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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 -helix and -sheet
Available proteins
Alpha-lytic protease
BPTI
Calbindin
Calmodulin
Calmodulin//M13
Cutinase
Cyclophyllin
Cyanivirin-N
Dehydrase
MBP
HIV protease
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
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
1gb3.pdb CS homology model
CS homology
LIM2