nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1....
Transcript of nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1....
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NMR-spectroscopy
of proteins in solution
- spectra and assignment
Peter Schmieder
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NMR-spectroscopy of proteins
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
The main problem
obtaining assignments
of NMR-spectra of
proteins result from the
fact that a protein is a
polymer, i.e. a repetition
of identical units
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
0.81.01.21.41.61.82.02.22.42.62.83.03.23.4 ppm
(-)-Menthol
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
11 10 9 8 7 6 5 4 3 2 1 ppm
HN-protonsIndol-HN
H-protons aliphatic protons
aromatic protons
cyclic hexapeptid
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
HN
Aromaten
Aliphaten
H CH3HN
Aromaten
Aliphaten
H CH3
1H NMR-spectrum of a protein
aromatic
aliphatic
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
Differences in the chemical shifts result from
defined elements of secondary structure
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
10 9 8 7 6 5 4 3 2 1 0 ppm
1H NMR-spectrum ofan unfolded protein
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
DO2
HO2
13C NMR-spectrum of a protein
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
DO2
HO2
15N NMR-spectrum of a protein
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
DO2
HO2
NMR-spectra of proteins are thus not that much
different from spectra of small molecules and show
similar features (chemical shift, joupling etc.).
Because of the large number of nuclei contributing to
the spectrum, the fact that they are polymers and their
size, one-dimensional spectra are not sufficient and we
need to use multidimensional ones.
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
In addition to the necessity to used multidimensional spectra the superior dispersion of the spectra of
carbon and nitrogen make heteronuclear experiments the methods of choice for protein NMR spectroscopy:
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
Recording heteronuclear spectra using the heteronucleus in natural abundance (13C=1.1% and
15N=0.4%) is not realistic with proteins. The proteins need to be labeled when expressed.
Plasmid
E.coli Zell-Lysat
Chromatographie
SDS-Gel
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
1 15H, N-HSQC 1 13H, C-HSQC
140
10.0 9.0 8.0 7.0
130
120
110
100
120
7.0 5.0 3.0 1.0
95
70
45
20
1H,15N and 1H,13C HSQC-spectra of proteins (schematic)
1H,15N HSQC 1H,13C HSQC
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
1H,15N HSQC-spectra are „fingerprints“ of proteins
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
NMR-spectroscopy of proteins
1H,13C HSQC-spectra of proteins
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Multidimensional NMR-spectroscopy
with more than two dimensions
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
Formally a 3D experiment is a combination of two
2D experiments
1. 2D-sequence
2. 2D-sequence
3D-sequence
Preparation
Preparation
Evolution
Evolution
Mixing
Mxing
Detection
Detection
Preparation Evolution (1) Mixing (1) Evolution (2) Mixing (2) Detection
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
The spectrum is then no longer a plane but
a cuboid with chemical shift on all
three axes. Intensity is then a „fourth
dimension“
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
Since the spectrum is difficult to analyze as a cuboid, planes are cut through at different chemical shifts of on
axis resulting in a stack of 2D spectra
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
3D-NMR
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
H
1D-1H-spectrum:
Region of the amino
protons, 4 signals can be
found, two of which
overlap.
2 signals
9 8 7
As a realistic example we look at an artificial region of amino protons, that are usually show overlap in the proton
spectrum of a protein.
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
H (ppm)9 8 7
8
10
6
4
2
0 Homonuclear1H-1H spectrum:
The overlap of the two
amino protons prevent
a distinction of the
otherwise resolved
protons in the aliphatic
region
H (ppm)
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
H (ppm)9 8 7
110
120
130
N (ppm)Heteronuclear
1H-15N-spectrum:
The overlap of the
two amino protons is
resolved due to
different 15N
chemical shifts.
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
In an 1H-1H-15N-3D-spectrum all overlap is resolved. Two of the faces of the
cuboid correspond to the original 2D
spectra.
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
Now we cut a „plane“ at a certain 15N chemical shift out of the cuboid.
„plane“
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
H(ppm) 9 8 7
8
10
6
4
2
0H(ppm)
9 8 7
2D „plane“
The overlap has been removed from the 1H-1H-2D spectrum
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Multidimensional NMR-spectroscopy
H (ppm)
8
10
6
4
2
0H (ppm)
9 8 7
„strip“
To handle the data in an
assignment software
they are further reduced
to „strips“.
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Sequence specific assignment
of proteins using
tripel-resonance-techniques
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
As with all other
molecules the first step
of an extraction of
information is the
assignment of
resonances – but we
have that „polymer-
problem“.
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
SH3 from
-spectrin
We need to get from here ....
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
SH3 from
-spectrin
to here ....
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
1. Which type of amino acid is present (color)2. Which aa is next to which (neighborhood)3. Comparison with the protein sequence to assign4. The order of (1) and (2) is irrelevant
A L F GA
The solution for the assignment problem is the
sequence-specific assignment
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
Besides the better dispersion of heteronuclear spectra that is utilized in 3D spectra a transfer of magnetization via scalar couplings between
heteronuclei is more efficient for labeled proteins than a transfer via proton-proton couplings.
To record spectra all three nuclei (1H, 13C and 15N) and the scalar couplings between them are therefor used. That’s why the group of NMR experiments are called:
“Tripel-resonance-experiments”
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
90 Hz
55 Hz 15 Hz
35 Hz11 Hz
7 Hz
140 HzH
HR
H H
CC
C
O
O
N
HC
R
N
H
C
C
J-couplings between heteronuclei in proteins
2JN,CO < 1Hz !!
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
Because of the differences between the aliphatic and the carbonly carbons in proteins both can be
treated separately spectroscopically:1. Chemical shiftCO ~ 170-180 ppmC ~ 10-70 ppm
2. Scalar carbon-carbon couplingJ(CO,C) ~ 55 Hz
J(C,C) ~35 Hz3. Carbonyl carbons have no protons attached.
Carbonyl carbons are a “fourth” type of nucleus.
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
H
HR
H H
CC
C
O
O
N
HC
R
N
H
C
C
HNCA
1JHN = 90 Hz
1JNC = 11 Hz
2JNC = 7 Hz
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
H
HR
H H
CC
C
O
O
N
HC
R
N
H
C
C
HN(CO)CA
1JHN = 90 Hz
1JCC = 55 Hz
1JNC = 15 Hz
2JNC < 1Hz !!
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Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
1H
15N
1/2
90x 90y
90x180x
180x
1/2 2Entkopplung
13C
180x
180x
90x
90x
3/2 3/2
180x 90x
90x 180x
3/2-t2/2
t1/2 t1/2
2
90y
90x
1/2
180x
180x
1/2
180x
Entk.
The pulse sequence of the HNCA
H N C N H
3/2+t2/2
taq
![Page 41: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/41.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
H1
C1
C3
H2 H3
C4
C2
H1
C1
C3
H2 H3
C4
C2
HNCA HN(CO)CA
= sequential signalsHN HN
C
![Page 42: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/42.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
H
HR
H H
CC
C
O
O
N
HC
R
N
H
C
C
HNCO
1JHN = 90 Hz1JNC = 11 Hz
2JNC < 1Hz !!
![Page 43: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/43.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
HN(CA)CO
H
HR
H H
CC
C
O
O
N
HC
R
N
H
C
C
1JHN = 90 Hz
1JNC = 11 Hz
2JNC = 7 Hz
1JCC = 55 Hz1JCC = 55 Hz
![Page 44: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/44.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
H1
C1
C3
H2 H3
C4
C2
HN(CA)CO
= sequential signals
H1
C1
C3
H2 H3
C4
C2
HNCO
HN
CO
HN
![Page 45: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/45.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
HNCACB
H
HR
H H
CC
C
O
O
N
HC
R
N
H
C
C
1JHN = 90 Hz
1JNC = 11 Hz
2JNC = 7 Hz
1JCC = 35 Hz
1JCC = 35 Hz
![Page 46: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/46.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
HN(CO)CACB
H
HR
H H
CC
C
O
O
N
HC
R
N
H
C
C
1JHN = 90 Hz
1JCC = 55 Hz
1JNC = 15 Hz
1JCC = 35 Hz
![Page 47: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/47.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
HN HN
① ② ③ ④ ① ② ③ ④
C
C
HN(CO)CACB HNCACB
![Page 48: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/48.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
H1
C1
C3
H2 H3
C4
C2
H1
C1
C3
H2 H3
C4
C2
HNCA HN(CO)CA
= sequential signalsHN HN
C
![Page 49: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/49.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
12 4
3
H2
C1
C3
H3 H4
C4
C2
To do the assignment we do a
„sequential walk“.Blue arrows correspond to blue peaks,
red arrows to red peaks.
The connection represented by the
green arrows can be made by keeping
the frequency (and thus the nucleus)
constant
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
Using the HNCA/HN(CO)CA there can be the problem
that two C shifts are identical.
Then it is possible to use the pair HNCO and
HN(CA)CO as well in a similar fashion and it is unlikely
that overlap occurs in both.
But it is even better to used C and C simultaneously
in the HNCACB and HN(CO)CACB pair.
![Page 51: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/51.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
HN HN
① ② ③ ④ ① ② ③ ④
C
C
HN(CO)CACB HNCACB
Sequential assignment
![Page 52: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/52.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
7.0 8.0 9.0 7.0 8.0 9.0
60.0
40.0
20.0
Sequentielle Zuordnung
HN(CO)CACB HNCACB
![Page 53: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/53.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
Sequentielle Zuordnung
60.0
40.0
8.87.67.98.0 8.57.37.67.7
20.0
13C
(ppm
)
1H (ppm)8.87.67.98.0 8.57.37.67.7
1H (ppm)
60.0
40.0
20.0
13C
(ppm
)
(113.49 ppm) (116.21 ppm) (111.16 ppm) (118.74 ppm) A56 Y57 V58 K59
HN(CO)CACB HNCACB
![Page 54: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/54.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
Using those pairs of triple resonance experiments it is
possible to establish a sequential neighborhood.
To be able to compare the stretches of amino acids with
the sequence in order to obtain the final assignment we
need information on the type of amino acid.
That can be obtained from the chemical shifts of the
C und C, that are available from the HNCACB or
HN(CO)CACB
![Page 55: nmr proteins assignment - schmieder.fmp-berlin.info · Sequence specific assignment of proteins 1. Which type of amino acid is present (color) 2. Which aa is next to which (neighborhood)](https://reader033.fdocuments.net/reader033/viewer/2022042921/5f67f1fc736d9d2e3163bff6/html5/thumbnails/55.jpg)
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
Sequence specific assignment of proteins
Amino acid „typing“Ala 53,170 18,990Arg 56,810 30,680Asn 53,550 38,710Asp 54,700 40,880Cys 58,190 32,810Gln 56,610 29,180Glu 57,360 30,000Gly 45,370His 56,490 30,220Ile 61,650 38,610Leu 55,660 42,300Lys 56,970 32,790Met 56,140 33,000Phe 58,130 39,950Pro 63,350 31,850Ser 58,760 63,800Thr 62,260 69,730Trp 57,730 29,970Tyr 58,140 39,300Val 62,530 32,720
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Beerbaum/SchmiederAG Solution-NMR
Practical course „Molekulare Pharmakologie und zelluläre Signaltransduktion : NMR-spectroscopy
http://schmieder.fmp-berlin.info/teaching/lehre_unis_berlin.htm
That‘s it