Makromolekulak_2010_12_07 Simon István

Prion protein

p27 Kip1 IA 3 FnBP Tcf3 Bound IUP structures

Aminosav összetételek Radivojac et al. Protein Sci. 2004;13: Rövid, hosszú, N- és C- terminális régiókban lévő részeknek más-más aminosav összetételük van

1.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 3.Machine learning algorithms (SVM, NN) Datasets PDB for ordered short and long disorder Prediction of protein disorder from the amino acid sequence Prediction of protein disorder from the amino acid sequence

Pairwise energy calculated from structure

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: P ij Estimation of pairwise energies from amino acid compositions

Estimated energies correlate with calculated energies Corr coeff: 0.74

Estimated pairwise energies of globular proteins and IUPs IUPs Glob

IUPred:

P53 Tumor antigen

IUPs: high frequency in proteomes coli yeast

Erdős-Rényi The yeast interactome Barabási-Albert Networks

The mediator complex

Hub proteins contain more disordered regions in all four genomes

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

Lack of segmentation of the interfaces of IUPs IUPs Glob

LM – average disorder profiles local drop in disorder

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

Predicting protein disorder - IUPred Back to p53: A – 10% C – 0% D – 12 % E – 10 % F – 2 % stb… Amino acid composition of the residue D: The predicted interaction energy: E = Interaction energies: 1.16*0.10+(-0.82)*0+… = %, that it is disordered

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 - ANCHOR Example: N terminal p53 Contains three binding sites: –MDM2: –RPA70N: –RNAPII: The three quantities are combined optimally to best distinguish binding sites. This is converted into a p-value (probability of the residue forming a disordered binding site). P = p1*S average + p2*E int + p3*E gain

Application: Segmented binding LONGER DISORDERED CHAINS: p27 – CDK2-CyclinA The predictor was also tested on binding regions longer than 30 amino acids. An example is human p27 that consists of a strongly interacting N-terminal domain (D1, residues 25-36) followed by a linker helix (LH domain, residues 38-60) followed by D2 domain (residues 62-90) containing 3 regions of strong interaction. Figure 4 shows the prediction results and their mapping onto the crystal structure of the complex. The correlation between the prediction score (shown in blue) and the number of atomic contacts (shown in green) is evident showing that the prediction identifies strongly interacting regions only. Figure 4: Prediction output for human p27 (upper) and the identified regions mapped to the structure (lower). CDK2-Cyclin complex is shown is blue, p27 is shown in yellow with the identifi- ed regions shown in red. PDB code: 1jsu LONGER DISORDERED CHAINS: p27 – CDK2-CyclinA The predictor was also tested on binding regions longer than 30 amino acids. An example is human p27 that consists of a strongly interacting N-terminal domain (D1, residues 25-36) followed by a linker helix (LH domain, residues 38-60) followed by D2 domain (residues 62-90) containing 3 regions of strong interaction. Figure 4 shows the prediction results and their mapping onto the crystal structure of the complex. The correlation between the prediction score (shown in blue) and the number of atomic contacts (shown in green) is evident showing that the prediction identifies strongly interacting regions only. Figure 4: Prediction output for human p27 (upper) and the identified regions mapped to the structure (lower). CDK2-Cyclin complex is shown is blue, p27 is shown in yellow with the identifi- ed regions shown in red. PDB code: 1jsu Example: human p27 Inhibitor of CDK2-CyclinA complex. 3 domains become ordered during binding: D1 binds strongly LH forms a helix, binds weakly and steers the third domain to place D2 binds strongly but not evenly – contains 3 subdomains that give the majority of binding energy We are able to identify strongly interacting regions separately

Rendezetlenség predikció - IUPred

„Ismeretlen” szekvencia – predikciók

ANCHOR PSIPRED

„Ismeretlen” szekvencia – predikciók A modellünk: DNS kötő, globuláris domén rendezetlen részek kötőhely, részben  -helikális kötőhely,  -helikális kötőhely, nincs szerkezeti info A valóság (p53): DNS kötő, globuláris domén MDM2 kötőhely RPA70N és RNAPII kötőhely (átfedőek) regulációs kötőhely, 4 partner (különböző konformációk) tetramerizációs régió,  -helikális