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Chemical Shift And its Use in Structure Determination. It has been know for a long while that: The chemical shift is dependant on the secondary structure, and Homologous proteins have homologous shifts. = W rc + W sec rc random coil shift sec secondary shift, Depends on

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Chemical Shift And its Use in Structure Determination

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Chemical shift and its use in structure determination

Chemical Shift

And its Use in Structure Determination

  • It has been know for a long while that:

  • The chemical shift is dependant on the secondary structure, and

  • Homologous proteins have homologous shifts


Chemical shift and its use in structure determination

  • = Wrc + Wsec

  • rc random coil shift

  • sec secondary shift,

    Depends on

    conformation

    H-bond(s)

    Neighboring residue type

    etc


Chemical shift and its use in structure determination

Secondary shifts for a-helix and b-sheet


Chemical shift and its use in structure determination

Available proteins

Alpha-lytic protease

BPTI

Calbindin

Calmodulin

Calmodulin//M13

Cutinase

Cyclophyllin

Cyanivirin-N

Dehydrase

MBP

HIV protease

Human carbonic anhydrase

Human thioredoxin red.

Serine Protease PB92

Staph nuclease

Ubiquitin

III-glc

Interleukin 1a

Metallo-lactamase

Profilin


Chemical shift and its use in structure determination

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

R1  0  1  1  1  1  1  2  1  2  1  0 1 1  3  1  2  1  1  2

D1  1  0  0  1  1  1  2  1  2  1  1  1  1  3  1  2  1  1  2

N1  1  0  0  1  1  1  2  1  2  1  1  1  1  3  1  2  1  1  2

C1  1  1  1  0  1  1  2  1  2  1  1  1  1  3  1  2  1  1  2

Q1  1  1  1  1  0  1  2  1  2  1  1  1  1  3  1  2  1  1  2

E1  1  1  1  1  1  0  2  1  2  2  2  1  1  3  1  2  1  1  2

G2  2  2  2  2  2  2  0  3  3  3  3  3  3  3  3  3  3  3  3

H1  1  1  1  1  1  1  3  0  2  1  2  2  1  3  2 2 1  1  2

I2  2  2  2  2  2  2  3  2  0  1  2  2  2  3  2  1  2  2  0

L1  1  1  1  1  1  2  3  1  1  0  1  1  1  3  2  2  1  1  2

K1  0  1  1  1  1  2  3  2  2  1  0  1  2  3  1  2  2  2  2

M1  1  1  1  1  1  1  3  2  2 1  1  0  2  3  1  2  2  2  2

F2  1  1  1  1  1  1  3  1  2  1  2  2  0  3  2  2  0  0  1

P3  3  3  3  3  3  3  3  3  3  3  3  3  3  0  3  3  3  3  3

S1  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

W2  1  1  1  1  1  1  3  1  2  1  2  2  0  3  2  1  0  0  1

Y2  1  1  1  1  1  1  3  1  2  1  2  2  0  3  2  1  0  0  1

V2  2  2  2  2  2  2  3  2  0  2  2  2  1 3  2  1  1  1  0


Chemical shift and its use in structure determination

Agreement between measured and predicted shifts Ubiquitin


Chemical shift and its use in structure determination

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’


Chemical shift and its use in structure determination

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,


Chemical shift and its use in structure determination

Gb3 protein: 56 aa


Cs homology

CS homology

CS homology model

1gb3.pdb


Chemical shift and its use in structure determination

LIM2


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