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Fehérjék 3. Simon Ist ván. Bound IUP structures. Tcf3. p27 Kip1. IA 3. FnBP. Bound IUPs – conformations. A1. A2. D. A1. IUPs – preformed elements. Prediction of protein disorder from the amino acid sequence. Dunker order promoting: W, C, F, I, Y, V, L, N

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bound iup structures
Bound IUP structures

Tcf3

p27Kip1

IA3

FnBP

slide8

Prediction of protein disorder

from the amino acid sequence

  • Dunker
  • order promoting: W, C, F, I, Y, V, L, N
  • disorder promoting: K, E, P, S, Q, G, R, G, A
  • 2. Uversky
  • High net charge/ low average hydrophobicity
  • Machine learning algorithms
  • (SVM, NN)
  • Datasets
  • PDB for ordered
  • short and long disorder
slide10

Estimation of pairwise energies from amino acid compositions

To take into account that the contribution of amino acid i depends on its interaction partners, we need a quadratic form in the amino acid composition

The connection between composition and energy is encoded by the 20x20 energy predictor matrix: Pij

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…..

slide16

Barabási-Albert

Erdős-Rényi

Networks

The yeast interactome

slide17

LM – average disorder profiles

local drop in disorder

slide19

Distinct interfaces of disordered proteins

  • More hydrophobic
  • More residue-residue contacts
  • Less segments