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Sequence Homology Treat or Trick?. Fine Grain Structural Classification using the T-RMSD method Cedric Notredame Luis Serrano Cedrik Magis François Stricher Almer van der Slot. Same sequence Same structure. Same Sequence. Same Origin. Same Function. Same 3D fold.

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sequence homology treat or trick

Sequence Homology Treat or Trick?

Fine Grain Structural Classification using the T-RMSD method

Cedric Notredame

Luis Serrano

Cedrik Magis

François Stricher

Almer van der Slot

same sequence same structure
Same sequence Same structure

Same

Sequence

Same

Origin

Same

Function

Same

3D fold

same sequence same structure1
Same sequence Same structure ???

Prion protein

PrP-c

(normal)

Prion protein

PrP-sc

(pathology)

100% Identical

Sequence

>P04156|23-230 / PRIO_HUMAN

KKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGS

100% Identical

Sequence

tnf receptors tnfrs
TNF Receptors (TNFRs)

Receptor

Ligand

Intra

Extra

Aggarwal, BB. Nat RevImmunol. 2003 Sep;3(9):745-56.

tnfr and crd collections
TNFR and CRD Collections

Domain Databases

UNIPROT

17

4

2

34

10

0

1

25 annotated

notidentified

6 putativesnotidentified

classifications
Classifications
  • If they are so different and diverse
    • Can we classify them?
    • Can this classification bring functional information?
structurally
Structurally?

Not really…

phylogeny
Phylogeny?

Not quite there…

add hoc
Add-hoc?

Maybe…

add hoc1
Add-hoc?

Maybe…

Bodmer, JL., Schneider, P., Tschopp, J. Trends Biochem. Sci. 2002 Jan;27(1):19-26.

add hoc2
Add-hoc?
  • Half Domains
  • Complex
  • Explains Little

Maybe…

a new classification
A new Classification ?
  • Is it possible to design a new classification
    • Structure based
    • Functionally informative
    • Predictive for TNFRs without a known structure
  • Yes if we can compare structures in a more informative way
the standard way rmsd root mean square deviation
The Standard Way: RMSD(Root Mean Square Deviation)
  • RMSD
    • Superpose the Structures
    • Measure The deviation

D1

D2

Z

X

D3

Y

W

t rmsd trees based on irmsd

UPGMA

C

A

B

D

T-RMSD: Trees based on iRMSD

Dd2

Dd1

A

B

C

D

P1

Distance

Matrix

P1

B

t rmsd trees based on irmsd1

C

A

B

D

T-RMSD: Trees based on iRMSD

Dd1

Dd2

A

B

C

D

P1

A

A

C

C

C

A

B

B

B

D

D

D

Consensus Tree

what does the new classification predict
What Does the New Classification Predict ?

Type I

Type II

Type III

Outliers

what does the new classification predict1
What Does the New Classification Predict ?

Type I

Type II

Type III

Outliers

Nter CRDs (Pre Ligand Assembly

Domains, PLAD) are involved in the

complex formation

slide26
Next ???
  • New Classes ?
  • New Functions ?
  • New Structures

???

slide27
Next ???
  • Which Ligand
  • How To Align These things
    • MSA problem

???

summary
Summary
  • T-RMSD
    • Fine Grain Structural Classification
  • TNFRs/CRD
    • New typology
    • Structurally meaningful
    • Functionally informative
    • Predictive
  • T-RMSD is available for download and part of the T-Coffee package (www.tcoffee.org)
  • Collaborators
    • Cedrik Magis
    • François Stricher
    • Almer van der Slot
    • Luis Serrano
    • Cedric Notredame
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