Protein quality-control decisions

1 · Start with a protein chain

New or damaged protein → inspection

Exposed hydrophobic regions and stalled synthesis can recruit distinct quality-control systems.

2 · Assist folding

Unfolded chain → folding cycles

DnaK/DnaJ/GrpE and GroEL/GroES are representative chaperone systems. ATP-driven cycles can help recover a native fold.

3 · Recover useful protein

Successful folding → functional protein

The folded chain can assemble with partners. Some proteins require repeated cycles; others fold without these chaperones.

4 · Remove irreparable protein

Damaged chain → peptides

ATP-dependent proteases, such as Clp systems, recognize and degrade selected substrates. Peptidases recycle amino acids.

5 · Rescue stalled translation

Stalled ribosome → release / recycling

tmRNA–SmpB is a bacterial example: a rescue template frees the ribosome and adds a degradation tag to the unfinished product.

6 · Maintain other molecular parts

RNA processing / ribosome maturation

Separate cleavage, modification and assembly reactions maintain RNA and ribosomes; they are not stages of protein folding.

Evidence and scope

Original explanatory diagram based on the sources below. These are selected documented biochemical routes or mechanisms, not a complete species-specific reconstruction. Each arrow can summarize several reactions; panels may represent branches or alternatives. Genome annotations, protein models and organism-specific evidence remain in the detailed system map.

• Chaperone-assisted refolding experiments
• Aquificales chaperone inventories