Protease Biochem March05
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Proteases
Dr. Jessica Bell Davies Laboratory NIDDK/NIH For the University of Richmond
What do proteases do? H
+
HN
3
H
O
C
C
R1
H N
C
H
R2
+
COO
+
H2O
3
HN
C R1
COO H
+ +
3
HN
C
COO
R2
∆Go for the rxn is 2kcal/mol But… Catalyzed rxn (chymotrypsin) at neutral pH, 37°C: 100/sec
Uncatalyzed rxn at neutral pH, 37°C: 1 X 1010 /sec
Conditions for chemically catalyzed reaction:
24hrs. @ 6M HCl, 110°C
Koshland, D. (1996) J. Cell. Comp. Phys. Suppl. 1 43:217.
Two types of cleavages endopeptidase
exopeptidase
Same rxn, Four mechanisms Named for residue/group in active site of enzyme essential for most effective catalysis Serine
OH
Cysteine/Thiol SH
Acid/Aspartic COO Metallo
Zn2+
Mechanistic Sets of Proteases set
feature
inhibitor
examples
function
Serine protease
active site serine H57, D102, S195
fluorophosphates
trypsin thrombin plasmin coccoonase subtilisin acrosin
digestion blood coagulation lysis of blood clots mechanical digestion sperm penetration
Cysteine protease
active site cysteine C25, H159, N175
iodoacetate
papain strept. proteinase cathepsin B
digestion digestion intracell. digestion
Acid protease
acidic pH optimum D32, D215
diazoketones
pepsin chymosin
digestion milk coagulation
Metalloproteases
Zn2+, E270 Zn2+, Ca2+ E143, H231
ophenanthroline ophenanthroline
carboxypeptidase thermolysin
digestion digestion
Secretion
signal peptidases
Development snake
Digestion
Adhesion
P. gingivalis protease
Immune Response
Tcell protease
Blood pressure regulation renin
trypsin
Coagulation
Complement Fixation CI protease
thrombin
Cell fusion
hemaglutinase
Tumor Invasion
Reproduction and Fertilization
collagenase
acronase
Fibrinolysis
tissue plasminogen actvator
Hormone Processing
Kex 2
Pain Sensing kallikrein
Animal Virus Replication HIV protease
6 Broad Categories Function Protease Nutrition trypsin, subtilisin, αlytic protease Invasion
matrix metallo proteases
Evasion
IgA protease
Adhesion P. gingivalis protease Processing signal peptidase, viral proteases, proteosome Signaling caspases, granzymes
Serine Protease Mechanism – The players
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Serine Protease Mechanism – Oxyanion Hole
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Serine inhibitors
CH3 O S O
O NH
CH
C
CH2
Cl
CH2 Peptide bond mimic
Chloromethyl ketone [CMK] TPCK
(L1Chloro3[4tosylamido]4phenyl2butanone)
Serine inhibitors
CH3 CH CH3
F O
P O
CH3 O
CH CH3
DFP Diisopropyl fluorophosphate
Divergent vs. Convergent Evolution Catalytic Triad Conserved
Trypsin
Elastase Same Fold
Subtilisin
Serpins Serine protease inhibitors Irreversible Disruption of 3º structure
Ecotin Serine Protease Inhibitor Unknown function Dimeric 1° and 2° binding sites Cleaved
Cysteine protease mechanism Michaelis Complex 159
H
N
Tetrahedral intermediate I 159
25 N: HN
S H
H
O
N
+
25 N
H
S
HN
P1
P1
159
H
O
159 25
25
N + N H
S
O
O
H Tetrahedral intermediate II
P1
NH2
H
N
N:
S
O
NH2
H2O
Acyl Intermediate
P1
Cysteine protease mechanism Michaelis Complex 159
H
N
N:
S H
H
O
N
+
25 N
H
S
HN
No Asp102 equivalent
159
159 25
25
N + N H
S
O
O
H Tetrahedral intermediate II
P1
O
P1
Covalent Intermediate
P1
159
25
HN
H
Tetrahedral intermediate I
NH2
H
N
N:
S
O
NH2
H2O
Acyl Intermediate
P1
Cysteine protease inhibitors
159
H
N
25 S
N
:
H
I CH2
O C
OH
Iodoacetic acid E64 (2S,3S)3(N(1S)1[N (4guanidinobutyl)carbamoyl]3methylbutyl)carbamoyl) oxirane2carboxylic acid
Cystatin Superfamily Cysteine protease inhibitors Noncanonical binding
Acid protease mechanism
O
Asp25’
H O
H
P1
O
H O
Asp25
H
H
O
O
Asp25’
P1’
Tetrahedral intermediate
O
P1’
O
O
O
N
O
H
Asp25
N
O
O
O
O
O
O O
H
H
H
Asp25’
P1
H
Asp25
O
Asp25
H
P1’
O
O
H
O
H
P1 O
N
H
O
H
N
Michaelis complex P1’ P1 H
Asp25’
Acid protease mechanism
H
O
O
O
O
O
O
O
Asp25’
H
H
Asp25
P1’
Asp25
O
O
H
O
H
P1 O
N
H
O
H
N
Michaelis complex P1’ P1 H
Asp25’
No covalent intermediate
Activated water H O
H
P1
O
H O
Asp25
H
H
O
O
Asp25’
P1’
Tetrahedral intermediate
O
O
H
P1’
O
O
N
O
O O
H
Asp25
H
N
P1
Asp25’
Acid protease inhibitors
Indinavir, Roche
CH3
H N
RHN O
O
HIV Protease Substrate
NHR’
N O
O H
Reiling, K. K. et al. Biochemistry (2002) 41:458294.
Movie of Multidrug resistant HIV Models: www.ucsf.edu Click on AZ listings Under C find Craik, Charles Within the Craik website there is section entitled movies Enjoy!
Pepsin
HIV Protease
Metallo protease mechanism H
His
H
His
Zn2+
His
His
O
O P1
O
O
P1
O
Zn2+
O
Glu
P1
O P1
O
O
O
H
N
His
His
H P1’
H P1’
Glu
Zn2+
O
Zn2+
His
His
H
O N
Glu
His
His
O
H O
Zn2+
H
His
O
Glu
N
Glu
O
Zn2+
His
H
P1’
Glu
O
O
Metallo protease mechanism H
O
Glu
Activated water
O
O
O
Glu
His
His
Zn2+
P1
O P1
O
O
O
H
N
His
His
O
P1
H P1’
H P1’
Glu
Zn2+
O
Zn2+
P1
No covalent intermediate
His
His
O
H O
Zn2+
H
His
O
Glu
H
O N
Zn2+
His
N
His
H
His
His
O
Glu
O
Zn2+
His
H
P1’
Glu
O
O
H2NAspArgValTyrIleProPheHisLeuCo2H Proangiotensin
H2NAspArgValTyrIleProPheCo2H Angiotensin
A
Zn2+
H
NH
H
O
C
C
R2
H
O
N
C
C
H
R1
H N
C
H
R1
O
H2N
C O
+
C
NH
Arg
H2N
carboxydipeptidase active site A
Zn2+
H S CH2
H
O
C
C
CH3
H N
C
O C
Captopril
O
H2N + C H2N
NH
Arg
Thermolysin
Carboxypeptidase A
Synopsis of Protease Mechanisms Serine
SerHis Asp Catalytic Triad covalent intermediate Cysteine CysHis covalent intermediate Acid AspAsp Activated water no covalent intermediate Metallo Zn2+ or equivalentGlu
Activated Water no covalent intermediate
How Proteases Order Off the Menu P2
P1
OH
N H
N H
O
P2’
CH3
O
H N
Peptide
P1’ H N
O
N H
O
Scissile Bond Subsite of Protease
OH
NH3+
S2
S1
S1’
S2’
Substrate Selection within One Tertiary Fold
Methods to Determine Specificity 1>
Synthesis of short peptides [15 to 20a.a.], check for cleavage with PAGE
2>
Phage display of short peptides
3> Positional scanning synthetic combinatorial libraries [PSSCL]
N H
O
X
AcXXXOAMC AcXXOXAMC AcXOXXAMC AcOXXXAMC
X
O
H N
N H
X
O
A K A K A K A K
R F R F R F R F
N P N P N P N P
H N
O
H N
O
X
D S D S D S D S
E T E T E T E T
Q W Q W Q W Q W
G Y G Y G Y G Y
H V H V H V H V
7amino4methyl coumarin
I m I m I m I m
L
L L L
Harris J. L. et al. Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. PNAS (2000) 97:77549.
400.0
0.06 0.058
300.0
0.056 0.054
200.0
0.052 0.05
100.0
0.048 0.046
0.0
0.044
A R N D Q E G H I L K F P S T WY V mM
P4 N H
O
A R N D Q E G H I L K M m F P S T W Y V
P2
O
H N
N H
P3
500.0
O
H N O
P1
200.0
400.0
150.0
300.0 100.0 200.0 50.0
100.0
0.0
A R N D Q E G H I L K F P S T W Y V mM
0.0
A R N D Q E G H I L K F P S T W Y V mM
Regulation of Proteases – A Few Examples Zymogens Propeptide that must be cleaved before protease becomes fully active Trypsinogen 16
1 Enteropeptidase
1
15
Trypsin 16
Zymogen form has distorted oxyanion hole and substrate binding pocket Compartmentalization Macromolecular Inhibitors Host and nonhost
Cytotoxic Lymphocytes
Molecular Biology of the Cell, Garland
Cytotoxic T Lymphocyte Apoptotic Pathway Cytotoxic T lymphocyte Granzymes Perforin Ca
2+
3
Fas DD
Ca2+
Ca2+ Ca2+
FADD
cleave procaspases
DED
Mito. apoptosis aggregrates procaspase 8, intermolecular cleavage to caspase 8, activation of effector caspases [3, 6, 7], apoptosis
GrnA
GrnB
MPR?
serpins Nuclease ?
Bcl2
Single stranded breaks in DNA nucleus
Granzymes: Lymphocyte Serine Proteases Name
Activity
Predicted P1
MW
cleavage site
A
Trypsinlike R/K
60 (Dimer)
B
Aspase
D/E
35
C
Unknown
N/S
27
D
Unknown
F/L
3550
E
Unknown
F/L
3545
F
Unknown
F/L
3540
G
Unknown
F/L
H
Chymase
F
I
Unknown
J
Unknown
K
Trypsinlike
M
Metase
M/L/norL
30 30
Granzyme Structure
Waugh et al. (2000) Nat. Struct. Biol. 7:762765
Granzyme A, Proposed Dimeric Structure
Granzyme A: Substrate Specificity and Macromolecule Substrates Substrate
Sequence P4
FLUOROGENIC LIBRARIES
P3
V/I G/A/S
P2
P1
N
R
PIL-1β
D
A
P
V
R
S
L
N
C
T
THROMBIN RECEPTOR
T
L
D
P
R
S
F
L
L
R
HISTONE H1
K
L
G
L
K
S
L
V
S
K
HISTONE H2b
A
P
A
P
K
K
G
S
K
K
SET
Q
T
Q
N
K
A
S
R
K
R
LAMIN B
V
T
V
S
R
A
S
S
S
R
Chasing the Crystals
Macromolecular Inhibition of Granzyme A 1.2
mOD/min @ 405nm
1
Control mM84R Eco
0.8
dM84R Eco
0.6
Tryp. Inh.
0.4
0.2
0
0
0.05
5
[Inhibitor], µM
50
Potential Effects of Oligomer on Macromolecular Inhibitors
grnA
Potential Effects of Oligomer on Macromolecular Inhibitors grnB:dEcotin
Potential Effects of Oligomer on Macromolecular Inhibitors mEcotin
Small Molecule Inhibitor of Granzyme A 0.8 0.7
O N
mOD/minute @405nm
0.6
C
C
O N
C
C
N
C
C
CH2Cl
O
0.5 0.4 0.3 0.2 0.1
0
0
50
100 [Inhibitor], nM
150
200
Crystallization Previous conditions: 0.1M Citrate, pH 5.6, 20% peg 4K, 20% Isopropanol New Conditions: 4M NaFormate 0.1M Citrate, pH 5.6, 2030% peg4K, 0.2M AmAcetate 0.1M Cacodylate, pH 6.5, 1520% peg4K, 0.2M AmSO4 0.1M Tris, pH8.5, 1318% peg4K, 0.2M LiSO4
Diffraction!!!
Substrate Selectivity
Granzyme A: Human and Mouse Human Mouse
MRNSYRFLAS MRNASGPRGP
SLSVVVSLLL SLATLLFLLL
IPEDVCEKII IPEGGCERII
GGNEVTPHSR GGDTVVPHSR
PYMVLLSLDR PYMALLKLSS
Human Mouse
KTICAGALIA NTICAGALIE
NLNKRSQVIL NVGKRSKFIL
GAHSITREEP GAHSINK-EP
TKQIMLVKKE EQQILTVKKA
Human Mouse
FPYPCYDPAT FPYPCYDETT
TEKAKINKYV KKKATVNRNV
TILHLPKKGD AILHLPKKGD
DVKPGTMCQV DVKPGTRCRV
Human Mouse
AGWGRTHNSA AGWGRFGNKS
KDWVLTAAHC KNWVLTAAHC # REGDLKLLQL REGDLQLVRL # SWSDTLREVN APSETLREVN
ITIIDRKVCN ITVIDRKICN
DRNHYNFNPV DEKHYNFHPV
IGMNMVCAGS IGLNMICAGD
Human Mouse
LRGGRDSCNG LRGGKDSCNG
VFRGVTSFGL ILRGITSFG*
ENKCGDPRGP GEKCGDRRWP *
GVYILLSKKH GVYTFLSDKH
Human Mouse
LNWIIMTIKG LNWIKKIMKG
DSGSPLLCEG DSGSPLLCDG # AV SV
68% Identical!
P4
P3
P2
P1
Human V/I G/A/S N
R
Mouse
R
G F/Y
F
Substrate Specificity of Granzyme A Species
D102 R99
H57
P2 P3
P4
D189
P1
S195
Substrate Specificity of Granzyme A Species
P4
W224
Substrate Specificity of Granzyme A Species
P4
W224
Substrate Specificity of Granzyme A Species
Native Human GrA
Relative Fluorescence Units
0.06 0.05
Human
Mouse
P2
N
F
P3
G/A/S
F/Y
P4
V/L
G
0.04 0.03 0.02 0.01 0 A
R
N
D
Q
E G H I L K F P1-Arg PS-SCL of Human GrA - P3 Amino Acid
P
S
T
W
Y
V
n
Relative Fluorescence Units
0.06 0.05 0.04 0.03 0.02 0.01 0 A
R
N
D
Q E G H I L K F P P1-Arg PS-SCL of Native Human GrA - P4 Amino Acid
S
T
W
Y
V
n
Relative Fluorescence Units
0.06 0.05 0.04 0.03 0.02 0.01
0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
H > M GrA
0.14 0.12 0.1
Human
Mouse
P2
N
F
P3
G/A/S
F/Y
P4
V/L
G
0.08 0.06 0.04 0.02 0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
0.14 0.12 0.1 0.08 0.06 0.04 0.02 0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
0.14 0.12 0.1 0.08 0.06 0.04
0.02
0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
Conclusions: Mutational Studies
The residues identified from the model of mouse granzyme A [∆ L201, G202, E203, W211] when mutated into the equivalent positions of the human homologue: 1> switch the substrate specificity at the P3 position, 2> increase the preference for small residues [A/G] over branched residues [I/V] at the P4 position and 3> broaden residue selection at the P2 position.
C. S. Craik Craik Lab Members Granzyme A Sandy Waugh Sami Mahrus Carly Klein MTSP1 Jeonghoon Sun Ami Bhatt
R. J. Fletterick Fletterick Lab Members
ALS 8.3.1
The Chemists Amy Barrios Alan Marnett
NIH: The $$$ people
James Holton
Dr. Jessica Bell Davies Laboratory NIDDK/NIH For the University of Richmond
What do proteases do? H
+
HN
3
H
O
C
C
R1
H N
C
H
R2
+
COO
+
H2O
3
HN
C R1
COO H
+ +
3
HN
C
COO
R2
∆Go for the rxn is 2kcal/mol But… Catalyzed rxn (chymotrypsin) at neutral pH, 37°C: 100/sec
Uncatalyzed rxn at neutral pH, 37°C: 1 X 1010 /sec
Conditions for chemically catalyzed reaction:
24hrs. @ 6M HCl, 110°C
Koshland, D. (1996) J. Cell. Comp. Phys. Suppl. 1 43:217.
Two types of cleavages endopeptidase
exopeptidase
Same rxn, Four mechanisms Named for residue/group in active site of enzyme essential for most effective catalysis Serine
OH
Cysteine/Thiol SH
Acid/Aspartic COO Metallo
Zn2+
Mechanistic Sets of Proteases set
feature
inhibitor
examples
function
Serine protease
active site serine H57, D102, S195
fluorophosphates
trypsin thrombin plasmin coccoonase subtilisin acrosin
digestion blood coagulation lysis of blood clots mechanical digestion sperm penetration
Cysteine protease
active site cysteine C25, H159, N175
iodoacetate
papain strept. proteinase cathepsin B
digestion digestion intracell. digestion
Acid protease
acidic pH optimum D32, D215
diazoketones
pepsin chymosin
digestion milk coagulation
Metalloproteases
Zn2+, E270 Zn2+, Ca2+ E143, H231
ophenanthroline ophenanthroline
carboxypeptidase thermolysin
digestion digestion
Secretion
signal peptidases
Development snake
Digestion
Adhesion
P. gingivalis protease
Immune Response
Tcell protease
Blood pressure regulation renin
trypsin
Coagulation
Complement Fixation CI protease
thrombin
Cell fusion
hemaglutinase
Tumor Invasion
Reproduction and Fertilization
collagenase
acronase
Fibrinolysis
tissue plasminogen actvator
Hormone Processing
Kex 2
Pain Sensing kallikrein
Animal Virus Replication HIV protease
6 Broad Categories Function Protease Nutrition trypsin, subtilisin, αlytic protease Invasion
matrix metallo proteases
Evasion
IgA protease
Adhesion P. gingivalis protease Processing signal peptidase, viral proteases, proteosome Signaling caspases, granzymes
Serine Protease Mechanism – The players
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Serine Protease Mechanism – Oxyanion Hole
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Adapted from Voet and Voet (1995) Biochemistry, 2nd ed. John Wiley and Sons, Inc. New York.
Serine inhibitors
CH3 O S O
O NH
CH
C
CH2
Cl
CH2 Peptide bond mimic
Chloromethyl ketone [CMK] TPCK
(L1Chloro3[4tosylamido]4phenyl2butanone)
Serine inhibitors
CH3 CH CH3
F O
P O
CH3 O
CH CH3
DFP Diisopropyl fluorophosphate
Divergent vs. Convergent Evolution Catalytic Triad Conserved
Trypsin
Elastase Same Fold
Subtilisin
Serpins Serine protease inhibitors Irreversible Disruption of 3º structure
Ecotin Serine Protease Inhibitor Unknown function Dimeric 1° and 2° binding sites Cleaved
Cysteine protease mechanism Michaelis Complex 159
H
N
Tetrahedral intermediate I 159
25 N: HN
S H
H
O
N
+
25 N
H
S
HN
P1
P1
159
H
O
159 25
25
N + N H
S
O
O
H Tetrahedral intermediate II
P1
NH2
H
N
N:
S
O
NH2
H2O
Acyl Intermediate
P1
Cysteine protease mechanism Michaelis Complex 159
H
N
N:
S H
H
O
N
+
25 N
H
S
HN
No Asp102 equivalent
159
159 25
25
N + N H
S
O
O
H Tetrahedral intermediate II
P1
O
P1
Covalent Intermediate
P1
159
25
HN
H
Tetrahedral intermediate I
NH2
H
N
N:
S
O
NH2
H2O
Acyl Intermediate
P1
Cysteine protease inhibitors
159
H
N
25 S
N
:
H
I CH2
O C
OH
Iodoacetic acid E64 (2S,3S)3(N(1S)1[N (4guanidinobutyl)carbamoyl]3methylbutyl)carbamoyl) oxirane2carboxylic acid
Cystatin Superfamily Cysteine protease inhibitors Noncanonical binding
Acid protease mechanism
O
Asp25’
H O
H
P1
O
H O
Asp25
H
H
O
O
Asp25’
P1’
Tetrahedral intermediate
O
P1’
O
O
O
N
O
H
Asp25
N
O
O
O
O
O
O O
H
H
H
Asp25’
P1
H
Asp25
O
Asp25
H
P1’
O
O
H
O
H
P1 O
N
H
O
H
N
Michaelis complex P1’ P1 H
Asp25’
Acid protease mechanism
H
O
O
O
O
O
O
O
Asp25’
H
H
Asp25
P1’
Asp25
O
O
H
O
H
P1 O
N
H
O
H
N
Michaelis complex P1’ P1 H
Asp25’
No covalent intermediate
Activated water H O
H
P1
O
H O
Asp25
H
H
O
O
Asp25’
P1’
Tetrahedral intermediate
O
O
H
P1’
O
O
N
O
O O
H
Asp25
H
N
P1
Asp25’
Acid protease inhibitors
Indinavir, Roche
CH3
H N
RHN O
O
HIV Protease Substrate
NHR’
N O
O H
Reiling, K. K. et al. Biochemistry (2002) 41:458294.
Movie of Multidrug resistant HIV Models: www.ucsf.edu Click on AZ listings Under C find Craik, Charles Within the Craik website there is section entitled movies Enjoy!
Pepsin
HIV Protease
Metallo protease mechanism H
His
H
His
Zn2+
His
His
O
O P1
O
O
P1
O
Zn2+
O
Glu
P1
O P1
O
O
O
H
N
His
His
H P1’
H P1’
Glu
Zn2+
O
Zn2+
His
His
H
O N
Glu
His
His
O
H O
Zn2+
H
His
O
Glu
N
Glu
O
Zn2+
His
H
P1’
Glu
O
O
Metallo protease mechanism H
O
Glu
Activated water
O
O
O
Glu
His
His
Zn2+
P1
O P1
O
O
O
H
N
His
His
O
P1
H P1’
H P1’
Glu
Zn2+
O
Zn2+
P1
No covalent intermediate
His
His
O
H O
Zn2+
H
His
O
Glu
H
O N
Zn2+
His
N
His
H
His
His
O
Glu
O
Zn2+
His
H
P1’
Glu
O
O
H2NAspArgValTyrIleProPheHisLeuCo2H Proangiotensin
H2NAspArgValTyrIleProPheCo2H Angiotensin
A
Zn2+
H
NH
H
O
C
C
R2
H
O
N
C
C
H
R1
H N
C
H
R1
O
H2N
C O
+
C
NH
Arg
H2N
carboxydipeptidase active site A
Zn2+
H S CH2
H
O
C
C
CH3
H N
C
O C
Captopril
O
H2N + C H2N
NH
Arg
Thermolysin
Carboxypeptidase A
Synopsis of Protease Mechanisms Serine
SerHis Asp Catalytic Triad covalent intermediate Cysteine CysHis covalent intermediate Acid AspAsp Activated water no covalent intermediate Metallo Zn2+ or equivalentGlu
Activated Water no covalent intermediate
How Proteases Order Off the Menu P2
P1
OH
N H
N H
O
P2’
CH3
O
H N
Peptide
P1’ H N
O
N H
O
Scissile Bond Subsite of Protease
OH
NH3+
S2
S1
S1’
S2’
Substrate Selection within One Tertiary Fold
Methods to Determine Specificity 1>
Synthesis of short peptides [15 to 20a.a.], check for cleavage with PAGE
2>
Phage display of short peptides
3> Positional scanning synthetic combinatorial libraries [PSSCL]
N H
O
X
AcXXXOAMC AcXXOXAMC AcXOXXAMC AcOXXXAMC
X
O
H N
N H
X
O
A K A K A K A K
R F R F R F R F
N P N P N P N P
H N
O
H N
O
X
D S D S D S D S
E T E T E T E T
Q W Q W Q W Q W
G Y G Y G Y G Y
H V H V H V H V
7amino4methyl coumarin
I m I m I m I m
L
L L L
Harris J. L. et al. Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. PNAS (2000) 97:77549.
400.0
0.06 0.058
300.0
0.056 0.054
200.0
0.052 0.05
100.0
0.048 0.046
0.0
0.044
A R N D Q E G H I L K F P S T WY V mM
P4 N H
O
A R N D Q E G H I L K M m F P S T W Y V
P2
O
H N
N H
P3
500.0
O
H N O
P1
200.0
400.0
150.0
300.0 100.0 200.0 50.0
100.0
0.0
A R N D Q E G H I L K F P S T W Y V mM
0.0
A R N D Q E G H I L K F P S T W Y V mM
Regulation of Proteases – A Few Examples Zymogens Propeptide that must be cleaved before protease becomes fully active Trypsinogen 16
1 Enteropeptidase
1
15
Trypsin 16
Zymogen form has distorted oxyanion hole and substrate binding pocket Compartmentalization Macromolecular Inhibitors Host and nonhost
Cytotoxic Lymphocytes
Molecular Biology of the Cell, Garland
Cytotoxic T Lymphocyte Apoptotic Pathway Cytotoxic T lymphocyte Granzymes Perforin Ca
2+
3
Fas DD
Ca2+
Ca2+ Ca2+
FADD
cleave procaspases
DED
Mito. apoptosis aggregrates procaspase 8, intermolecular cleavage to caspase 8, activation of effector caspases [3, 6, 7], apoptosis
GrnA
GrnB
MPR?
serpins Nuclease ?
Bcl2
Single stranded breaks in DNA nucleus
Granzymes: Lymphocyte Serine Proteases Name
Activity
Predicted P1
MW
cleavage site
A
Trypsinlike R/K
60 (Dimer)
B
Aspase
D/E
35
C
Unknown
N/S
27
D
Unknown
F/L
3550
E
Unknown
F/L
3545
F
Unknown
F/L
3540
G
Unknown
F/L
H
Chymase
F
I
Unknown
J
Unknown
K
Trypsinlike
M
Metase
M/L/norL
30 30
Granzyme Structure
Waugh et al. (2000) Nat. Struct. Biol. 7:762765
Granzyme A, Proposed Dimeric Structure
Granzyme A: Substrate Specificity and Macromolecule Substrates Substrate
Sequence P4
FLUOROGENIC LIBRARIES
P3
V/I G/A/S
P2
P1
N
R
PIL-1β
D
A
P
V
R
S
L
N
C
T
THROMBIN RECEPTOR
T
L
D
P
R
S
F
L
L
R
HISTONE H1
K
L
G
L
K
S
L
V
S
K
HISTONE H2b
A
P
A
P
K
K
G
S
K
K
SET
Q
T
Q
N
K
A
S
R
K
R
LAMIN B
V
T
V
S
R
A
S
S
S
R
Chasing the Crystals
Macromolecular Inhibition of Granzyme A 1.2
mOD/min @ 405nm
1
Control mM84R Eco
0.8
dM84R Eco
0.6
Tryp. Inh.
0.4
0.2
0
0
0.05
5
[Inhibitor], µM
50
Potential Effects of Oligomer on Macromolecular Inhibitors
grnA
Potential Effects of Oligomer on Macromolecular Inhibitors grnB:dEcotin
Potential Effects of Oligomer on Macromolecular Inhibitors mEcotin
Small Molecule Inhibitor of Granzyme A 0.8 0.7
O N
mOD/minute @405nm
0.6
C
C
O N
C
C
N
C
C
CH2Cl
O
0.5 0.4 0.3 0.2 0.1
0
0
50
100 [Inhibitor], nM
150
200
Crystallization Previous conditions: 0.1M Citrate, pH 5.6, 20% peg 4K, 20% Isopropanol New Conditions: 4M NaFormate 0.1M Citrate, pH 5.6, 2030% peg4K, 0.2M AmAcetate 0.1M Cacodylate, pH 6.5, 1520% peg4K, 0.2M AmSO4 0.1M Tris, pH8.5, 1318% peg4K, 0.2M LiSO4
Diffraction!!!
Substrate Selectivity
Granzyme A: Human and Mouse Human Mouse
MRNSYRFLAS MRNASGPRGP
SLSVVVSLLL SLATLLFLLL
IPEDVCEKII IPEGGCERII
GGNEVTPHSR GGDTVVPHSR
PYMVLLSLDR PYMALLKLSS
Human Mouse
KTICAGALIA NTICAGALIE
NLNKRSQVIL NVGKRSKFIL
GAHSITREEP GAHSINK-EP
TKQIMLVKKE EQQILTVKKA
Human Mouse
FPYPCYDPAT FPYPCYDETT
TEKAKINKYV KKKATVNRNV
TILHLPKKGD AILHLPKKGD
DVKPGTMCQV DVKPGTRCRV
Human Mouse
AGWGRTHNSA AGWGRFGNKS
KDWVLTAAHC KNWVLTAAHC # REGDLKLLQL REGDLQLVRL # SWSDTLREVN APSETLREVN
ITIIDRKVCN ITVIDRKICN
DRNHYNFNPV DEKHYNFHPV
IGMNMVCAGS IGLNMICAGD
Human Mouse
LRGGRDSCNG LRGGKDSCNG
VFRGVTSFGL ILRGITSFG*
ENKCGDPRGP GEKCGDRRWP *
GVYILLSKKH GVYTFLSDKH
Human Mouse
LNWIIMTIKG LNWIKKIMKG
DSGSPLLCEG DSGSPLLCDG # AV SV
68% Identical!
P4
P3
P2
P1
Human V/I G/A/S N
R
Mouse
R
G F/Y
F
Substrate Specificity of Granzyme A Species
D102 R99
H57
P2 P3
P4
D189
P1
S195
Substrate Specificity of Granzyme A Species
P4
W224
Substrate Specificity of Granzyme A Species
P4
W224
Substrate Specificity of Granzyme A Species
Native Human GrA
Relative Fluorescence Units
0.06 0.05
Human
Mouse
P2
N
F
P3
G/A/S
F/Y
P4
V/L
G
0.04 0.03 0.02 0.01 0 A
R
N
D
Q
E G H I L K F P1-Arg PS-SCL of Human GrA - P3 Amino Acid
P
S
T
W
Y
V
n
Relative Fluorescence Units
0.06 0.05 0.04 0.03 0.02 0.01 0 A
R
N
D
Q E G H I L K F P P1-Arg PS-SCL of Native Human GrA - P4 Amino Acid
S
T
W
Y
V
n
Relative Fluorescence Units
0.06 0.05 0.04 0.03 0.02 0.01
0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
H > M GrA
0.14 0.12 0.1
Human
Mouse
P2
N
F
P3
G/A/S
F/Y
P4
V/L
G
0.08 0.06 0.04 0.02 0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
0.14 0.12 0.1 0.08 0.06 0.04 0.02 0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
0.14 0.12 0.1 0.08 0.06 0.04
0.02
0 A
R
N
D
Q
E
G
H
I
L
K
F
P
S
T
W
Y
V
n
Conclusions: Mutational Studies
The residues identified from the model of mouse granzyme A [∆ L201, G202, E203, W211] when mutated into the equivalent positions of the human homologue: 1> switch the substrate specificity at the P3 position, 2> increase the preference for small residues [A/G] over branched residues [I/V] at the P4 position and 3> broaden residue selection at the P2 position.
C. S. Craik Craik Lab Members Granzyme A Sandy Waugh Sami Mahrus Carly Klein MTSP1 Jeonghoon Sun Ami Bhatt
R. J. Fletterick Fletterick Lab Members
ALS 8.3.1
The Chemists Amy Barrios Alan Marnett
NIH: The $$$ people
James Holton
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