Team:TU-Munich/Modeling/Protein Predictions

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Prediction of Protein Structures

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Table 1:

Predicted Structures

Search for Homologous Structures using HHprd

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figure

Prediction of Possible Structure using iTasser

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figure



Analysis of Receptor Sequences

For several purposes in our project we needed a synthetic receptor that enables us to express protein-domains at the cellular or extracellular side of the cell membrane. As a template we investigated several different plant-receptors form the well understood dicotyledon Arabidopsis thaliana and the moss we are currently using as our chassis Physcomitrella patens. The A. taliana-receptors have the advantage that their transgenic expression has successfully been demonstrated (Ref.) whereas the P. patens-receptors bear less risk that they do not function in the evolutionary distant moss (Ref).
As there were many different availible receptors that we could use as a template for our synthetic receptor we applied bioinformatical methods to evaluate the suitability of thes receptors. From this work the three examples ERF, FLS2 and SERK are shown (see Table 2).

Table 2:

Examined Receptors

Receptor Organism Length (aa) Sequence reference
ERF A. thaliana 1031 [http://www.ncbi.nlm.nih.gov/protein/NP_197548.1 NP_197548.1]
FLS2 A. thaliana 1173 [http://www.ncbi.nlm.nih.gov/protein/NP_199445.1 NP_199445.1]
SERK P. patens 625 [http://www.ncbi.nlm.nih.gov/protein/XP_001759122.1 XP_001759122.1]


Prediction of Signal Peptides

Introduction: The first analysis were performed to identify the signal-peptide that is bound by the cellular signal recognition particle and lead to the translocation of the polypeptide into the ER. The signal peptide becomes afterwards cleaved by a signal peptidase at a distict site. The analysis of the signal peptides was carried out using the [http://www.cbs.dtu.dk/services/SignalP SignalP 4.1 Server].
Results: The prediction of the signal peptides was carried out for different receptors and will be illustrated for the three mentioned examples for which a signal peptide could be identified (see fig. 3).
The figure shows the N-terminal sequence of the receptors together with three scores: (1) the C-score (raw cleavage site score) in red, (2) the S-score (signal peptide score) in green and (3) the Y-score (combined cleavage site score) in blue.
The C-score shows the most probable cleavage site for the signal peptidase that could be identified for all shown receptors with a unclear result with two possible cleavage sites for the SERK-receptor. The amino acid with the highest C-score is according to the algorithm predicted to be the first amino acid of the cleaved receptor. The S-score was developed to identify amino acid sequences the lie in a polypeptide and others that do


Discussion:

Figure 3:

Prediction of Transmembrane Regions

Introduction: [http://www.cbs.dtu.dk/services/TMHMM TMHMM]
Results:
Discussion:

Figure 4:


Prediction of Cellular Localization

Introduction: [http://wolfpsort.org Wolfpsort]
Results:
Discussion:

figure



Choice of the SERK Receptor

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figure

Analysis of Protein-Ligand Interaction

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Structure based prediction using PDBePISA

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figure

References:

http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984

  1. http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984 Edens, L., Bom, I., Ledeboer, A. M., Maat, J., Toonen, M. Y., Visser, C., and Verrips, C. T. (1984). Synthesis and processing of the plant protein thaumatin in yeast. Cell, 37(2):629–33.




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