Chemical Shift
And its Use in Structure Determination
It has been know for a long while that:
1. The chemical shift is dependant on the secondary structure,
and
2. Homologous proteins have homologous shifts
= rc + sec
rc random coil shift
sec secondary shift,
Depends on
conformation
H-bond(s)
Neighboring residue type
etc
Secondary shifts for a-helix and b-sheet
Available proteins
Calmodulin//M13 MBP
Alpha-lytic protease Cutinase
HIV protease
BPTI
Cyclophyllin
Calbindin
Cyanivirin-N
Calmodulin
Dehydrase
Human carbonic
anhydrase
Human thioredoxin
red.
III-glc
Interleukin 1a
Metallo-lactamase
Profilin
Serine Protease
PB92
Staph nuclease
Ubiquitin
Residue
A
R
D
N
C
Q
E
G
H
I
L
K
M
F
P
S
T
W
Y
V
A
0
1
1
1
1
1
1
2
1
2
1
1
1
2
3
1
2
2
2
2
R
1
0
1
1
1
1
1
2
1
2
1
0
1
1
3
1
2
1
1
2
D
1
1
0
0
1
1
1
2
1
2
1
1
1
1
3
1
2
1
1
2
N
1
1
0
0
1
1
1
2
1
2
1
1
1
1
3
1
2
1
1
2
C
1
1
1
1
0
1
1
2
1
2
1
1
1
1
3
1
2
1
1
2
Q
1
1
1
1
1
0
1
2
1
2
1
1
1
1
3
1
2
1
1
2
E
1
1
1
1
1
1
0
2
1
2
2
2
1
1
3
1
2
1
1
2
G
2
2
2
2
2
2
2
0
3
3
3
3
3
3
3
3
3
3
3
3
H
1
1
1
1
1
1
1
3
0
2
1
2
2
1
3
2
2
1
1
2
I
2
2
2
2
2
2
2
3
2
0
1
2
2
2
3
2
1
2
2
0
L
1
1
1
1
1
1
2
3
1
1
0
1
1
1
3
2
2
1
1
2
K
1
0
1
1
1
1
2
3
2
2
1
0
1
2
3
1
2
2
2
2
M
1
1
1
1
1
1
1
3
2
2
1
1
0
2
3
1
2
2
2
2
F
2
1
1
1
1
1
1
3
1
2
1
2
2
0
3
2
2
0
0
1
P
3
3
3
3
3
3
3
3
3
3
3
3
3
3
0
3
3
3
3
3
S
1
1
1
1
1
1
1
3
2
2
2
1
1
2
3
0
1
2
2
2
T
2
2
2
2
2
2
2
3
2
1
2
2
2
2
3
1
0
1
1
1
W
2
1
1
1
1
1
1
3
1
2
1
2
2
0
3
2
1
0
0
1
Y
2
1
1
1
1
1
1
3
1
2
1
2
2
0
3
2
1
0
0
1
V
2
2
2
2
2
2
2
3
2
0
2
2
2
1
3
2
1
1
1
0
Agreement between measured and predicted shifts Ubiquitin
Limitation:
Size of the Database: 20.pbd files
Solution:
The Database can be ‘extrapolated’
By constructing Surfaces that describe the
(f,y) Dependance of the Secondary Shift
Shifts can be simulated for arbitrary .pdb files
.pdb database can be mined for fragments of arbitrary length
‘Inverse Talos’
Problems:
When Shifts do not depend on backbone conformation
(Cofactors, Metal Centers, Hyperfine Shifts, H-bonds)
Gly surfaces have two-fold symmetry
(potential source of errors)
No ‘long range information’
Only secondary structure information,
Tertiary structure requires additional constraints
NOE at the interfaces, RDC, etc …
Can be combined with methods of Bioinformatics,
Sequence alignment, Structure prediction,
Gb3 protein: 56 aa
CS homology
1gb3.pdb
CS homology model
LIM2