Protein Degradation

Copyright © 2000-2008 by Joyce J. Diwan. All rights reserved.

Molecular Biochemistry II

There are several classes of proteolytic enzymes.

Serine proteases include digestive enzymes trypsin, chymotrypsin, & elastase.

Different serine proteases differ in substrate specificity. For example:

Chymotrypsin prefers an aromatic side chain on the residue whose carbonyl carbon is part of the peptide bond to be cleaved.

Trypsin prefers a positively charged Lys or Arg residue at this position.

serine (Ser, S)

During catalysis, there is nucleophilic attack of the hydroxyl O of a serine residue of the protease on the carbonyl C of the peptide bond that is to be cleaved.

An acyl-enzyme intermediate is transiently formed.

In this diagram a small peptide is shown being cleaved, while the usual substrate would be a larger polypeptide.

Hydrolysis of the ester linkage yields the second peptide product.

During attack of the serine hydroxyl oxygen, a proton is transferred from the serine hydroxyl to the imidazole ring of the histidine, as the adjacent aspartate carboxyl is H-bonded to the histidine.

The active site in each serine protease includes a serine residue, a histidine residue, & an aspartate residue.

Asp102

His57

Ser195

Catalytic residues in trypsin

PDB 3BTK

Aspartate proteases include the digestive enzyme pepsin Some proteases found in lysosomes the kidney enzyme renin HIV-protease.

Two aspartate residues participate in acid/base catalysis at the active site.

In the initial reaction, one aspartate accepts a proton from an active site H2O, which attacks the carbonyl carbon of the peptide linkage.

Simultaneously, the other aspartate donates a proton to the oxygen of the peptide carbonyl group.

aspartate (Asp)

Zinc proteases (metalloproteases) include: digestive enzymes carboxypeptidases matrix metalloproteases (MMPs), secreted by cells one lysosomal protease.

Some MMPs (e.g., collagenase) are involved in degradation of extracellular matrix during tissue remodeling.

Some MMPs have roles in cell signaling relating to their ability to release cytokines or growth factors from the cell surface by cleavage of membrane-bound pre-proteins.

During catalysis, the Zn++ promotes nucleophilic attack on the carbonyl carbon by the oxygen atom of a water molecule at the active site.

An active site base (Glu in Carboxypeptidase) facilitates this reaction by extracting H+ from the attacking H2O.

zinc

water oxygen

Carboxypeptidase

PDB 1YME

A zinc-binding motif at the active site of a metalloprotease includes two His residues whose imidazole side-chains are ligands to the Zn++. Colors in Carboxypeptidase image at right: Zn, N, O.

Cysteine proteases have a catalytic mechanism that involves a cysteine sulfhydryl group.

Deprotonation of the cysteine SH by an adjacent His residue is followed by nucleophilic attack of the cysteine S on the peptide carbonyl carbon.

A thioester linking the new carboxy-terminus to the cysteine thiol is an intermediate of the reaction (comparable to acyl-enzyme intermediate of a serine protease).

cysteine

Cysteine proteases:

Papain is a well-studied plant cysteine protease.

Cathepsins are a large family of lysosomal cysteine proteases, with varied substrate specificities.

Caspases are cysteine proteases involved in activation & implementation of apoptosis (programmed cell death).

Caspases get their name from the fact that they cleave on the carboxyl side of an aspartate residue.

Calpains are Ca++-activated cysteine proteases that cleave intracellular proteins involved in cell motility & adhesion.

They regulate processes such as cell migration and wound healing.

Activation of proteases:

Most proteases are synthesized as larger pre-proteins.

During activation, the pre-protein is cleaved to remove an inhibitory segment.

In some cases activation involves dissociation of an inhibitory protein.

Activation may occur after a protease is delivered to a particular cell compartment or the extracellular milieu.

Caspases involved in initiation of apoptosis are activated by interaction with large complexes of scaffolding & activating proteins called apoptosomes.

See diagram of apoptosome in a Univ. London website.

Protease Inhibitors:

Most protease inhibitors are proteins with domains that enter or block a protease active site to prevent substrate access.

IAPs are proteins that block apoptosis by binding to & inhibiting caspases.

The apoptosis-stimulating protein Smac antagonizes the effect of IAPs on caspases.

TIMPs are inhibitors of metalloproteases that are secreted by cells.

A domain of the inhibitor protein interacts with the catalytic Zn++.

Cystatins are inhibitors of lysosomal cathepsins. Some (also called stefins) are found in the cytosol, and others in the extracellular space. Cystatins protect cells against cathepsins that may escape from lysosomes.

Serpins use a unique suicide mechanism to inhibit serine or cysteine proteases.

• A large conformational change in the serpin accompanies cleavage of its substrate loop.

• This leads to disordering of the protease active site, preventing completion of the reaction.

• The serpin remains covalently linked to the protease as an acyl-enzyme intermediate.

• Movie depicting the conformational changes.(University of Cambridge website)

• Serpins are widely distributed within & outside of cells, and have diverse roles, including regulation of blood clotting, fibrin cleavage, & inhibition of apoptosis.

plasma membrane may be processed first in an endosomal compartment and then delivered into the lumen of a lysosome by fusion of a transport vesicle.

Solute transporters embedded in the lysosomal membrane catalyze exit of products of lysosomal digestion (e.g., amino acids, sugars, cholesterol) to the cytosol.

H+ Lysosome

ATP ADP + Pi

Vacuolar ATPase

low internal

pH

Lumen contains

hydrolytic enzymes.

Lysosomes contain a large variety of hydrolytic enzymes that degrade proteins & other substances taken in by endocytosis.

Materials taken into a cell by inward budding of vesicles from the

Lysosomal proteases include many cathepsins (cysteine proteases), some aspartate proteases & one zinc protease.

Activation of lysosomal proteases by cleavage may be catalyzed by other lysosomal enzymes or be autocatalytic, promoted by the internal acidic pH.

H+ Lysosome

ATP ADP + Pi

Vacuolar ATPase

low internal

pH

Lumen contains

hydrolytic enzymes.

Lysosomes have a low internal pH due to vacuolar ATPase, a H+ pump homologous to mitochondrial F1Fo ATPase.

All intra-lysosomal hydrolases exhibit acidic pH optima.

In autophagy, part of the cytoplasm may become surrounded by two concentric membranes.

Fusion of the outer membrane of this autophagosome with a lysosomal vesicle results in degradation of enclosed cytoplasmic structures and macromolecules.

Genetic studies in yeast have identified unique proteins involved in autophagosome formation.

autophagosome autophagic vacuole

(lysosome)

One model for autophagic vacuole formation

Protein turnover; selective degradation/cleavage

Individual cellular proteins turn over (are degraded and re-synthesized) at different rates.

E.g., half-lives of selected enzymes of rat liver cells range from 0.2 to 150 hours.

N-end rule: On average, a protein's half-life correlates with its N-terminal residue. Proteins with N-terminal Met, Ser, Ala, Thr, Val, or

Gly have half lives greater than 20 hours. Proteins with N-terminal Phe, Leu, Asp, Lys, or Arg

have half lives of 3 min or less.

PEST proteins having domains rich in Pro (P), Glu (E), Ser (S), Thr (T), are more rapidly degraded than other proteins.

Most autophagy is not a mechanism for selective degradation of individual macromolecules.

However, cytosolic proteins that include the sequence KFERQ may be selectively taken up by lysosomes in a process called chaperone-mediated autophagy.

This process, which is stimulated under conditions of nutritional or oxidative stress, involves interaction of proteins to be degraded with:

• Cytosolic chaperones that unfold the proteins.

• A lysosomal membrane receptor (LAMP-2A) that may provide a pathway across the membrane.

• Chaperones in the lysosomal lumen that may assist with translocation across the membrane.

Intramembrane-cleaving proteases (I-CLiPs) cleave regulatory proteins such as transcription factors from membrane-anchored precursor proteins.

E.g., precursors of SREBP (sterol response element binding protein) transcription factors are integral proteins embedded in endoplasmic reticulum membranes.

The released SREBP can then translocate to the cell nucleus to regulate transcription of genes for enzymes involved, e.g., in cholesterol synthesis.

S2P (site 2 protease, an I-CLiP) is a membrane-embedded metalloprotease that cleaves an α-helix of the SREBP precursor within the transmembrane domain.

N C

membrane

cytosol

lumen

S2P cleavage releasing SREBP

SCAP-activated S1P cleavage Activation of SREBP

involves its translocation to golgi membranes where sequential cleavage by 2 proteases releases to the cytosol a domain with transcription factor activity.

Ubiquitin:

Proteins are usually tagged for selective destruction in proteolytic complexes called proteasomes by covalent attachment of ubiquitin, a small, compact, highly conserved protein.

ubiquitin PDB 1TBE

However, some proteins may be degraded by proteasomes without ubiquitination.

An isopeptide bond links the terminal carboxyl of ubiquitin to the ε-amino group of a lysine residue of a "condemned" protein.

lysine

The joining of ubiquitin to a condemned protein is ATP-dependent.

Three enzymes are involved, designated E1, E2 & E3.

Initially the terminal carboxyl group of ubiquitin is joined in a thioester bond to a cysteine residue on Ubiquitin-Activating Enzyme (E1). This is the ATP-dependent step.

The ubiquitin is then transferred to a sulfhydryl group on a Ubiquitin-Conjugating Enzyme (E2).

A Ubiquitin-Protein Ligase (E3) then promotes transfer of ubiquitin from E2 to the ε-amino group of a Lys residue of a protein recognized by that E3, forming an isopeptide bond.

There are many distinct Ubiquitin Ligases with differing substrate specificity.

• One E3 is responsible for the N-end rule. • Some are specific for particular proteins.

ubiquitin C S

O

Cys E2 H2N Lys protein to be degraded

ubiquitin C

O

HS Cys E2N Lys protein to be degraded

H

+

E3

+

(Ubiquitin-Protein Ligase)

H2N COO−

destruction box

chain of ubiquitins

Primary structure of a protein targeted for degradation

More ubiquitins are added to form a chain of ubiquitins.

The terminal carboxyl of each ubiquitin is linked to the ε-amino group of a lysine residue (Lys29 or Lys48) of the adjacent ubiquitin.

A chain of 4 or more ubiquitins targets proteins for degradation in proteasomes. (Attachment of a single ubiquitin to a protein has other regulatory effects.)

H2N COO−

destruction box

chain of ubiquitins

Primary structure of a protein targeted for degradation

Some proteins (e.g., mitotic cyclins involved in cell cycle regulation) have a destruction box sequence recognized by a domain of the corresponding Ubiquitin Ligase.

Ubiquitin Ligases (E3) mostly consist of two families:

Some Ubiquitin Ligases have a HECT domain containing a conserved Cys residue that participates in transfer of activated ubiquitin from E2 to a target protein.

Some Ubiquitin Ligases contain a RING finger domain in which Cys & His residues are ligands to 2 Zn++ ions.

A RING (Really Interesting New Gene) finger is not inherently catalytic. It stabilizes a characteristic globular domain conformation that serves as a molecular scaffold for residues that interact with E2.

Regulation of ubiquitination:

Some proteins regulate or facilitate ubiquitin conjugation.

Regulation by phosphorylation of some target proteins has been observed. E.g., phosphorylation of PEST domains activates ubiquitination of proteins rich in the PEST amino acids.

Glycosylation of some PEST proteins with GlcNAc has the opposite effect, prolonging half-life of these proteins. GlcNAc attachment increases with elevated extracellular glucose,suggesting a role as nutrition sensor.

A ubiquitin-like protein called Nedd8 may be attached to ubiquitin ligases (E3) that have a "cullin" subunit including a RING finger domain.

De-neddylation (removal of the Nedd8 protein), catalyzed by a metalloprotease subunit of a complex called the COP9 signalosome, activates the E3 ligases.

Some disease-causing viruses target host cell proteins for degradation in the proteasome.

They either activate a host cell Ubiquitin Ligase to ubiquitinate host proteins, or encode their own Ubiquitin Ligase.

The proteasome core complex, with a 20S sedimentation coefficient, contains 2 each of 14 different polypeptides.

7 α-type proteins form each of the two α rings, at the ends of the cylindrical structure.

7 β-type proteins form each of the 2 central β rings.

Proteasomes: Selective protein degradation occurs in the proteasome, a large protein complex in the nucleus & cytosol of eukaryotic cells.

20 S Proteasome (yeast) closed state

two views PDB 1JD2

α β β α

The 20S proteasome core complex encloses a cavity with 3 compartments joined by narrow passageways.

Protease activities are associated with 3 of the β subunits, each having different substrate specificity.

20 S Proteasome (yeast) closed state

two views PDB 1JD2

α β β α

1. One catalytic β-subunit has a chymotrypsin-like activity with preference for tyrosine or phenylalanine at the P1 (peptide carbonyl) position.

2. One has a trypsin-like activity with preference for arginine or lysine at the P1 position.

3. One has a post-glutamyl activity with preference for glutamate or other acidic residue at the P1 position.

Different variants of the 3 catalytic subunits, with different substrate specificity, are produced in cells of the immune system that cleave proteins for antigen display.

The proteasome hydrolases constitute a unique family of threonine proteases. A conserved N-terminal threonine is involved in catalysis at each active site.

The 3 catalytic β subunits are synthesized as pre-proteins. They are activated when the N-terminus is cleaved off, making threonine the N-terminal residue.

Catalytic threonines are exposed at the lumenal surface.

threonine (Thr)

Proteasomal degradation of particular proteins is an essential mechanism by which cellular processes are regulated, such as cell division, apoptosis, differentiation and development.

E.g., progression through the cell cycle is controlled in part through regulated degradation of proteins called cyclins that activate cyclin-dependent kinases.

Several subunits of the proteasome are glycosylated with GlcNAc when extracellular glucose is high, leading to decreased intracellular proteolysis.

Conversely, under conditions of low nutrition, decreased modification by GlcNAc leads to increased proteolysis.

Thus protein degradation is responsive to nutrition via glycosylation of Ubiquitin Ligase & the proteasome itself.

Many inhibitors of proteasome protease activity are known, some of which are natural products and others experimentally produced.

E.g., TMCs are naturally occurring proteasome inhibitors.

They bind with high affinity adjacent to active site threonines within the proteasome core complex.

TMCs have a heterocyclic ring structure derived from modified amino acids.

Proteasome inhibitors cause cell cycle arrest and induction of apoptosis (programmed cell death) when added to rapidly dividing cells.

The potential use of proteasome inhibitors in treating cancer is being investigated.

Proteasome evolution:

Proteasomes are considered very old.

They are in archaebacteria, but not most eubacteria, although eubacteria have alternative protein-degrading complexes.

The archaebacterial proteasome has just 2 proteins, α & β, with 14 copies of each.

The eukaryotic proteasome has evolved 14 distinct proteins that occupy unique positions within the proteasome (7 α-type & 7 β-type).

The ends of the cylindrical complex are blocked by N-terminal domains of α subunits that function as a gate.

Interaction with a cap complex causes a conformational change that opens a passageway into the core complex.

Regulatory cap complexes:

In crystal structures of the proteasome core alone, there is no apparent opening to the outside.

20 S Proteasome (yeast) closed state

two views PDB 1JD2

α β β α

The 19S regulatory cap complex recognizes multi-ubiquitinated proteins, unfolds them, removes ubiquitin chains, and provides a passageway for threading unfolded proteins into the core complex.

The 19S cap is a 20-subunit 700 kDa complex, also referred to as PA700. When combined with a 20S core complex, it yields a 26S proteasome.

Only low-resolution structural information, obtained by electron microscopy, is available for the 19S cap.

Location and roles of some constituent proteins have been established.

The outermost "lid" of the 19S cap is a ring of eight proteins.

The innermost "base" of the 19S cap includes a ring of six members of the AAA family of ATPases.

These are chaperones that carry out ATP-dependent unfolding of proteins prior to their being threaded into the core complex.

It is typical of AAA ATPases that they assemble into hexameric rings

Isopeptidases in the 19S cap disassemble ubiquitin chains. Ubiquitins can then be re-used.

At least one deubiquitylating enzyme is located between the lid & base regions of the 19S cap.

A simpler archaebacterial cap complex called PAN consists only of a hexameric ring of AAA ATPases, comparable to the base of the 19S regulatory cap.

PAN, in the presence of ATP, was found to cause opening of a gate at the end of the 20S proteasome through which an unfolded protein could enter.

The base of the 19S cap is assumed to do the same, although high resolution structural evidence is still lacking.

A high resolution structure has been achieved for a complex of the 20S proteasome with an 11S regulatory cap.

The 11S cap is a heptameric complex of a protein PA28.

The 11S cap allows small, non-ubiquitinated proteins & peptides to pass into the core complex.

This does not require ATP hydrolysis.

The 11S cap is dome-shaped, with a wide opening at each end.

20 S Proteasome (yeast), with

11S Regulator (Trypanosome)

two views

PDB 1FNT

Binding of the 11S cap alters conformation of N-terminal domains of core complex α subunits, opening a gate into the proteasome core. For images see a website.

There have been many structural studies of isolated core complex with 19S or 11S cap.

Formation of mixed complexes of proteasome core sandwiched between 19S & 11S caps has been shown by EM.

20 S Proteasome (yeast), with

11S Regulator (Trypanosome)

two views

PDB 1FNT

In vivo a 19S cap may recognize, de-ubiquitinate, unfold & feed proteins into a core complex, while an 11S cap at the other end may provide an exit path for peptide products. See an animation.

Compare with Chime the yeast 20S proteasome core complex, with and without the 11S regulatory cap.

11S-20S-11S complex

20 S Proteasome

α β β α