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Protein Targeting and Degradation. David Shiuan Department of Life Science Institute of Biotechnology Interdisciplinary Program of Bioinformatics National Dong Hwa University. Protein Targeting and Degradation. Targeting mechanism involved a peptide signal sequence

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Protein targeting and degradation
Protein Targeting and Degradation

David Shiuan

Department of Life Science

Institute of Biotechnology

Interdisciplinary Program of Bioinformatics

National Dong Hwa University

Protein targeting and degradation1
Protein Targeting and Degradation

  • Targeting mechanism involved a peptide signal sequence

  • SRP (signal recognition particle) – move to ER then Gorgi  lysosome, plasma membrane, transport vesicles

  • Amino-terminal sequence – mitochondria, chloroplast, bacterial export

  • Internal signal sequence – nucleus proteins

  • Degradation – ubiquitin-dependent proteolysis at proteasome

Glycosylation plays a key role in protein targeting

In the ER leumen, signal sequence is removed, protein are

folded, disulfide bond formed and many are glycosylated

A donor molecule brings

the oligo to Asn

Tunicamycin mimics UDP-acetylglucosamine

and block the first of oligo synthesis

Synthesis of the core oligosaccharide of glycoprotein

Pathway taken by proteins destined for lysosomes,

the plasma membrane, or secretion

Phosphorylation of mannose residues on lysosome-targeted enzymes

(hydrolase, the best understood) in Golgi  target to lysosome

Targeting of nucleus proteins enzymes

Ribosomal proteins are imported into nucleus and assembled into 60s and 40s. The complete subunits are transported back to cytosol. Nuclear proteins synthesized in cytosol and imported via importin into nucleus. NLS - nucleus localization signal

Sanning EM of nucleus surface, showing enzymes

numerous nuclear pores

Signal sequences that target proteins to enzymesdifferent

locations in bacteria


+ charge

Model for protein export in bacteria enzymes

Soluble chaperon proteinSecB;

membrane associated SecA(receptor and translocating ATPase)

SecYEG form translocating complex

Cells import proteins by enzymesreceptor-mediated endocytosis

Some Proteins (LDL low density lipoprotein, transferrin, peptide

hormone and circulating proteins) destined for degradation – bind to

endocytic receptors concentrated on the protein lattice : clathrin



Input Sequence enzymes

QUERY (348 aa)


TargetP enzymes

  • TargetP 1.1 predicts the subcellular location of eukaryotic proteins

  • The location assignment is based on the predicted presence of any of the N-terminal presequences:

    1. Chloroplast transit peptide(cTP)

    2. Mitochondrial targeting peptide(mTP)

    3. Secretory pathway signal peptide(SP)

Targetp predictions of unannotated a thaliana and h sapiens sequences
TargetP enzymespredictions of unannotated A. thaliana andH. sapiens sequences

Death by proteases
Death by enzymesProteases

Ubiquitin 2004 nobel prize in chemistry
Ubiquitin enzymes2004 Nobel Prize in Chemistry

  • Cells are continually building proteins, usingthem for a single task, and then discarding them.

  • Signaling or controlling proteins (eg. transcription regulators and the cyclins) - lead very brief lives, carrying their messages and then being thrown away.

  • Specialized enzymes - built just when they are needed, allowing cells to keep up with their minute-by-minute synthetic needs.

  • The approach may seem wasteful, but it allows each cell to respond quickly to constantly changing requirements.

Ubiquitin 2004 nobel prize in chemistry1
Ubiquitin enzymes2004 Nobel Prize in Chemistry

  • The small protein ubiquitin plays a central role. Ubiquitin attached to obsolete proteins to dissemble.

  • Ubiquitin is found in all eukaryotic cells and in cells throughout your body.

  • The Nobel Prize in Chemistry 2004 was awarded to the Aaron Ciechanover, Avram Hershko , Irwin Rosewho discovered its essential function in 1980.

Human ubiquitin nmr structure
Human Ubiquitin NMR Structure enzymes

mqifvktltg ktitleveps dtienvkaki qdkegippdq qrlifagkql edgrtlsdyn iqkestlhlv lrlrggakkr kkksyttpkk nkhkrkkvkl avlkyykvde ngkisrlrre cpsdecgagv fmashfdrhy cgkccltycf nkpedk156 aa,8.5 kD

Eukaryotic enzymesProteosome

Protein degradation at lysosome
Protein Degradation at enzymesLysosome

Sumo small ubiquitin like modifier
SUMO enzymes(Small Ubiquitin-like Modifier)

  • SUMO is member of ubiquitin and ubiquitin - like superfamily

  • Most SUMO proteins contain tetrapeptide motif B-K-x-D/E(B: a hydrophobic residue, K: lysine and D/E: an acidic residue)

  • Substrate specificity is derived from ubc9 and the respective substrate motif

Sumo and ubiquitin
SUMO and Ubiquitin enzymes

  • Alignments of ubiquitin and SUMO-1 indicate only 18% identical in amino acid sequence

  • These two proteins have remarkably similar secondary and tertiary structures

  • Unlike the ubiquitin system, which primarily targets substrate proteins to the proteasome, SUMO-1 conjugation has diverse cellular functions

Sumo small ubiquitin like modifier1
SUMO enzymes(Small Ubiquitin-like Modifier)

  • Unlike ubiquitin modification which targets proteins for degradation, SUMOylation

    1. increases a protein's lifetime.

    2. change a protein's location in the cell

  • SUMO modification of proteins has many functions. Among the most frequent and best studied are protein stability, nuclear-cytosolic transport, transcriptional regulation (mostly transcriptional repression).

Sumo small ubiquitin like modifier2
SUMO enzymes(Small Ubiquitin-like Modifier)

Human SUMO1: 101 aa; 11.6 kD kD; PDB1A5R

Steven shoei lung li
李 水 龍 enzymes(Steven Shoei-Lung Li)高雄醫學大學醫學研究所 講座教授

Daxx is a shuttle protein participating in biological functions on various subcellular localizations.Human Fas death domain-associated protein (Daxx) is a 740-amino acids protein mainly localized in nucleus. It functioned as a transcriptional repressor when associated with chromatin in nucleus.