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Fehérjék 4 Simon István. Estimate the interaction energy between the residue and its sequential environment. A – 10% C – 0% D – 12 % E – 10 % F – 2 % etc …. Decide the probability of the residue being disordered based on this. Amino acid composition of environ-ment:.

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Presentation Transcript
predicting protein disorder iupred

Estimate the interaction energy between the residue and its sequential environment

A – 10%

C – 0%

D – 12 %

E – 10 %

F – 2 %

etc…

Decide the probability of the residue being disordered based on this

Amino acid composition of environ-ment:

Predicting protein disorder - IUPred
  • Basic idea:

If a residue is surrounded by other residues such that they cannot form enough favorable contacts, it will not adopt a well defined structureit will be disordered

  • The algorithm:

…..QSDPSVEPPLSQETFSDL

WKLLPENNVLSPLPSQAMDDLMLSP

D

DIEQWFTEDPGPDEAPRMPEAAPRVA

PAPAAPTPAAPAPA…..

predicting protein disorder iupred1

Amino acid composition of the residue D:

Interaction energies:

A – 10%

C – 0%

D – 12 %

E – 10 %

F – 2 %

stb…

97%, that it is disordered

Predicting protein disorder - IUPred
  • Back to p53:

E =

1.16

*0.10

+

(-0.82)

*0

+…

The predicted interaction energy:

=1.138

predicting binding sites anchor
Predicting binding sites - ANCHOR
  • 3 – Interaction with globular proteins

We consider the average amino acid composition of a globular dataset instead of the own environment:

A – 10%

C – 0%

D – 12 %

E – 10 %

F – 2 %

stb…

A – 7.67%

C – 2.43%

D – 4.92 %

E – 5.43 %

F – 3.19 %

stb…

Composition calculated on a large globular dataset

The thus gained energy:

where

predicting binding sites anchor1
Predicting binding sites - ANCHOR
  • Example: N terminal p53

Contains three binding sites:

    • MDM2: 17-27
    • RPA70N: 33-56
    • RNAPII: 45-58

P = p1*Saverage+ p2*Eint+ p3*Egain

transzmembr n feh rj k

Anyagcsere folyamatok

Transzporterek

Ion csatornák

Hordozók

Információ csere

Receptorok

Transzmembrán fehérjék
slide16

O

o

H

i

I

A HMMTOP algoritmus

slide18

Intracellular domain Q

Pfam

Prosite

Prints

Smart

Intracellular domain Q

Intracellular domain Q

Intracellular domain Q

C

Protein A

N

C

N

Protein B

S c a n n i n g

Protein C

TM selection of UniProtKB

N

C

?

?

C

TOPDOM

Unknown

Protein

N

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