[jfarlow]

Brownian motion dominates at the scale of a protein. In other words, the energy imparted by the ambient temperature is orders of magnitude greater than that that could be established through momentum of objects with that little mass. So everything bumps into everything, and the only distinguishing factor between various bumps is how long they stay stuck together. Most things just bounce right off. Sometimes they are repulsed, and in rare cases (when they've been selected for), multiple proteins can meet in just the right orientation that they stay stuck for a while (now scale this so that 3 or 4 objects must meet at the same time, and now you get into the 'regulation' of a cell at perception-relevant time-scales). This measurement of stickiness is called the "dissociation constant (Kd)" and is a measurement of what concentration of component A you need alongside component B such that half of component A is bound to component B. It is one of the primary drivers of most biochemical processes in a cell.

https://en.wikipedia.org/wiki/Dissociation_constant

[stillsut]

Is there not some local disturbances in the circulation of cell contents that not all interactions are i.i.d? Some kind of repelling force on a large molecule that would keep similarly charged molecules at arms length. And in some cases act as a cell wide tidal force to diffusion?

I'm thinking of the atari pong ball where you can ricochet the ball between the top of the court and bricks repeatedly; is there some locality in the cell which takes advantage of positioning to increase likelihood of collision?

[Reelin]

> local disturbances in the circulation of cell contents that not all interactions are i.i.d?

Sure, in the sense that the cell isn't actually a single homogeneous compartment the way it's often portrayed.

There are numerous organelles, most (all?) separated by lipid bilayer membranes. (https://en.wikipedia.org/wiki/Lipid_bilayer) There are various transporters (ie protein machines) embedded in the different membranes that move specific things from one side to the other. There are also complex transport systems that move packets of things from one organelle to another. (https://www.nature.com/scitable/topicpage/endoplasmic-reticu...)

The end result is that the contents and chemical conditions of compartments are quite different from one another. As a concrete example, this is actually one of the ways that viruses know when to "wake up" and start doing things. (https://www.uniprot.org/keywords/KW-1170)

> Some kind of repelling force on a large molecule that would keep similarly charged molecules at arms length.

It's more that proteins get "sorted" into the appropriate locations where they aren't reactive with anything except their intended targets. If they react with things they aren't supposed to then (over generalizing to an absurd degree for illustrative purposes) everything stops working, that organism dies, evolution continues, and one way or another eventually we're back at that protein only reacting with the things it's supposed to react with.

[jszymborski]

tl;dr very much so, yes

Cells are very subdivided, and the ease with which macromolecules traverse these spaces varies greatly. There are organelles and the nucleus that require only let certain proteins in and and out and at certain rates.

There are also kinds of tar-pits that keep certain proteins around for longer.

Stress granules and vesicles also gobble-up macromolecules into these fun party bags that burst in certain contexts.

Sometimes you even have complexes of macromolecules like ribosomes whose entire job is to intercept other macromolecules so that they might interact (there is a subtle difference between enzymes/catalysis here if I understand correctly)