Team:TU-Munich/Modeling/Protein Predictions

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==Analysis of Receptor Sequences==
==Analysis of Receptor Sequences==
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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.<br>
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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).<br>
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 1).
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 1).

Revision as of 20:14, 2 July 2013


Prediction of Protein Structures

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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 1).

Table 1:

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: [http://www.cbs.dtu.dk/services/SignalP SignalP 4.1 Server]
Results:
Discussion:

TUM13 Modeling Signal-P.png

Prediction of Transmembrane Regions

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

TUM13 Modeling TMHMM.png


Prediction of Cellular Localization

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

figure



Choice of the SERK Receptor

Text
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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