the three classical mechanisms for protein folding (fersht and daggett, cell 108, 573-582, 2002)...
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![Page 1: The three classical mechanisms for protein folding (Fersht and Daggett, Cell 108, 573-582, 2002) (hierarchial)](https://reader036.vdocuments.us/reader036/viewer/2022062407/56649d4b5503460f94a28f13/html5/thumbnails/1.jpg)
The three classical mechanisms for protein folding
(Fersht and Daggett, Cell 108, 573-582, 2002)
(hierarchial)
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Energy landscape of protein folding
rugged landscape: multi-state folding
A rugged landscape with kinetic traps, energy barriers, and some narrow throughway paths to native. Folding can be multistate
idealized funnel landscape
(K. Dill)
As the chain forms increasing numbers of intrachain contacts, and lowers its internalfree energy, its conformational freedom is also reduced
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The folding energy landscape of a protein
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Goodsell 1991, TiBS(16): 203-206
Macromolecular crowding
(approx. 300 mg/ml)
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Major chaperones and their interactions with substrates
?
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The GroEL-GroES chaperone machine
GroEL proteins(subunits)
GroEL complex (double ring with 7 GroEL/ring)
Active complex
GroES complex (single ring with 7 GroES/ring)
GroES proteins(subunits)
ATP
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Protein folding by GroEL and GroES
GroELGroEL with
unfolded polypeptideGroEL:GroES with
enclosed polypeptide
The folding activity is ATP-dependent!
U. Hartl
∆t = 15 sec
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H. Saibil
Conformational changes induced by nucleotide and GroES(model based on cryo electron microscopy)
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Hsp70
Cellular roles of Hsp70 chaperone systems
aggregation prevention
disaggregation
refolding
degradation
stress-related functions
de novo folding
translocation
assembly and disassembly
regulation of activity
regulated degradation
house-keeping functions
wide range of substrate conformers
unfolded - folding intermediates - aggregated - native
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Functional cycle of DnaK
ATP
ADP + P
ATP
ADP·P
Unfolded protein substrate
ATPase domain Substrate binding domain
DnaJGrpE
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Substrate binding domain of DnaK
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activity & stability controlof folded proteins(Hsp70 & Hsp90)
regular folding pathways
quality control of misfolded proteins
chaperones
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Hsp70-Hsp90 activation cycle
ligandactive
Hsp90
client
Hsp70
Function of cochaperones:
> Targeting factor> Adaptor> Regulator Hsp40
Hip
Bag-1
Hop
Aha1
p23
immunophilinscdc37
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The Hsp70-Hsp90 chaperone machine:a regulator for signal transduction and cell cycle
Mayer & Bukau 1999 Curr. Biol.
c-Src control of cell proliferation
plasma membrane90
37
stressHSF
nucleus
activation ofgene expression
steroid
SHRnucleus
Cdk4
cyclin D
control of G1-progression
nucleus
hemeP
eIF-2-kinase control of translation
initiation
cytosol
Ras
Raf-1activation ofMAP-kinase pathway
plasmamembrane
P
9037
9037
9037
9037
90
9023
inactive active
activation ofgene expression
Hsp70Hsp90
>120 different targets!!!!
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Transcription factorsSteroid hormone receptors: AR, ER, GR, MR, PROther nuclear receptors: AhR, RARHeme activator protein (Hap1)HSF-1Hypoxia-inducible factor-1aMTG8 myeloid leukemia proteinp53SimSV40 large T antigenTumor promotor-specific binding proteinv-erbA
PolymerasesTelomeraseHepatitis B virus reverse transcriptaseDNA-polymerase
3-Phosphoinositide-dependent kinase-1AktAurora BBcr-AblCalmodulin-regulated eEF-2 kinaseCasein kinase IIChk1c-MosDeath domain kinase RIPFlt3Focal adhesion kinaseGRK2Ire1IB kinases ,,,Kinase suppressor of ras (KSR)MEK (MAP kinase kinase)MEKK1, MEKK3Mik1MOK, MAK, MRKPhosphatidylinositol 4-kinasePim-1Polo mitotic kinaseSevenless PTKTAK1TBK1trkBWee1, Swe1
KinasesSrc-family kinases: Fps, Fes, Fgr, v-Src, c-Src, Hck, p56lck, YesCycline dependent kinases: Cdc2, Cdk4, Cdk6, Cdk9Receptor tyrosin kinases: EGFR, ErbB2, IGF-R, Insulin receptor,PDGFR, VEGFR2Raf family kinases: v-Raf, c-Raf, B-Raf, Gag-Mil, Ste11eIF-2 kinases: HRI, Gcn2, Perk, PKR
Hsp70/Hsp90 clients
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OthersAminoacyl t-RNA synthetaseApaf-1Apoprotein BAtrial natriuretic peptide receptorBidCalponinCentrin/centrosomeCna2 (catalytic subunit of calcineurin)CFTRCtf13/Skp1 component of CBF3Cytoskeletttal proteins: actin, tubulin, myosineNOS, iNOS, nNOS Erythrocyte membrane protein (Plasmodium falciparum)Fanconi anemia group C proteinG protein G0, G12Guanylate cyclase (-subunit)HETE binding complexHistones H1, H2A, H2B, H3, H4Lysosomal membraneMacrophage scavenger receptorMdm2MMP2MTG8NB-LRR proteins RPM1 and RPS2Neuropeptide Y
P2X7 purinergic receptor Pancreatic bile salt-dependent lipasePB2 subunit of influenza RNA pol.Protease-activated receptor 1 (PAR-1)ProteasomeRab-GDIRal-binding protein 1Reovirus protein s1SKP2 complexiessurvivinTau proteinThiopurine S-methyltransferaseThyroglobulinTLR4/MD-2 complexVaccinia core protein 4a
http://www.picard.ch/downloads/downloads.htmWegele, et al. 2004 Rev. Physiol. Biochem. Pharmacol.
Hsp70/Hsp90 clients
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E-Cadherin
Frizzo
ed
IGF
-R EG
FR
Cyt
oki
ne-
R
Fas
Wnt
Cell Adhesion
Survival Receptor
Growth Receptor Cytokines
Death Factor
Disheveled
GSK-3
APC
-Catenin
-Catenin
-Catenin/LEF
PI3K
PDK1
AKT
IKK
IB
NFB
Src Grb2SOS
RAS
RalRaf
Cdc42
MEK
Erk
Elk
JAKs
Stat3,5
Bcl2/Bax FADD
CytC Casp 8
Apaf-1/CytC/Casp 9
Casp 3
Gene expression
Zhang & Burrows 2004 J. Mol. Med.
Signal transduction pathways related to tumor progression
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E-Cadherin
Frizzo
ed
IGF
-R EG
FR
Cyt
oki
ne-
R
Fas
Wnt
Cell Adhesion
Survival Receptor
Growth Receptor Cytokines
Death Factor
Disheveled
GSK-3
APC
-Catenin
-Catenin
-Catenin/LEF
PI3K
PDK1
AKT
IKK
IB
NFB
Src Grb2SOS
RAS
RalRaf
Cdc42
MEK
Erk
Elk
JAKs
Stat3,5
Bcl2/Bax FADD
CytC Casp 8
Apaf-1/CytC/Casp 9
Casp 3
Gene expression
Zhang & Burrows 2004 J. Mol. Med.
Signal transduction pathways related to tumor progression
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ClpB structure
N-terminal domain (NTD)
1st ATPase (D1)
2nd ATPase (D2)
middle domain (M)
Lee et al. Cell 2003
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ClpB Protomers form hexameric rings (in ATP)
top side
3D model
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Mechanism of ClpB/KJE-mediated protein disaggregation
Weibezahn et al., Cell 2004
ClpB
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Protein aggregates in neurodegenerative diseases
Plaques and tangles Lewy bodies
Amyloid plaques
Aggregates
Intranuclear inclusions
Alzheimer’s Parkinson’s
PolyQ diseases Prions
Amyotrophic lateral sclerosis
E. Nollen
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Polyglutamine aggregation
glutamine residue
other residue
Disease > 35 residues
Wild type < 35 residues
Aggregate
Folded protein
E. Nollen
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Caenorhabditis elegans
*lives in the ground *size 1mm*has 959 cells*has a transparent body, observable in light microscope*life span: 20 days
Perfect tool: - easy genetic manipulation
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C. elegans, a model system to study Dementia
GFPQn
Protein aggregates: Huntington
Promotor
Unc-54
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Length dependent aggregation of polyQ-YFP in C. elegans
GFPQn
Unc-54
Morley et al., 2002
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Q19-expressing animals Q82-expressing animals
0
20
40
60
80
100
Morley&Morimoto
PolyQ of a length of n≥35 cause:- protein aggregation- drastic impaired mobility
3-4 days old C. elegans
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Luciferin + ATP + O2 Oxoluciferin + CO2 Luciferase
Light emission
Firefly Luciferase