Biochemistry 530 NMR Theory and...
Transcript of Biochemistry 530 NMR Theory and...
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Biochemistry 530
NMR Theory and Practice
Gabriele Varani
Department of Biochemistry
and
Department of Chemistry
University of Washington
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1D spectra contain structural information .. but is hard to
extract: need multidimensional NMR
1D spectrum
Dispersed amides:
protein is folded
Ha: protein contains b-sheet
Downfield CH3:
Protein is folded
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1D vs 2D homonuclear NMR Spectroscopy
preparation
1D NMR
detection
t
FID
Basic structure of 1D
experiment
preparation evolution detection
t1
2D NMR
m
mixing
t2
Basic structure of 2D
experiment (e.g.
NOESY)
Jeener and Ernst, 1972
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2D homonuclear NMR Spectroscopy
preparation evolution detection
t1
2D NMR
m
mixing
t2 Basic
structure
90 90
COSY t1
t1 m
90 90 90
NOESY FID
Two basic
experiments:
NOESY and
COSY
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How to generate a 2D experiment: NOESY
1. Record numerous 1D experiments by
systematically incrementing time t1 from 0 to
tmax; the experiment generates a matrix of
points S(t1,t2) which encodes the frequency
information with respect to both t1 and t2
Typical
number of
repetitions (t1
increments)
for
homonuclear
NMR: 256-512
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How to process the data to obtain a 2D spectrum
2. Execute the FT for each experiment (each t1 value) with
respect to time t2 to generate an interferogram S(t1, w2)
3. Execute the FT with respect to t1 (for each w2 value) to
generate the final 2D spectrum S(w1,w2)
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1D vs 2D NMR spectra of a protein
1D spectrum
amides Ha Side chain CH2
Side chain CH3
NH2
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1D vs 2D NMR spectra of a protein
2D projection
representation
2D contour
representation
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“cross-peaks” in multidimensional NMR carry structural
information
2D contour
representation:
peaks outside
diagonal are called
cross-peaks
Diagonal is closely
related to 1D
spectrum
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Nuclear Overhauser Effect SpectroscopY (NOESY)
The NOESY experiments detects interactions between
spins that are close in space and dipolar coupled: the
magnetization transfer mechanism is essentially the
same as FRET in optical spectroscopy (fluorescence)
preparation evolution detection
t1
2D NMR
m
mixing
t2
x
y
zB
t1 free
precession
Iy
Sy
x
zA
SzIz
90x
90x
x
y
x
zD
mixingm
Iz cos I t1
Sz cos S t1
SI
Sy cos S t1
SI
C z
x
yIx sin I t1Sx sin S t1
Iy cos I t1
zF
x
yI
S
Sy (aSS cos S t1 + aIS cosI t1)Iy (aII cos I t1 + aSI cosS t1)
90x
x
zE
y
SI
Iz cos I t1
Sz cos S t1
(mixing)
consider a two spin system, I & S:
B
90x 90x90x
t2
A
t1
mixing
m
acquireC D FE
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1. Excite with 90o
pulse
2. During t1, spins are
labeled with their
Larmor frequency
3. The second 90o
pulse exchanges
rotates magnetization
to -z
5. The final 90o pulse
makes the signal
observable and signal
is acquired in t2
Nuclear Overhause Effect SpectroscopY (NOESY)
x
y
zB
t1 free
precession
Iy
Sy
x
zA
SzIz
90x
90x
x
y
x
zD
mixingm
Iz cos I t1
Sz cos S t1
SI
Sy cos S t1
SI
C z
x
yIx sin I t1Sx sin S t1
Iy cos I t1
zF
x
yI
S
Sy (aSS cos S t1 + aIS cosI t1)Iy (aII cos I t1 + aSI cosS t1)
90x
x
zE
y
SI
Iz cos I t1
Sz cos S t1
(mixing)
consider a two spin system, I & S:
B
90x 90x90x
t2
A
t1
mixing
m
acquireC D FE
4. Magnetization is
exchanged between
spin I and S during
the mixing time
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Cross-peaks appear between
spins which are close in space
(<5-6 A) (assignments and
structure)
When magnetization is
exchanged, spin I signal
contains information on spin
S and viceversa (cross-
peaks)
Nuclear Overhause Effect SpectroscopY (NOESY)
90x free precessiont1
90x acquiret2
90x mixingm
[Iy aII cosI t1 + Sy aSS cosS t1 + Iy aSI cosS t1 + Sy aIS cosI t1]
.[ cos I t2 + cos S t2 ]
I
S
IS
crosspeaks
diagonal peaks
IS
aIS
aSI
aSS
aIII,I)
S,I)
S,S)I,S)
F2
F1
I
I
S
S
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The mixing coefficients, aIS =
aSI are proportional to the NOE
between these two nuclei
The NOE is related to the
distance r between the two
spins and the correlation
time tc (the time for
reorientation of the IS vector
in the molecule): structure
and motion
Nuclear Overhause Effect SpectroscopY (NOESY)
90x free precessiont1
90x acquiret2
90x mixingm
[Iy aII cosI t1 + Sy aSS cosS t1 + Iy aSI cosS t1 + Sy aIS cosI t1]
.[ cos I t2 + cos S t2 ]
I
S
IS
crosspeaks
diagonal peaks
IS
aIS
aSI
aSS
aIII,I)
S,I)
S,S)I,S)
F2
F1
I
I
S
S
NOE r IS-6f (tc) m
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A simple example: a small immunogenic peptide
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A simple example: a small immunogenic peptide
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COSY and NOESY connectivities in the polypeptide unit
COSY (broken lines) and NOESY (continuous lines)
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Protein chemical structure dictates ‘local’ NOE interactions
Sequential and medium range interactions in polypeptides
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Protein secondary structure determines local NOE
interactions
Sequential and
medium range NOE
interactions in
regular turns
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Protein 3D structure determines local NOE interactions
Sequential and medium
range NOE interactions in
an a-helix
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Protein 3D structure determines NOE interactions
Medium and long range NOE interactions
in a parallel and anti-parallel b-sheets
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Patterns of NOE interactions define protein secondary
structure
Observable NOE interactions (<5 A) in
regular protein secondary structures
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NOE interactions, scalar couplings (and chemical shifts)
can be combined to define protein secondary structure
NOE interactions (<4.5 A) and scalar
coupling patterns in regular protein
secondary structures
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A simple example: a small immunogenic peptide
![Page 24: Biochemistry 530 NMR Theory and Practicecourses.washington.edu/bioc530/2011_Lectures/nmr_530.04... · 2012. 10. 26. · NMR Theory and Practice Gabriele Varani Department of Biochemistry](https://reader033.fdocuments.us/reader033/viewer/2022052023/60385663ce706314ac78a15c/html5/thumbnails/24.jpg)
A simple example: a small immunogenic peptide
![Page 25: Biochemistry 530 NMR Theory and Practicecourses.washington.edu/bioc530/2011_Lectures/nmr_530.04... · 2012. 10. 26. · NMR Theory and Practice Gabriele Varani Department of Biochemistry](https://reader033.fdocuments.us/reader033/viewer/2022052023/60385663ce706314ac78a15c/html5/thumbnails/25.jpg)
COherence transfer SpectroscopY (COSY)
Cross-section of cross-peak between HN
and Ha proton allows measurement of
scalar couplings for residue C57
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COherence transfer SpectroscopY (COSY)
The COSY experiments detects interactions
(correlation) between spins that are scalar
coupled: beware, it can only be understood
through quantum mechanics
Sx
Ix sin (I _ JIS)t1++Sx sin (S _ JIS)t1 I
Cz
ySy cos (S _ JIS)t1+
Iy cos (I _ JIS)t1+90x
x
SI
yIx sin (I _ JIS)t1+
+Sx sin (S _ JIS)t1
Dz
t2acquire
B
90x 90x
t2
C DA
t1
acquire
consider a two spin system, I & S:
x
zA
90x
x
y
zB
free precessionSzIz
Iy
Sy
t1
preparation evolution detection
t1
2D NMR
m
mixing
t2
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COherence transfer SpectroscopY (COSY)
1. Excite with 90o pulse
Sx
Ix sin (I _ JIS)t1++Sx sin (S _ JIS)t1 I
Cz
ySy cos (S _ JIS)t1+
Iy cos (I _ JIS)t1+90x
x
SI
yIx sin (I _ JIS)t1+
+Sx sin (S _ JIS)t1
Dz
t2acquire
B
90x 90x
t2
C DA
t1
acquire
consider a two spin system, I & S:
x
zA
90x
x
y
zB
free precessionSzIz
Iy
Sy
t1
2. During t1, spins are
labeled with their
Larmor frequency
3. During t1, if spins
are scalar coupled, the
signal encodes this
information as well
4. The second 90o pulse
exchanges
magnetization between
spins: spin I now has
memory of spin S and
viceversa
5. Signal is acquired in t2
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COherence transfer SpectroscopY (COSY)
Cross-peaks appear between
spins which are scalar
coupled (assignments)
90x free precessiont1
acquiret2
90x
Ix .1/2[sin (I - JIS) t1 - sin (I + JIS) t1]
.1/2[sin (I - JIS) t2 - sin (I + JIS) t2]
Sx .1/2[sin(S - JIS) t1 - sin (S + JIS) t1]
.1/2[sin (S - JIS) t2 - sin (S + JIS) t2]
I
S
IS
crosspeaks
diagonal peaks
ISISJ ISJ
F2
I,S)
I,I)
S,I)
S,S)
S ± JIS/2 I ± JIS/2
I ± JIS/2
S ± JIS/2
F1
The cross-peak fine
structure contains
information on scalar
coupling (structure)
When magnetization is
exchanged, spin I signal
contains information on spin
S and viceversa (cross-
peaks)
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Structural information: scalar couplings directly gives
you the torsion angles that define protein or n.a. structure
(Karplus, 1958)
3JHaN=5.9cos2f-1.3cosf +2.2
N
C
Ca
N
C
O
Cb
CaO
HH
H
R
Ca
H
H
f
1
3Jab=9.5cos21-1.6cos1+1.8
Cross-peaks in COSY
experiments occur only
between residues that are
scalar coupled; in turns, these
couplings can be measured in
COSY experiments
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COSY and NOESY connectivities in the polypeptide unit
COSY (broken lines) and NOESY (continuous
lines)
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Amino acid chemical structure
Different pattern of
scalar couplings
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Amino acid identification from scalar coupling patterns
Different pattern
of scalar
couplings allows
amino acid type
identification in
correlated
spectra (COSY,
2QF-COSY,
TOCSY)
This is the first
step towards
complete spectral
assignments of a
protein spectrum
(at least before
heteronuclear
NMR)
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Amino acid chemical structure leads to distinct shift for
each residue: random coil chemical shift values
Residue NH aH bH Others
Gly 8.39 3.97
Ala 8.25 4.35 1.39
Val 8.44 4.18 2.13 CH3 0.97, 0.94
Ile 8.19 4.23 1.90 CH2 1.48, 1.19
CH3 0.95
CH3 0.89
Leu 8.42 4.38 1.65,1.65 H 1.64
CH3 0.94, 0.90
Prob 4.44 2.28,2.02 CH2 2.03, 2.03
CH2 3.68, 3.65
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NOE interactions, scalar couplings (and chemical shifts)
can be combined to define protein secondary structure
NOE interactions (<4.5 A) and scalar
coupling patterns in regular protein
secondary structures