r pharmaceuticals d. ambrosius; slide 1 proteine/ramc-presentation-9-01 various strategies used to...
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D. Ambrosius; slide 1 Proteine/RAMC-Presentation-9-01
Various Strategies Used to Obtain Proteins for
Crystallization and Biostructural Studies
Dorothee Ambrosius, R. Engh, F. Hesse,
M. Lanzendörfer, S. Palme, P. Rüger
Roche Pharmaceutical Research, Penzberg
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D. Ambrosius; slide 2 Proteine/RAMC-Presentation-9-01
Protein Classes
extracellular proteins
plasma protein concentration: 70 mg/ml
•transporter (albumin)•immuno-globulin•enzymes, enzyme-inhibitors•coagulation factors,
lipoproteins
protein characteristics/
stability •often monomeric proteins•contain disulfide bridges•protease resistant •stable fold
intracellular proteins
cytoplasma and organelles: 300-800 mg/ml
•multi-enzyme complexes•enzyme cascades•transcription complexes•focal adhesion/integrins•cytoskeleton, heat-shock
proteins
protein characteristics/stability
•often multimeric complexes•no disulfide bridges•very labile proteins; short
half-life •require stabilization:
interaction with other proteins
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D. Ambrosius; slide 3 Proteine/RAMC-Presentation-9-01
Protein Sources/Expression Systems
Expression system Advantages Examples Structure
E. coli soluble inclusion bodies
rapid cloning/ expression high yield isotope labeling possible
G-CSF; IBsPEX, IBsMIA, IBsIL-16, solubleMDM2, IBsPKA, soluble
NMRX-rayNMRNMRX-ray, NMRX-ray
Baculo/Insect cells
expression of active protein modifications
most Tyr kinases(RTK: IRK,c-met,SRC, LCK, etc.)Ser/Tyr kinasese.g. cdks, cAPK
X-ray/NMR
X-ray/NMR
RTS: E. coli parallel expression high throughput proteomics
see talk & posterJ . Stracke
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D. Ambrosius; slide 4 Proteine/RAMC-Presentation-9-01
Biological Function of Cytokines
G-CSFNeutrophils
Source: Herrmann/Lederle
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D. Ambrosius; slide 5 Proteine/RAMC-Presentation-9-01
Development Goals for Recombinant Human G-CSF
native sequence: without additional N-terminal Met
reduction of immunogenicity risk
potency: equal to Amgen´s Neupogen
low production cost: E. coli as host strain in vitro refolding
consistent quality: robust downstream scheme analytical methods
established
Hu-G-CSF: hematopoietic growth factor (174 aa)2 S-S bridges, one single Cys 17
Clinical use: patients with neutropenia: after chemotherapy improved haemotopoietic recovery
reduction of infectious risks
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D. Ambrosius; slide 6 Proteine/RAMC-Presentation-9-01
Genetic engineering of an economic downstream process
Strategy: Development of Recombinant Human G-CSF
Fusion Peptide
high level expression
improved refolding
efficient separation of cleaved and uncleaved protein
optimized cleavage site
Human G-CSFFusion Peptide
Protease
specific
efficient
recombinant
consistent quality
rhG-CSF
low production costs
without N-terminal Met
equal potency/efficiency
consistent quality
improved quality
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D. Ambrosius; slide 7 Proteine/RAMC-Presentation-9-01
Cleavage
-
++
++
+
+++
++
+++
Expression
(%)
100
30
100
100
25
10
100
Renaturation
(%)
10
20
20
50
90
80
80
Fusion Peptide
Met G-CSF
Met-Thr-Pro-Leu G-CSF
Met-Thr-Pro-Leu-His-His G-CSF
Met-Thr-Pro-Leu-Lys-Lys G-CSF
Met-Thr-Pro-Leu-Glu-Glu-Gly G-CSF
Met-Thr-Pro-Leu-Glu-Glu-Gly-Thr-Pro-Leu G-CSF
Met-Lys-Ala-Lys-Arg-Phe-Lys-Lys-His G-CSF
Cleavage Site (Pro-Arg-Pro-Pro)
Optimization of rhG-CSF Fusion Proteins
Source: EP 92102864.3 ; DE 4104580
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D. Ambrosius; slide 8 Proteine/RAMC-Presentation-9-01
Refolding Kinetics of rhG-CSF Fusion Protein
Solubilization6,0 M Gdn/HCl, pH 8.0 100 mM Tris,/HCl100 mM DTE 1 mM EDTATemperature: RTc= 20 mg/ml
Renaturation0,8 M Arginine/HCl100 mM Tris/HCl, pH 8.00.5 / 0.5 mM = GSH / GSSG10 mM EDTATemperature: RTProtein conc. 0.5 -1.0 mg /mlTime: 1- 2 hours
native
denat.
Source: EP 92102864.3 ; DE 4104580
Pellet SN
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D. Ambrosius; slide 9 Proteine/RAMC-Presentation-9-01
Role of p53 in cell cycle control:“guardian of the genome”
latent p53 active p53
activationaccumulation
h
stress factorsor oncogenic proteins mdm2
cell type level of p53 extent of DNA damage genetic background
cell cycle arrest: repair defective genes
apoptosis: kill harmful deregulated cells
negative feedback loop !!
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D. Ambrosius; slide 10 Proteine/RAMC-Presentation-9-01
Engineering of MDM2 for biostructural purposes
The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor.
Goal: Improvement of biophysical properties of HDM2
(human MDM2) by “crystal engineering”
Known: XDM2 (Xenopus laevis MDM2): - better solubility, suitable for biostructural
investigations - wrong species and reduced binding affinity HDM2 (25-108): - high binding affinity to p53 peptide - prone to aggregation, not suitable for
biostructural studies
Strategy: use XDM2 as scaffold and humanize its p53-binding site
introduce point mutations in HDM2 to increase solubility
remove flexible ends at both sides of structured p53-binding
region
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D. Ambrosius; slide 11 Proteine/RAMC-Presentation-9-01
Figures taken from Kussie et al., Science 274 (1996) 948.
Structure of MDM2/p53-peptide complex
Resolution X-ray structures:
human MDM2/p53: 2.6 Å Xenopus MDM2/p53: 2.3 Å
p53
mdm2
17-29
26-108
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D. Ambrosius; slide 12 Proteine/RAMC-Presentation-9-01
MDM2 variants created by protein engineering
human MDM21 26 108 125 185 240 300 330 350 440 491
p53 binding
HDM2 (17-125) X-ray published
HDM2 (25-108) X-ray
HDM2 (25-108) mutants X-ray
XDM2 (13-119) X-ray published, NMR
XDM2 (13-119) LHI NMR, X-ray
XDM2 (21-105) LHI X-ray
I50L P92H
L95I
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D. Ambrosius; slide 13 Proteine/RAMC-Presentation-9-01
Step 15N-labeled non-labeled (LB)
(minimal medium)
Fermentation 10 L 10 L
E. coli (wet weight) 90 g 600 g
Inclusion bodies (w.w.) 3.5 g 85 g
IB total protein content 1.3 g 30 g
MDM2 (50-70% yield) 0.8 g 18 g
Renaturation (~25%) 0.2 g 4.5 g
MDM2 (Purification) 0.16 g 3.6 g
Final product 0.1 g 2.2 g
Human MDM2: Yields & Upscale
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D. Ambrosius; slide 14 Proteine/RAMC-Presentation-9-01
Crystals of hXDM/peptide
Some crystals comply withcorporate identity rules
hXDM2/p53 peptide
Patience might be rewarded
Conditions: 0.1 M MES pH 6.2, 4.0 M NaOOCH 3 days after micro seeding at 13 °C 4 months at 4 °C
hXDM2/phage-peptide
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D. Ambrosius; slide 15 Proteine/RAMC-Presentation-9-01
I: Ser/Thr-Kinase Families Subfamilies/StructuresIa: Non Receptor Ser/Thr-Kinase familiy
cAPK: cAMP dependent protein kinase PKA, PKB, PKCcdks: Cyclin dependent kinase cdk2, cdk4, cdk6
MAPK: Mitogen activated protein kinase Erk, Erk2, Jnk, p38(,,)
MLCK: Myosine light chain kinase Twitchin, TitinCK: Casein kinase Ck-1, Ck-2PhK: Phosphorylase kinase (tetramer: , , , ) PhK
CaMK: Calcium/calmodulin dependen kinase CaMK
Ib: Receptor Ser/Thr-Kinase familyTGF1-R Kinase TGF1-ßRII: Tyr-Kinase Families
Subfamilies/StructuresIIa: Non receptor Tyr-Kinase family
SRC-family SRC, c-SRC, CSK, HCK
LCK: humam lymphocyte kinase: LCK, c-Abl
IIb: Receptor Tyr-Kinase familyEGFR-family: EGFR, ErbB2-4InsR-family IRK, IGF1R, IRRPDGFR-, CSFR-, Met-, Ron-familiy, FGF1-R, VEGFR-KEphA1….EphB1, Trk A, B, C, etc.
Protein Kinase Families (incomplete list)
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D. Ambrosius; slide 16 Proteine/RAMC-Presentation-9-01
PKA: 2 Å X-ray StructureFurther details for crystallization see poster of Ch. Breitenlechner
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D. Ambrosius; slide 17 Proteine/RAMC-Presentation-9-01
PKA: cyclic AMP Dependent Protein KinaseExpression: E. coli, solubly expressed in phosphorylated,
active form 20-50 mg purified protein (10 l fermentation)
Purification: affinity chromatography with inhibitory peptide (PKI)
mimicking substrate binding Ref.: R. Engh & D. Bossemeyer, Adv. Enz. Reg.
41, 2001
Binding Affinity: 20 nM of inhibitory peptide (PKI)
Protein: MW: 35 kDa Ser/The kinase monomeric 2 domain (C- and N-lobe) protein
without additional regulatory domains (SH2, SH3, etc.) extended structured C- and N-Terminus, which
possibly stabilizes the overall kinase structure
Ideal model: Ser/Thr protein kinase inhibitor studies generation of other Ser/The kinase (e.g. PKB, Aurora) structures
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D. Ambrosius; slide 18 Proteine/RAMC-Presentation-9-01
Major Components of the Cell Cycle Machinery
mitogen induced progression through the cell cycle requires timely controlled activation of different cyclin-dependent kinases (CDKs)
cyclins (D, E, A, B), periodically expressed throughout the cycle, are the regulatory subunits of CDKs (activation)
members of the p16(INK4)- and p21(KIP)-protein family inhibit CDKs and CDK-cyclin complexes and arrest inappropriate cell cycle progression
G1
S
M
G2
Cell Cycle
G0
CDK2
cyclin A
CDC2
cyc. A/B CDK2
cyclin E
CDK4/6
cyclin D
CDC2
cyclin BMitosis
DNA Replication
INK4
Kip/Cip
Kip/Cip
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D. Ambrosius; slide 19 Proteine/RAMC-Presentation-9-01
Cyclin Dependent Kinases: CDK2 and CDK4/6
N. Pavletich, JMB 287, 821-828, 1999
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D. Ambrosius; slide 20 Proteine/RAMC-Presentation-9-01
Structural investigations of cdks (incomplete list) Structure Method Protein Expression system Referencep16p16
Folding studiesNMR
p16GST-p16
E. coli (IBs)E. coli (soluble)
Tang, 1999Byeon, 1998
p18
p18
NMR
X-ray: 1.95 Å
GST-p18
p18
E. coli (soluble)
BL21 (soluble)
Yuan, 1999
Venkataramani, 1998p19 NMR p19 E. coli (IBs) Baumgartner, 1999p19/cdk6, p16/cdk6
p19/cdk6
X-ray: 2.8 ÅX-ray: 3.4 Å
X-ray: 1.9 Å
cdk6GST-p19/p16
p19GST-cdk6
Baculo/insect cellsE. coli (soluble)
E. coli (soluble)Baculo/insect cells
Russo, 1998
Brotherton, 1998p18/cdk6/cycK X-ray: 2.9 Å GST-cycK
GST-p18cdk6
E. coli (soluble)E. coli (soluble)Baculo/insect cells
Jeffrey, 2000
cycA-cdk2cycA-ATPS-cdk2
X-ray: 2.3 ÅX-ray: 2.6 Å
cdk2cycA:
Baculo/insect cellsE.coli (soluble)
Jeffery, 1995Russo, 1996
cycA-ckk2-p27 X-ray: 2.3 Å p27 E. coli (soluble) Russo, 1996No strcuture GST-cdk4; cdk4 Baculo/insect cellscdk4 (mimic cdk2) X-ray cdk2, engineered
cdk4 pocketBaculo/insect cells Ikuta, 2001
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D. Ambrosius; slide 21 Proteine/RAMC-Presentation-9-01
Summary
Proteins show a tremendous diversity with respect to - biological function and cellular location- structure, conformation and stability
E. coli is a very attractive expression system with respect to time, yield, costs and production of isotope labeled proteins
Application of in vitro protein refolding is a powerful tool to generate native structured proteins and should be considered as alternative
The protein kinase family is regulated by multiple mechanism and show conformational diversity of catalytic cores; high degree of flexibility
- e.g. IRK(3P) and LCK (Tyr kinases) show structural homology to
cAPK and cdks (Ser/Thr kinases)
Until today, most kinases successfully applied for structural research are expressed as active P--enzyme in baculo/insect cells; exception PKA
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D. Ambrosius; slide 22 Proteine/RAMC-Presentation-9-01
Acknowledgement
PEX: S. Kanzler, H. Brandstetter (MPI)
MDM2: G. Saalfrank, Ch. Breitenlechner (MPI), U. Jacob (MPI)
IL-16: B. Essig , P. Mühlhahn (MPI), T. Holak (MPI)
MIA: G. Saalfrank, C. Hergersberg, R. Stoll (MPI), T. Holak (MPI)
cAPK: G. Achhammer, E. Liebig, Ch. Breitenlechner (MPI)
cdks: H. Hertenberger, J. Kluge, U. Jucknischke
G-CSF: S. Stammler, M. Leidenberger, U. Michaelis, T. Zink (MPI), T. Holak (MPI)