Fold Commons

BeadFold · part 2

CoreFold

In BeadFold, the oily beads end up tucked together and the watery beads end up on the outside. Does a real protein do the same? Find out with myoglobin.

1. The beads

Toy model A simplified picture to show one idea. Not a measurement, and not a prediction. Of protein folding: two kinds of bead on a flat grid, where real proteins have twenty kinds of building block and fold in 3D.

Here is a best fold of a 12-bead chain from BeadFold. The filled beads are oily. In this fold 5 pairs of oily beads touch.

2. A real protein

the Sketcher's drawing Prediction Computed by a model, with how sure it is. Not an experiment.

This is myoglobin from a sperm whale (Physeter macrocephalus), 154 building blocks long. It keeps oxygen in muscles. The picture is AlphaFold's 3D prediction, squashed flat onto the page. Each dot is one building block.

Ten building blocks are marked with a number. For each one, is it inside the protein or on the outside? Careful: the picture is flat, so a dot in the middle is not always deep inside.

How we check

A building block counts as inside when it has a lot of neighbours: we count the other building blocks whose centres sit within 10 ångströms (1 nanometre, a millionth of a millimetre) of it in the model. If it has at least as many as the middle building block of the chain, it is inside. Oily here means A, V, L, I, M, F, W or C, the same as in ProteinQuest.

Real myoglobin also holds a haem, the part that holds the oxygen. The model is the chain on its own, so the haem is not in it. A few oily building blocks that look outside here may sit next to where the haem goes.

Sources