nmr in biophysical chemistry preview: ligand binding and
TRANSCRIPT
![Page 1: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/1.jpg)
ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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NMR in BiophysicalChemistry
Erik Zuiderweg and David Case
Preview:
Ligand Binding andAllosterics
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ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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Simple Ligand Binding:Two-site exchange
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fA=fB=0.5 kex=10-1 s-1
![Page 5: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/5.jpg)
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fA=fB=0.5 kex=100 s-1
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fA=fB=0.5 kex=101 s-1
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fA=fB=0.5 kex=102 s-1
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fA=fB=0.5 kex=103 s-1
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fA=fB=0.5 kex=104 s-1
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fA=fB=0.5 kex=105 s-1
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fA=fB=0.5 kex=106 s-1
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Fast exchange titration
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kex=106 s-1 fA=1.00 fB=0.00
! = fFREE!BOUND + fBOUND!BOUND
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kex=106 s-1 fA=0.67 fB=0.33
! = fFREE!BOUND + fBOUND!BOUND
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kex=106 s-1 fA=0.50 fB=0.50
! = fFREE!BOUND + fBOUND!BOUND
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kex=106 s-1 fA=0.33 fB=0.67
! = fFREE!BOUND + fBOUND!BOUND
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kex=106 s-1 fA=0.00 fB=1.00
! = fFREE!BOUND + fBOUND!BOUND
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SIMPLE USE:Chemical Shift Mapping
Complex:15N-2H Flavodoxin 14N-1H Methionine
SynthaseAmide H
Amide
15N
15N
14N
15N
14N
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Quantitating Fast Exchange Binding Constants
[LP] =[L]
TOT+ [P]
TOT+ K
D( ) ± [L]TOT
+ [P]TOT
+ KD( )
2
! 4[L]TOT[P]
TOT
2
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Slow exchange Titration
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kex=0.1 s-1 fA=1.00 fB=0.00
IA = fFREE IFREE IB = fBOUNDIBOUND
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kex=0.1 s-1 fA=0.67 fB=0.33
IA = fFREE IFREE IB = fBOUNDIBOUND
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kex=0.1 s-1 fA=0.50 fB=0.50
IA = fFREE IFREE IB = fBOUNDIBOUND
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kex=0.1 s-1 fA=0.33 fB=0.67
IA = fFREE IFREE IB = fBOUNDIBOUND
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ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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kex=0.1 s-1 fA=0.00 fB=1.00
IA = fFREE IFREE IB = fBOUNDIBOUND
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Quantitating Slow Exchange Binding Constants
Saturation =IBOUND
IBOUND
+ IFREE
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Range of Quantitation
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Range of Quantitation
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Range of Quantitation
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Intermediate exchangetitration
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kex=103 fA=1.0 fB=0.0
LW = fALWA + fBLWB + fA fB!A "!A( )
2
kex
![Page 32: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/32.jpg)
ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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kex=103 fA=0.9 fB=0.1
LW = fALWA + fBLWB + fA fB!A "!A( )
2
kex
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kex=103 fA=0.8 fB=0.2
LW = fALWA + fBLWB + fA fB!A "!A( )
2
kex
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kex=103 fA=0.5 fB=0.5
LW = fALWA + fBLWB + fA fB!A "!A( )
2
kex
![Page 35: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/35.jpg)
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kex=103 fA=0.2 fB=0.8
LW = fALWA + fBLWB + fA fB!A "!A( )
2
kex
![Page 36: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/36.jpg)
ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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kex=103 fA=0.1 fB=0.9
LW = fALWA + fBLWB + fA fB!A "!A( )
2
kex
![Page 37: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/37.jpg)
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kex=103 fA=0.0 fB=1.0
LW = fALWA + fBLWB + fA fB!A "!A( )
2
kex
![Page 38: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/38.jpg)
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Quantitating Kinetics
Slow Exchange : Upper limit on kex (typical: kex << 10 s-1)
Fast Exchange : Lower limit on kex (typical: kex >> 104 s-1)
Intermediate Exchange : quantify kex
(typical: 102 s-1 < kex < 104 s-1)
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Simulating two-site exchange
dMx
A(t)
dt= !"AMy
A(t) ! R
2
A+ kAB( )Mx
A(t) + kBAMx
B(t)
dMy
A(t)
dt= +"AMx
A(t) ! R
2
A+ kAB( )My
A(t) + kBAMy
B(t)
dMx
B(t)
dt= !"BMy
B(t) ! R
2
B+ kBA( )Mx
B(t) + kABMx
A(t)
dMy
B(t)
dt= +"BMx
B(t) ! R
2
B+ kBA( )My
B(t) + kABMy
A(t)
![Page 40: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/40.jpg)
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Simulating two-site exchange
i!A " R2A " kAB kBA
kAB i!B " R2B " kBA
#
$%&
'(M
+
A
M+
B
#
$%&
'(=
pAMtot
pBMtot
#$%
&'(
Steady-state solution
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ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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Simulating two-site exchange
S !( ) = Im Mtot
pA ! "!!B( ) + pB ! "
!!A( ) + i kAB + kBA( )
! "!!A( ) + ikAB( ) ! "
!!B( ) + ikBA( ) + kABkBA
#$%
&%
'(%
)%
Steady-state solution
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More Possibilities in 2D
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Ligand Binding:Three-site exchange
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Curved traces insequential 3-site exchange
2L + P ! " L + LP ! "L2P
P PL PL2
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ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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Sometimes, a two-site exchange
must be three-site exchange
KD=10-9 M
Δω=200 r/s
IHPFree
IHPBound
31P NMR
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ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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kon_max =108 M-1 s-1
KD =10-9 M
koff_max =0.1 s-1
!" =100 rs-1
IHP
Hemoglobin
IHP
Hemoglobin
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ENC-tutorial 2006:Erik RP Zuiderweg, U Michigan
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Sometimes, a two-site exchange
must be three-site exchange
KD=10-9 M
Δω=200 r/s
IHPFree
IHPBound
31P NMR
![Page 48: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/48.jpg)
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k =108 M-1 s-1
KD =10-9
M
k =104 s-1
KDa =10-4 M
k =104 s-1
k =10 9 s-1
KDb =10-5
Solution: one ligand,
two consecutive fast processes
“entry site”
![Page 49: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/49.jpg)
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Simulating three-siteexchange
d
dt
M+
A(t)
M+
B(t)
M+
C(t)
!
"
###
$
%
&&&=
i'A( R
2
A ( kAB( k
ACkBA
kCA
kAB
i'B( R
2
B ( kBA( k
BCkCB
kAC
kBC
i'C( R
2
C ( kCA
( kCB
!
"
###
$
%
&&&
M+
A(t)
M+
B(t)
M+
C(t)
!
"
###
$
%
&&&
![Page 50: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/50.jpg)
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Solution
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Ligand Binding:four-site exchange
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Ligand-binding-induced conformationalchange = 4-site exchange
k =105 M-1 s-1
k =108 M-1 s-1
k =103 s-1
k =103 s-1
k =10-2 s-1 k =10-1 s-1
k =10-1 s-1 k =10-3 s-1
![Page 53: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/53.jpg)
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k =105 M-1 s-1
k =108 M-1 s-1
k =103 s-1
k =103 s-1
k =10-2 s-1 k =10-1 s-1
k =10-1 s-1 k =10-3 s-1
![Page 54: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/54.jpg)
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k =105 M-1 s-1
k =108 M-1 s-1
k =103 s-1
k =103 s-1
k =10-2 s-1 k =10-1 s-1
k =10-1 s-1 k =10-3 s-1
![Page 55: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/55.jpg)
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k =105 M-1 s-1
k =108 M-1 s-1
k =103 s-1
k =103 s-1
k =10-2 s-1 k =10-1 s-1
k =10-1 s-1 k =10-3 s-1
![Page 56: NMR in Biophysical Chemistry Preview: Ligand Binding and](https://reader038.vdocuments.net/reader038/viewer/2022103106/586b62fc1a28abdf0a8bb7f6/html5/thumbnails/56.jpg)
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Allosterics
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Allosterics is wide-spread
•Site “b” knows whether site “a” is occupied
•“Intra-molecular signal transduction”
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e.g. signal transduction
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NMR allows delineation of theallosteric mechanism of a
cytidylyltransferase
Stevens, S.Y., Sanker, S., Kent, C. and Zuiderweg, E.R.P.,
Nature Structural Biology 8, 947-952 (2001)
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Crystal structure of CTP:glycerol-3-phosphate cytidylyltransferase
(GCTase)+ 2CTP
Courtesy ofMartha LudwigChris Weber
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An Allosteric Enzyme
CTP
CTP CTP
CTP CTP
CTP CTP
G3P
G3P G3P
G3P
G3P
G3P G3P
G3P
CTP
G3P
G3P
CTP
1 µM
(1 µM)
300 µM (300 µM)
(1500 µM)
(100 µM) (100 µM)
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CTP
CTP CTP
CTP CTP
CTP CTP
G3P
G3P G3P
G3P
G3P
G3P G3P
G3P
CTP
G3P
G3P
CTP
1 µM
(1 µM)
300 µM (300 µM)
(1500 µM)
(100 µM) (100 µM)
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CTP CHEMICAL SHIFT MAPPING
First CTPKD < 5 µM
Second CTPKD = 500 µM
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CTP
CTP CTP
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+S
+S
or
or
or
DEFINING THE KNF-ALLOSTERIC MODEL
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Where is the negative cooperativitycoming from?
First CTPΔG = -7.3 Kcal/M
Second CTPΔG = -4.6 Kcal/M
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First CTPΔG = -7.3 Kcal/M
Second CTPΔG = -4.6 Kcal/M
Binding sites identical,Expect identical localbinding free energies
Thus:2.7 Kcal/M of bindingfree energy lost on
interface
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15N R2 relaxation with and without exchange broadening suppression
GCT GCT(CTP)2GCT(CTP)
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Therefore, the allosteric free energyof negative cooperativity
has an entropic component.
GCT
Dynamic
GCT(CTP)2GCT(CTP)
Dynamic Rigid
ΔS = 0 ΔS = neg
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Other example:Allosteric energy is (partially)
dynamic in origin
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Mäler, L., Blankenship, J., Rance, M. & Chazin, W. J. Nature Struct. Biol. 7, 245 – 250 (2000).
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1 2L
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The allosteric free energy ofpositive cooperativity
has an entropic component.
Calb
Dynamic
Calb(Ca2+)2Calb(Ca2+)
Rigid Rigid
ΔS = 0ΔS = neg
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Cooper A, Dryden DT: Allostery without conformational change. A plausible model.
Eur Biophys J 1984, 11:103-109.
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Thank you for your attentionI hope this was useful…