1 / 19

Fehérjék 3. Simon Ist ván

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

ginger-mcdowell
Download Presentation

Fehérjék 3. Simon Ist ván

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Fehérjék 3.Simon István

  2. Bound IUP structures Tcf3 p27Kip1 IA3 FnBP

  3. Bound IUPs – conformations A1 A2 D A1

  4. IUPs – preformed elements

  5. 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

  6. Pairwise energy calculated from structure

  7. 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

  8. Estimated energies correlate with calculated energies Corr coeff: 0.74

  9. Estimated pairwise energies of globular proteins and IUPs IUPs Glob

  10. 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…..

  11. Globular proteins are not representative of full genomes Human genome Probable IUPs TM ? GLOB

  12. IUPs: high frequency in proteomes yeast coli

  13. Barabási-Albert Erdős-Rényi Networks The yeast interactome

  14. LM – average disorder profiles local drop in disorder

  15. Distinct interfaces of disordered proteins • More hydrophobic • More residue-residue contacts • Less segments

More Related