Molecular Biology: Chapter 9 — Protein folding and the fate of a new chain

9.1 What is left to cell biology #

9.1.1 The address is not this chapter #

Secretory and membrane proteins are recognised by the signal-recognition particle and enter the endoplasmic reticulum. Nuclear proteins use importins and Ran.

This chapter is the fold, and the decision to destroy a chain. Anfinsen’s refolding of ribonuclease showed that for many small proteins the native structure is encoded in the sequence. Chaperones do not add information the sequence lacks.

9.2 Chaperones #

9.2.1 Hsp70 #

Hsp70 (DnaK in bacteria) binds short hydrophobic stretches. Hsp40 (DnaJ) delivers substrate and stimulates ATP hydrolysis. If the chain has not folded, it can rebind. It does not impose a shape.

In bacteria, trigger factor on the ribosome often meets the chain first, and Hsp70 acts next. Eukaryotic cytosolic chains meet a ribosome-associated Hsp70 system. Hsp70 also holds mitochondrial precursors until the translocase takes them. The family is named for heat shock because unfolded protein induces it.

9.2.2 GroEL and TriC #

Some proteins need isolation rather than repeated release. GroEL, a group I chaperonin, is two rings of seven subunits.

TriC, or CCT, is the eukaryotic cytosolic chaperonin, group II. Each ring has eight different subunits and a built-in lid, with no GroES. Actin and tubulin do not fold without it, so the cytoskeleton in the cell-biology notes depends on this cage. Hsp90, later and with its own co-chaperones, holds a narrower set of clients, many of them signalling proteins, until they bind a partner.

9.3 Ubiquitin and the proteasome #

9.3.1 E1, E2, and E3 #

Ubiquitin has 76 amino acids. Its C-terminal glycine is joined to a lysine of the substrate, or of another ubiquitin, by an isopeptide bond. E1 uses ATP to make a thioester with ubiquitin. E2 receives that thioester. E3 selects the substrate. RING E3s bring charged E2 and substrate together. HECT E3s take ubiquitin onto their own cysteine first. A few E1 enzymes, several dozen E2 enzymes, and hundreds of E3 enzymes exist. Specificity is in the E3s. SCF ligases and the anaphase-promoting complex are E3s whose cell-cycle substrates are followed in the cell-biology notes.

9.3.2 Why a polyubiquitin chain is a degradation signal #

One ubiquitin is not an order to destroy the protein. Monoubiquitin can mark histones or a trafficking event. Chains joined through lysine 48, usually four or more ubiquitins, are the canonical proteasome signal. Lysine-11 chains also mark some proteins for destruction. Lysine-63 chains more often signal DNA-damage responses or endocytosis, and they are not by themselves a degradation mark. “Ubiquitinated” has the same fault as “methylated” in Chapter 2.

🔬 Key Illustrated Scientific Figure

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The 26S proteasome reads the K48 chain. The 20S core is four rings, α then β then β then α. Protease sites are N-terminal threonines of β subunits, inside a closed chamber, so a folded neighbour is not chewed by proximity. A 19S cap recognises the chain, removes ubiquitin for reuse, and unfolds the substrate with AAA ATPases. This is not the lysosome, which degrades material delivered by endocytosis, phagocytosis, or autophagy.

9.4 Key terms, summary, and self-check #

Key terms. Anfinsen; Hsp70; GroEL; TriC; ubiquitin; E3; K48; 26S proteasome.

Summary. Where a new chain is sent is cell biology. Whether it folds is a kinetic problem, even though the sequence encodes the structure. Hsp70 binds hydrophobic peptides and releases them on an ATP cycle. GroEL–GroES and TriC isolate clients in a chamber; actin and tubulin require TriC. E1 activates ubiquitin, E2 carries it, and an E3 chooses the substrate. A K48-linked polyubiquitin chain delivers the protein to the 26S proteasome, which recycles ubiquitin, unfolds the chain, and hydrolyses it in a sealed core. Other ubiquitin linkages are not degradation signals, and the lysosome is a different compartment.

Self-check.

1. If the sequence encodes the fold, why does the cell need chaperones?

2. What does ATP hydrolysis do to an Hsp70-bound chain, and how is a GroEL cage different?

3. Which enzyme, E1, E2, or E3, chooses the substrate?

4. Why is a K48 chain a degradation signal when a single ubiquitin, or a K63 chain, is not automatically one?

5. Where are the proteasome’s active sites, and why is that machine not a lysosome?

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