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Unnatural Protein Unnatural Protein Engineering:Engineering:Biochemical and Medicinal Biochemical and Medicinal ApplicationsApplications
Youngha RyuYoungha Ryu
Department of Chemistry Department of Chemistry Texas Christian UniversityTexas Christian University
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Methods of Protein Modification
• Chemical modification of the reactive side chains
• Total chemical synthesis
• Ligation of synthetic peptide to a
truncated protein
• In vitro transcription/translation
• Expression in living organisms
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Protein biosynthesis machineryDNA
mRNA
acylated tRNA
peptide chain
ribosome
H2N
mRNA
tRNA aa~AMP
Aminoacyl-tRNA synthetase (aaRS)
R
NH2
O
O
R
NH2
O
O
EF-Tu
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“Standard” Genetic Codes
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PNAS 48, 1086 (1962)
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Suppressor tRNAs
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Nonsense Suppressors in E. coli
Suppressor Type Anticodon change tRNA Gene Efficiency
supE Amber CUG --> CUA tRNAGln glnV 0.8-20%
supP Amber CAA --> CUA tRNALeu leuX 30-100%
supD Amber CGA --> CUA tRNASer serU 6-54%
supU Amber CCA --> CUA tRNATrp trpT
supF Amber GUA --> CUA tRNATyr tyrT 11-100%
supZ Amber GUA --> CUA tRNATyr tyrU
supB Ochre UUG --> UUA tRNAGln glnU
supL Ochre UUU --> UUA tRNALys lysT
supN Ochre UUU --> UUA tRNALys lysV
supC Ochre GUA --> UUA tRNATyr tyrT
supM Ochre GUA --> UUA tRNATyr tyrU
glyT Opal UCC --> UCA tRNAGly glyT
trpT Opal CCA --> UCA tRNATrp trpT 0.1-30%
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In vitro System
P. G. Schultz et al. Science 1989, 244, 182
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Incorporation of unnatural amino acids into proteins in living organisms
• Efficient transport or biosynthesis of unnatural amino acids
• Unique codons (nonsense, four base, etc)
• tRNA/aminoacyl-tRNA synthetase pair that is orthogonal to the endogenous system
• Directed evolution of the aminoacyl-tRNA synthetase to selectively charge the orthogonal tRNA with an unnatural amino acid
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An “Orthogonal” pair from M. jannaschii
• M. jannaschii tRNATyr is orthogonal to E. coli synthetases
• M. jannaschii TyrRS is orthogonal to E. coli tRNAs
• M. jannaschii TyrRS has minimal interaction with anticodon
• M. jannaschii TyrRS has no proofreading activity
AOH
CCAGGCCGCC
pCCGGCGG
C G G C C
G C U G G
U U G
A A CCGCCU
GCGGA
T AA
A
CU UC
GG
UA
UACAG
G
GA G
CU
CU A
G
A
3'
5'
G
CA
G U
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Directed Evolution of Mj TyrRS
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Selection strategy
Wang, Brock, Herberich & Schultz Science 292, 498, (2001)
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Synthetases for Unnatural amino acids
H2NOH
OH2N
OH
O
O
Turner, Graziano, Spraggon & Schultz J. Am. Chem. Soc., 127, 14976 (2005) Proc. Natl. Acad. Sci., 103, 6483 (2006)
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Expanded Genetic Code in E. coli
H2NOH
O
O
H2NOH
O
H2NOH
O
O
H2NOH
O
O
H2NOH
O
I
H2NOH
O
NH2
H2NOH
O
N3
H2NOH
O
O
H2NOH
O
CO2H
H2NOH
O
C
H2NOH
O
NO2
H2NOH
O
B(OH)2
H2NOH
O
O
H2NOH
O
OH
OH
H2NOH
O
NN
H2NOH
O
O
NO2
SO
O
O-
H2NOH
O
N
H2NOH
O
N
N
H2NOH
O
CF3
NN
H2NOH
O
OO OH
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Sub-optimal yields of proteins in E. coli
• Non-versatile two plasmid system? – Integration of the synthetase and tRNA genes into a single plasmid, which is compatible with most E. coli expression vectors and strains
• Intrinsic low efficiency due to the competition with termination? – High suppression efficiency is achieved by naturally occuring non-sense suppressors (e.g. XL1-Blue)
• Inefficient transcription and processing of tRNA? – New promoter and flanking sequence
• Inefficient expression of aminoacyl-tRNA synthetase? – New promoter
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New Mj tRNA expression cassette
ACCAGGCCGCC
ACCAGGCCGCC
CCGGCGG
CCGGCGG
C G G C C
G C U G G
U U G
A A CCGCCU
CGCCU
GCGGA
GCGGA
U
A A
A
CU UC
GG
UA
UACAG
GG
A G
C
UC U A
A
A
3'
5'
G
CA
GC
U
A A U U C G A A A A G C C U G C U C
U
A
A
CU U U U U C G G A C G A GU
RNAse P RNAse E
RNAse T, PH etc
RNAse III
JYTRN
Terminator
• E. coli prolyl tRNAs have C1-G72 pair, which is major identity determinant of MjtRNA – Important context for the precise tRNA processing
• proK tRNA is most frequently used in E. coli
• FIS enhances tRNA transcription
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Mutant glnS promoter enhances the synthetase expression
AAAAAACTAACAGTTGTCATTGTCAGCCTGTCCCGCTTATAAGATCATACGCCGTTATACGTT
AAAAAACTAACAGTTGTCAGCCTGTCCCGCTT-TAATATCATACGCCGTTATACGTT
-35 region -10 region +1
WT
Mutant
BpaRS
WT Mutant
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Asp286Arg (D286R) substitution enhances tRNA(CUA) binding affinity
Asp286
His283
G34
Phe261
Asp286 Arg286
G34C34 C34
TyrRS (WT) – tRNATyr (WT)
Asp286
TyrRS (WT) – tRNATyr (CUA) TyrRS (D286R) – tRNATyr (CUA)
Km= 0.35 Mkcat= 0.19 s-1
kcat/Km (relative) = 1
Km= 39 Mkcat= 0.070 s-1
kcat/Km (relative) = 0.0033
Km= 0.68 Mkcat= 0.079 s-1
kcat/Km (relative) = 0.22
Kobayashi et. al. Nat. Struct. Biol. 10, 425 (2003)
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Polycistronic expression of MjtRNA
tRNA copy #
tRNA promoter
0 1 1 1 3 6
lpp proK proK proK proK
aaRS promoter glnS glnS’ glnS’ glnS’glnSglnS
-
JYTRN
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-Galactosidase assay for suppression efficiency
araBAD promoter leader
TAG
lacZ
proK
proK + D286R
proK + glnS’
proK + glnS’ + D286R
+ 3TRN
+ 6TRN
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Efficient incorporation of many different unnatural amino acids
H2N CO2H
O
H2N CO2H
O
H2N CO2H
N3
H2N CO2H
I
Bpa pAcPhe pAzPhe pIPhe
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Efficiency and fidelity
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Optimizing protein yields in E. coli
• E. coli prolyl-tRNA promoter and terminator for the amber suppressor tRNA
• Mutated form of the glnS promoter for the synthetase
• D286R substitution in the synthetase gene
• Multiple copies of the suppressor tRNA gene
• Yield of adiponectin (Glu123Bpa) mutant: 0.4g/L
Ryu & Schultz Nat. Methods 3, 263 (2006)
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Site-selective modification of proteins
NH
O
O
H2NO PEG
NH
O
NO PEG
pAcPhe
NH
O
Lys
NH2
NH
O
HN
O
PEGO PEG
O
N
O
O
http://www.ambrx.com
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Photocaged Tyrosine
Tyr503
lactose
H2N CO2H
O
O2N
H2N CO2H
OH
ONBY Tyrosine
h
365nm
Deiters, Groff, Ryu, Xie & Schultz Angew. Chem. Int. Ed. 45, 2728 (2006)
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Incorporation of a distance probe into proteins
H2N CO2H
NO2
pNO2Phe
Tsao, Summerer, Ryu & Schultz J. Am. Chem. Soc. 128, 4572 (2006)
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Incorporation of an IR probe into proteins
__O2
[2230 cm-1]
Cyanide [2236 cm-1]
NO [2230 cm-1]
Azide [2234 cm-1]
CO [2239 cm-1]
Met-ferric [2248 cm-1]
Deoxyferrous[2233 cm-1]
Ferric (Fe3+) adducts
Ferrous (Fe2+) adducts
Wavenumber (cm-1)
2160 2180 2200 2220 2240 2260
Re
lati
ve
Ab
so
rba
nc
e
0.0
0.2
0.4
0.6
0.8
1.0
FeII(CO) pCNPhe64 Mb
FeII(NO) pCNPhe64 Mb
FeII(O2) pCNPhe64 Mb
2230 2239B
H2N CO2H
CN
Schultz, Supekova, Ryu, Xie, Perera & Schultz J. Am. Chem. Soc. 128, 13984 (2006)
pCNPhe
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Co-translational protein modification
H2N
OH
OH
O
Tyrosine
Desulfo-hirudine Sulfo-hirudine
Liu & Schultz, Nat. Biotech. 24, 1436 (2006)
Thrombin Thrombin
Ki = 307 fM Ki = 26 fM
H2N
O
OH
O
Sulfotyrosine
S
O
O
O-
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Incorporation of an NMR probe
Cellitti et. al. J. Am. Chem. Soc. 130, 9268 (2008)TE domain of the human FAS
H2N CO2H
O F
FF
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Unnatural amino acids incorporated by the mutant TyrRS in E. coli
H2NOH
O
O
H2NOH
O
H2NOH
O
O
H2NOH
O
O
H2NOH
O
I
H2NOH
O
NH2
H2NOH
O
N3
H2NOH
O
O
H2NOH
O
CO2H
H2NOH
O
C
H2NOH
O
NO2
H2NOH
O
B(OH)2
H2NOH
O
O
H2NOH
O
OH
OH
H2NOH
O
NN
H2NOH
O
O
NO2
SO
O
O-
H2NOH
O
N
H2NOH
O
N
N
H2NOH
O
CF3
NN
H2NOH
O
OO OH
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Identification of the protein modification and secretion pathways by photo-crosslinking in E. coli
N-Acetylation of recombinant proteins in E. coli• N-Acetylation (e.g. Z-domain etc)
• N-Acetylation of lysine side chains (e.g. Porcine and bovine somatotropins)
Secretion pathway of the YebF protein in E. coli
NH
O
O NH
O
HO NH
R
O
Bpa
O
H
R
NH
h
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N-Terminal acetylation of the Z-domain depends on E. coli strains and expression plasmids
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N-Terminal acetylation of the Z-domainis context-dependent
Position Amino acidObserved
M.W.- Met1 N-Acetylation
S3Bpa 7968.3
Yes YesTyrosine 7886.5
V4Bpa 7913.9
Yes NoTyrosine 7827.4
D5Bpa 7898.2
Yes NoTyrosine 7811
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Photo-crosslinking and proteomics analysis
Band S3Bpa V4Bpa D5Bpa
1 Protein A Protein AProtein A
EF-Ts
2Protein A
Hsp70PBP
EF-TuProtein F
3EF-Tu
Protein A
V4BpaS3BpaControl D5Bpa
10 -
15 -20 -
30 -
50 -
80 -
220 -
kDa Marker
1
23
1 1
2
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Strategy to identify the YebF transporter
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Unnatural protein medicinal chemistry
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Directed evolution of the archaea LeuRS system
H2N
NH
N
S OO
O
OHH2N
O
OH
HN
O
H2N
O
OH
HN
H2NOH
OH2N
N
OH
O
H2NOH
O
N
NO
OH
H2N
HN
OH
O
N ON
NO2
H2NOH
O
S
O2N
H2N
B
OH
O
OH
OH
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Selection with a single reporter plasmid
Positive selection + Unnatural amino acid+ Cm + Uracil
Survivors containing aaRS capable of charging any natural or unnatural aa on the orthogonal tRNA
Negative selection- Unnatural amino acid
+ 5-FU
Cells that incorporate natural amino acids make toxic product from 5-FU and die;
Cells that incorporate unnatural amino acid only survive on 5-FU
Nex
t rou
nd o
f pos
itive
sel
ectio
n
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Deletion of the upp and pyrF genes by the recombinase-based gene replacement
Minimal media+ Uracil
+ Uridine
Minimal media+ Uracil
GeneHog upp pyrF
OMP UMPpyrF
de novo synthesis
Bicarbonate
Uridine
Uracil
uppSalvage Pathway
UDP
UTP
CTP
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Summary
• A single plasmid system for the high yield expression of proteins containing unnatural amino acids
• Broad applications depending on the physicochemical properties of unnatural amino acids – chemical and photochemical reactions, spectroscopic probes, novel therapeutics etc.
• Ongoing projects
– Identification of the protein acetylation and secretion pathways
– Unnatural protein medicinal chemistry
– Directed evolution of the leucyl-tRNA synthetase
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Acknowledgments
• Minoro Aoshima• Lina Bernal-Perez• Pradeep Budhathoki• Aery Lee
• Kiran Butt• Michael Foster• Brett McKnight• Fatima Sahyouni• Diana Tran
• Dr. Laszlo Prokai (UNTHSC)• Dr. Peter Schultz (TSRI)
TCU (Start-up, RCAF, SERC)
Graduate Students
Undergraduate Students
Collaborators
Financial Support