Biosynthesis and degradation of proteins

Bruno Sopko

Content

• Proteosynthesis• Post-translation processing of proteins• Protein degradation

Proteosynthesis

• Aminoacyl-tRNA formation• Iniciation• Elongation• Termination

Aminoacyl-tRNA formationAmino acid + ATP ↔ Aminoacyl-AMP + PPi

Aminoacyl-AMP + tRNA ↔ Aminoacyl-tRNA + AMP

• Each amino acid has „its own“ tRNA and aminoacyl-tRNA synthetase (ARS)

• Reactions are cytosolic• Errors are corrected by specific correcting enzymes• ARS have other enzyme activity (other signaling molecule?)

Other ARS functions

Proteosynthesis Iniciation

Elongation

Termination

Post-translation processing of proteins

• Secondary structure and role of the chaperons• Proteolytic modifications• Glycosylation• Other modifications (hydroxylation,

phosphorylation, acetylation, methylation, carboxylation)

Protein transfer after translation

Contranslational translocation

Contranslational translocation –transmembrane proteins

Transmembrane proteins - examples

• Type I – glycophorin, LDL receptor, influenza HA protein, insulin receptor, growth hormone receptor …

• Type II – transferrin receptor, influenza HN protein, Golgi sialyltransferase, Golgi galactosyltranferase …

• Type III – cytochrome P450 …• Type IV – G-protein, glucose receptors (GLUT 1

…), connexin, voltage gated Ca2+ channel …

Secondary structure

Secondary structure –HSP70 chaperon cycle

Secondary structure – GroEL/GroES system

Secondary structure – overview

Protein disulfid isomerase (PDI) and peptidyl prolyl cis-izomerase

PPI:

Proteolytic modification - insulin

N-Glycosylation

Other modifications

• O-glycosylation• Hydroxylation (hydroxyproline, hydroxylysine)• Methylation (mono- , di- and even trimethyllysine)• PHOSPHORYLATION• Carboxylation (γ-carboxyglutamate, vitamin K,

fibrinogen)• Acetylation• ……..

Protein degradation

• Proteases• Protein degradation systems• Ubiquitin and proteasome• Activation of proteases• Protease inhibitors

Proteases

• Serine proteases (trypsin, chymotrypsin, elastase ….)

• Aspartate proteases (pepsin, some proteases found in lysosomes, renin, HIV-protease …)

• Metalloproteases (carboxypeptidases, various matrix metalloproteases …)

• Cysteine proteases (papain, cathepsins, caspases, calpains …)

Protein degradation systems

• Vacuolar (lysosomes, endosomes, ER, …)

• Ubiquitin pathway (proteasome)

Ubiquitin pathway

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 compartment within a cell or to the extracellular milieu.

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

Protease inhibitors• IAPs are proteins that block apoptosis by binding to and 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 Zn2+.

• Cystatins are inhibitors of lysosomal cathepsins. Some of these (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 are widely distributed proteins that utilize 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.

• Non-specific: α2-macroglobulin

Fate of the protein

Literature

• Marks´ Basic Medical Biochemistry, A Clinical Approach, third edition, 2009 (M. Lieberman, A.D. Marks)

• B. Wilkinson, H.F. Gilbert / Biochimica et Biophysica Acta 1699 (2004) 35–44

• F. Ulrich Hartl, Andreas Bracher & Manajit Hayer-Hartl, Molecular chaperones in protein folding and proteostasis, Nature 475 (2011)