flavins and electrochemical methods proline metabolism...
TRANSCRIPT
![Page 1: Flavins and electrochemical methods Proline Metabolism ...genomics.unl.edu/RBC_2012/COURSE_FILES/mon3.pdf · (5 mM) Time (s) PutA (ox) Zhang and Becker (2004) Biochemistry 43, 13165-13174.;](https://reader033.vdocuments.mx/reader033/viewer/2022041900/5e5fb777e86d153a793668d8/html5/thumbnails/1.jpg)
Flavin Redox Switching and Proline
June 11, 2012
• Flavins and electrochemical methods
• Proline Metabolism
• Proline Utilization A (PutA)
• Flavin redox switching of PutA
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Flavin Enzyme Diversity 1. Flavins support one-electron and two-electron transfer processes
2. Reactions catalyzed by flavoenzymes:
Dehydrogenation
Electron transfer
Hydroxylation
Dehalogenation
DNA repair
Disulfide reduction
Luminescence
Histone demethylation
3. Biological Processes
energy metabolism, amino acid metabolism, DNA synthesis, fatty acid
metabolism, cholesterol, neuroactive compounds, chromatin remodeling, and
bioremediation of polychlorinated aromatics
4. Regulate protein function- protein interactions, DNA binding, membranes
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Discovery of flavin mononucleotide
(FMN) by a Swedish biochemist
Showed the biochemical basis for riboflavin as a vitamin
Nobel Prize in Physiology or Medicine 1955
Axel Hugo Theodor Theorell N
N
NH
NH3C
H3C
O
O
CH2
CHHO
CHHO
CH
H2C
HO
O P O P O
O-
O O
O-
CH2O
H
OH OH
H
N
N
N
N
NH2
FAD
Nobelprize.org
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Redox Chemistry of Flavin
Flavin semiquinone is EPR active (S=1/2).
Flavins support one-electron and two-electron transfer processes involving the N(1), C(4a) and N(5)
positions of the isoalloxazine ring system.
Because flavins are involved in catalyzing oxidative and reductive mechanisms, characterizing the redox potentials of the
substrates, products, and flavins are important. The redox potential of free flavin is -219 mV (pH 7). However, when bound to an
enzyme, the redox potential can vary anywhere from + 100 mV to – 400 mV. Thus, the active site environment has a tremendous
influence on the redox and electronic properties of the flavin coenzyme in order to optimize catalysis.
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Electrochemistry Methods for Studying Redox Proteins
Coulometry
Potentiometry
An important thermodynamic parameter is the establishment of equilibrium between all
redox active species. The redox potential (Eo’) or midpoint potential (Em) is determined
along with the number of electrons (n) transferred in the reduction step. Measurement is
taken at zero current flow.
Emeas = Eo’ +(RT/nF) ln (ox/red)
number of electrons (n) transferred to a protein
molar absorptivity ()
Q = nFVC
Spectroelectrochemistry
Combines electrolysis, potentiometry, and spectroscopy
(UV-visible, electron spin resonance, IR, etc.)
Cyclic voltammetry
“Electronic scanning” Potential is scanned while current
is measured
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Prosthetic Groups are buried in Proteins FAD
Space-Filling
Model
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Electrochemical Methods
E meas =
m(free) + ln [ox]
[red] RT nF
E
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Redox potential of bound FAD in PutA
Wavelength (nm)
300 400 500 600
0
2
4
6
8
10
12
14
m
M-1
cm
-1
Becker and Thomas (2001) Biochemistry 40, 4714-4721.; Vinod et al. (2002) Biochemistry 41, 6525-6532.;
Lee et al., (2003) Nat. Struct. Biol. 10, 109-114; Zhang et al., (2004) Biochemistry 43, 12539-12548.
Wavelength (nm)
300 400 500 600 700
Ab
sorb
an
ce
0.00
0.05
0.10
0.15
0.20
0.25
0.30
percent reduced
0 20 40 60 80 100
po
ten
tia
l (V
)
-0.14
-0.12
-0.10
-0.08
-0.06
-0.04
-0.02
7
1
2e-
N
N
NH
N
O
O
R
H
H
N
N
NH
N
O
O
R
2e-
N
N
NH
N
O
O
R
H
H
N
N
NH
N
O
O
R
Em(free) = -0.076 V (pH 7.5)
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Redox linked protein-ligand interactions
The binding of molecule (L) to the oxidized and reduced forms of a protein
can be linked to differences in the potential of the protein in the presence
(Em(bound)) and absence (Em(free)) of the ligand by the following
thermodynamic box.
Kd(ox) L L
Em(free)
Em(bound)
Kd(red)
*L + 2e- Proteinox
+ 2e- Proteinox
* L Proteinred
Proteinred
There are two binding equilibria:
Pox + L Pox*L Pred + L Pred*L
Kdox = [Pox][L]
[Pox*L]
Kdred = [Pred][L]
[Pred*L]
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Flavin Redox Switch
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NADP+ + Pi
- H2O
g-GP
ADP
ATP
NADPH
Proline
P5C
Glutamate
P5CR FAD
NADPH
NADP+
PRODH
GSA
FADH2
PutA
P5CDH P5CS
GPR
GK
+ H2O
NAD+ + H2O
NADH + H+
Proline Metabolism
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Human enzymes in proline metabolism
Mitsubuchi et al., 2008. J. Nutr.
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Nat Genet. 2009 Sep;41(9):1016-21. Mutations in PYCR1 cause cutis laxa with progeroid features
PYCR1-related autosomal recessive cutis laxa a.k.a wrinkly skin syndrome
• P5CR localizes to mitochondria.
• Fibroblasts from affected individuals have altered mitochondrial morphology
• Increased membrane potential and apoptosis upon oxidative stress
Mutations in the PYCR1 gene (P5CR) found in wrinkly skin syndrome
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Organization of PRODH and P5CDH
Bradyrhizobium japonicum (BjPutA) short bifunctional
Escherichia coli (EcPutA) trifunctional (Functional switching)
Tanner and Becker, Proline Metabolism and PutA. Handbook of Flavins, (2012) in press.
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15
PutA (PRODH/P5CDH) and bioenergetics
COO-COO- COO-COO-
PRODH FAD FADH2
CoQ
COO-COO-
± H2O
-OOC COO--OOC COO-
NAD+, H2O NADH + H+
PutA
Pro P5C
GSA Glu
reductive
half-reaction
CoQH2
P5CDH
oxidative
half-reaction kcat = 5 s-1
Km (pro) = 34 mM
Km (CoQ1) = 124 mM
kcat/Km = 1400 M-1s-1
Proline is an important energy
source in various species
Bacteria (e.g., H. pylori)
Cuttlefish
Insects
Beetle:www.reptileforums.co.uk
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Reductive Half-Reaction
E + Pro E-Pro k (506 M-1s-1) 1
f + P5C k (255 s-1) -1
k (27.5 s-1) 2
k (1.6 s-1) -2
k (2.2 s-1) 3
k (0.19 s-1) -3
F-P5C f-P5C k (95.5 s-1) 4
k (4600 M-1s-1) -4
Oxidative Half-Reaction
f + CoQ f-CoQ k (2100 M-1s-1) 5
k (2.9 s-1) -5
k (5.4 s-1) 6 k (4.7 s-1) 7 e-CoQH2 E-CoQH2
Moxley and Becker (2012) Biochemistry 51:511-520.
Stopped-flow kinetics of PutA
Slow step in the overall reaction is k6.
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PROLINE
FADH2
FAD
P5C PRODH
PROLINE ETCox
ETCred
ATP/NADPH
Apoptosis
Cell Survival
ROS
cyt c release Nrf2
AKT/Foxo3a
Proline/PRODH and Cell Survival
Prostate cancer cells (PC3)
Knockdown of
PRODH decreases
P-AKT and stress
survival of PC3 cells In worm, PRODH
activates Nrf2 leading to
increased catalase/SOD
and lifespan
Cell Metab. 15:451-65; 2012. FRBM. In revision, 2012.
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PROLINE
FADH2
FAD
P5C PRODH
PROLINE ETCox
ETCred
ATP/NADPH
Apoptosis
Cell Survival
ROS
cyt c release Nrf2
AKT/Foxo3a
Proline/PRODH and Cell Death
The gene encoding PRODH is
inducible by p53
Upregulation of PRODH by p53
results in formation of proline-
dependent ROS and induction of
intrinsic and extrinsic apoptotic
pathways
Co-expression of Mn-SOD blocks
apoptosis induced by PRODH
Overexpression of PRODH
suppresses tumorigenesis in
xenografted nude mice
Nature. 389:300-5. 1997; Cancer Res. 61:1810-5. 2001; Oncogene. 25:5640-7. 2006;
Cancer Res. 69:6414-22. 2009; PNAS USA. Epub ahead of print May, 2012.
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PutA Functional Switching L-proline
PutP
PutA
red
red
red
red
H+
red red
red red putP
putA
red
red
red red
ox
ox
ox
ox
putP
putA
Ubiquinone Ubiquinol
O
O
CH3
R
O
O
H3C
H3C
OH
OH
CH3
R
O
O
H3C
H3C
NH
N
NH
HN
O
O
R
N
N
NH
N
O
O
R
FADox FADred
P5C Proline
Inner
Membrane
- proline + proline
Becker, DF and Thomas, E. (2001) Biochemistry 40, 4714-4721.
Flavin Redox Switch
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Structures of PutA
Mem CoQ4 CoQ2 CoQ1 Mena Duro DCPIP
Wt PutA
Km
(pro, mM)
1.5 ± 0.29
2.25 ± 0.53
9.38 ± 1.6
35 ±4
67 ± 6
27 ± 2
100
kcat
(s-1)
0.40 ± 0.02
0.18 ± 0.01
0.4 ± 0.01
1.3 ± 0.03
2.4 ± 0.06
0.99 ± 0.02
5-8
kcat/Km
(mM-1 s-1)
0.293 0.08 0.043 0.04 0.036 0.0372 0.03-0.08
Mem CoQ4 CoQ2 CoQ1 Mena Duro DCPIP
Wt PutA
Km
(pro, mM)
1.5 ± 0.29
2.25 ± 0.53
9.38 ± 1.6
35 ±4
67 ± 6
27 ± 2
100
kcat
(s-1)
0.40 ± 0.02
0.18 ± 0.01
0.4 ± 0.01
1.3 ± 0.03
2.4 ± 0.06
0.99 ± 0.02
5-8
kcat/Km
(mM-1 s-1)
0.293 0.08 0.043 0.04 0.036 0.0372 0.03-0.08
E. coli
PRODH P5CDH D 1 - - 1320 PRODH P5CDH D 1 - - 1320
P5CDH
PRODH PRODH
P5CDH
PRODH PRODH
PRODH P5CDH 1 - - 999 PRODH P5CDH
B. jap . B. jap .
1 - - 999
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PutA-DNA Binding
Zhou et al., J Mol Biol. 2008 Aug 1;381(1):174-88.
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PRODH Active Site
Becker and Thomas (2001) Biochemistry 40, 4714-4721.; Vinod et al. (2002) Biochemistry 41, 6525-6532.;
Lee et al., (2003) Nat. Struct. Biol. 10, 109-114; Zhang et al., (2004) Biochemistry 43, 12539-12548.
(S)-Tetrahydro-2-furoic acid (THFA)
Kd =0.24 mM
O C O O H
R555
R556
R431
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Structure of full-length bifunctional PutA
P5CDH
PRODH PRODH
P5CDH
PRODH PRODH
Tanner, JJ. PNAS 2010.
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Model of EcPutA and EcPutA-DNA complex
Singh et al. J. Biol. Chem. 2011. 286: 43144-43153.
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A
Non-Channeling Control
PRODH
S I P
Channeling
C792A
Channeling Test in PutA
R456M
P5CDH
PRODH
S I
P5CDH
PRODH P5CDH
I P
B
Channeling in PutA Enzymes
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PutA Functional Switching L-proline
PutP
PutA
red
red
red
red
H+
red red
red red putP
putA
red
red
red red
ox
ox
ox
ox
putP
putA
Ubiquinone Ubiquinol
O
O
CH3
R
O
O
H3C
H3C
OH
OH
CH3
R
O
O
H3C
H3C
NH
N
NH
HN
O
O
R
N
N
NH
N
O
O
R
FADox FADred
P5C Proline
Inner
Membrane
- proline + proline
Becker, DF and Thomas, E. (2001) Biochemistry 40, 4714-4721.
Flavin Redox Switch
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PutA Redox Properties in the Presence
of put Intergenic DNA
Wavelength (nm)
300 400 500 600 700
0.00
0.05
0.10
0.15
0.20
percent reduced 0 20 40 60 80 100
pote
nti
al
(V)
-0.14
-0.12
-0.10
-0.08
-0.06
-0.04
-0.02
8
1
Wavelength (nm)
Ab
sorb
an
ce
PutAox-DNA
Kd = 45 nM DNA DNA
2 e-
2 e- PutAox PutAred
PutAred-DNA
Em = -76 mV
Em = -86 mV
Kd = 98 nM
Becker and Thomas. (2001) Biochemistry 40, 4714-4721.
Em(bound) = -0.086 V (pH 7.5)
Only ~ 2-fold increase in Kd
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Proline Dependent Binding to Lipid Bilayers (Surface Plasmon Resonance Study)
Res
po
nse
(R
U)
Time (s)
-100 0 100 200 300 400 500
-40
-20
0
20
40
60
80
100
120
PutA + proline (5 mM)
Time (s)
PutA (ox)
Zhang and Becker (2004) Biochemistry 43, 13165-13174.; Zhang et al., (2007) Biochemistry 46:483-91.
Sensorgrams of oxidized PutA (20 nM) and PutA (20 nM) with 5 mM
proline binding on E. coli polar extract lipids. The arrows indicate the
starting and ending of injection of protein sample. Buffer: 10 mM
HEPES, 150 mM NaCl, pH 7.4
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Where is the membrane binding domain?
Conserved C-terminal Motif (CCM)
Zhou et al., Amino Acids. 2008 35:711.
PutA 1-1308 BjPutA
EcPutA
Singh et al. J. Biol. Chem. 2011. 286: 43144-43153.
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PutA1-1308
55-fold lower activity
PutA1-1308 Deficient in Membrane Associations
M S L S L S L S L
OX RED OX RED
WT 1-1308
Zhu, unpublished, 2012
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Conformational change in PutA with FAD
reduction
po
ten
tia
l (V
)
Emeas (mV) OX -31 -36 -48 -60 –66 -74 -85 RED Re-OX
135 kDa
119 kDa 111 kDa
log ([ox]/[red])
-1.0 -0.5 0.0 0.5 1.0
-0.09
-0.08
-0.07
-0.06
-0.05
-0.04
-0.03
Em(Conf) = - 58 mV
(pH 7.5)
Em (FAD) = - 76 mV
Zhu, W. and Becker, D. F. (2003) Biochemistry 42, 5469-5477.
PRODH P5CDH D 1 - - 1320
PutA
- -
Conformational
change
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Trp 211
Ser 216
Arg234
Wavelength (nm)
300 350 400 450 500 F
luo
rescen
ce in
ten
sit
y (
au
)
0
50
100
150
200
250
ox
red 0 2 4 6 8 10
B 1
2
Fl (a
u)
0.04
0.08
0.12
0.16
Time (s)
kobs = 0.6 s-1
Kinetics of Conformational Change
Zhu and Becker, (2005) Biochemistry 44, 12297.
PRODH P5CDH D 1 - - 1320
E. coli
- -
PutA switching from a transcriptional repressor to a membrane-bound
enzyme most likely occurs on the timescale of seconds, which is
consistent with movements of large domains and the folding and
unfolding of sections of the polypeptide chain.
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33
How does FAD control PutA conformation
and function?
Yellow
Oxidized EcPutA PRODH domain
(PDB code 1TIW)
Gray
Reduced EcPutA PRODH domain
(PDB 3ITG)
Structural changes induced by reduction of the FAD in PutA
Structural changes: 2’-OH group rotates 90o
FAD(N)5-R431 and
R431-D370 interactions are
disrupted
Srivastava et al. 2010 Biochemistry 49:560. Tanner and Becker, Proline Metabolism and PutA. Handbook of Flavins, (2012) in press.
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putC:lacZ
PutA R431M
PutA + pro
- PutA
Zhang et al., (2007) Biochemistry 46:483-91.
FAD N(5)-R431 is important for activation of membrane binding
Removal of 2’-OH group (2’-deoxyFAD) and D370 (D370A) also disrupt membrane
binding
N(5) Position is Critical
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35
Working model of redox switch in PutA
FAD reduction leads to release of C-terminal peptide
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Summary • Flavins support one-electron and two-electron transfer processes
involving the N(1), C(4a) and N(5) positions of the isoalloxazine ring system.
• Electrochemistry is a versatile tool for studying redox regulation and conformational changes
• Proline/PRODH generates mitochondrial ROS and influences signaling pathways that determine cell survival and cell death outcomes
• PutAs have fused PRODH and P5CDH domains that are connected by a substrate channeling cavity
• FAD reduction induces conformational changes in EcPutA that lead to activation of membrane binding
• Hydrogen bonding interactions at the flavin N(5) are disrupted in reduced structures of the EcPutA PRODH domain
• Redox signals originating at the flavin N(5) are likely transmitted to the surface of EcPutA via internal hydrogen bond rearrangements
• C-terminal domain of EcPutA may be involved in membrane binding