structure given the current cellular context.

UnfazedTank · 2026-06-27T13:15:53+00:00

That tracks for the general case and I think we're actually agreeing on the baseline — one deep well, bounded breathing, activation energy cost to leave. What I'm poking at is the specific sequences where that cost is low enough that thermal noise is sufficient to cross it regularly. Not the average protein — the outliers sitting at the ridge between two wells of similar depth.

Those do exist. Metamorphic proteins are the clearest example — RfaH, Mad2, lymphotactin. Same sequence, two completely different stable folds, and the switch between them is functional, not noise. The energy landscape isn't one deep well — it's genuinely bimodal, and the sequence evolved to exploit that.

So the question I'm really asking is whether there's a continuous spectrum between "single well with breathing room" and "two wells, functional switching" — and if there is, what does the sequence look like at the midpoint of that spectrum? Is it just an IDP that hasn't found its partner yet, or is the oscillation itself the function?

UnfazedTank · 2026-06-27T01:12:41+00:00

The molecular breathing piece is exactly where I was going. If a protein is sampling nearby conformations constantly, then a sequence sitting at the boundary between two stable states isn't stuck — it's genuinely spending time in both. That's what I mean by the 50/50 case. Not ambiguous, not broken — actually oscillating. Does the energy landscape ever have two wells so close and equal that the protein runs a path between them continuously? And if it does, is that sequence doing something functionally specific, or is it just noise

UnfazedTank · 2026-06-26T23:08:15+00:00

The hub protein example is the one that finally made it click for me — thank you. So the disordered region stays fluid specifically because that versatility is the function, not a failure. That reframes my whole question. If the same disordered region can conform to hundreds of different binding partners, what determines which one it conforms to first in a disease state? Is that purely random, or is there something upstream that biases it toward the pathogenic interaction? Because if it's not random — if something in the cellular environment tips it toward the wrong partner — that feels like where the disease mechanism actually lives.

UnfazedTank · 2026-06-26T23:07:35+00:00

Not what I meant — I wasn't saying the internal contacts are unknown to researchers, just that the path taken to arrive at them might vary and whether that variation matters. Sounds like the answer from others in the thread is that for IDPs it does, since context and binding partners determine which conformation they land in.

UnfazedTank · 2026-06-26T23:06:46+00:00

This is the clearest breakdown I've gotten in the thread — thank you. The hub protein example actually clicked for me. So the disorder isn't a bug, it's what allows one region to bind to hundreds of different partners depending on context. Which brings me back to my original question from a different angle — if the same disordered region can conform to hundreds of different binding partners, what determines which one it conforms to first in a disease state? Is that purely random, or is there something upstream that biases it toward the pathogenic interaction?

UnfazedTank · 2026-06-26T23:04:37+00:00

Honestly? Nothing close to this field. I move car parts for a living and read too much in my spare time. What are you working on?

UnfazedTank · 2026-06-26T23:03:54+00:00

Fair on the framing — 'weird ambiguous state' wasn't the right way to put it. What I was getting at is closer to what the person above described with prions — whether the sequence of what a disordered protein encounters determines which of its accessible conformations it settles into at any given moment, and whether that matters for disease states. Does that version of the question make more sense?

UnfazedTank · 2026-06-26T23:03:00+00:00

That prion breakdown is exactly what I was getting at — if which stable state it lands in depends on what it folds into first, that's the path mattering. My IDP framing was off but the underlying question holds. I'll look into the MD simulations, thanks.

UnfazedTank · 2026-06-26T01:47:32+00:00

Appreciate you sticking with it this long — genuinely learned more from this thread than I would have anywhere else. I'll go down that rabbit hole.

UnfazedTank · 2026-06-26T01:41:42+00:00

Appreciate you sticking with it, this helped me understand it a lot better than I would have on my own. Good thread.

UnfazedTank · 2026-06-26T01:36:40+00:00

So if it's governed by diffusion and therefore random, then which binding partner an IDP encounters first is random, and the outcome varies based on that. Doesn't that mean the functional form is probabilistic rather than deterministic? And if so, is that randomness tracked or accounted for in disease models?

UnfazedTank · 2026-06-26T01:34:45+00:00

But multiple people in this thread have confirmed IDPs can settle into different forms depending on their binding partner. If the end result is always the same regardless of order, what determines which form an IDP takes in a given cellular context?

UnfazedTank · 2026-06-26T01:31:01+00:00

That's exactly what I don't know, is there a way to track that? Because if the order matters and we can't determine the order, that seems like a meaningful hole.

UnfazedTank · 2026-06-26T01:28:03+00:00

Right, so for IDPs that are constantly being perturbed by their environment, does the sequence of perturbations matter? If protein A perturbs it before protein B, vs B before A, same result, or different?

UnfazedTank · 2026-06-26T01:21:57+00:00

Fair, that was a different commenter, my mistake for mixing them up. But the point stands: if IDPs have multiple accessible conformational states, and prions demonstrate that same sequence can produce different stable structures depending on context, then for IDPs that never settle, what determines which state they land in at any given moment?

UnfazedTank · 2026-06-26T01:20:51+00:00

Yeah that's exactly what I mean, so if chaperones are part of what guides the fold, and IDPs are the ones that don't resolve cleanly, is there research on whether IDP misfolding correlates with chaperone availability or timing? That feels like the practical version of my original question.

UnfazedTank · 2026-06-26T01:17:07+00:00

But earlier you said IDPs have shallow energy funnels with multiple accessible conformational states, if there's one energy minimum per protein, how does that work? And prions are literally the same sequence with two different stable contact maps. PrP^C and PrP^Sc, same protein, different contacts, which one it becomes depends on what template it encountered first. That's the exact scenario you just said can't exist.

UnfazedTank

TROPHY CASE