Team:TU-Eindhoven/ProteinSelection

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{{:Team:TU-Eindhoven/Template:FloatEnd | caption=Plot of the Lysine ratio and Length of a broad range of proteins from PDB.org. Red dots represent potentially interesting proteins. | id=arginineRatioPlot }}
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{{:Team:TU-Eindhoven/Template:FloatEnd | caption=Plot of the Arginine ratio and Length of a broad range of proteins from PDB.org. Red dots represent potentially interesting proteins. | id=arginineRatioPlot }}
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Using this data a selection of interesting proteins was made for further analysis. The selection is shown below:
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{|class="table table-striped"
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! PDB ID
 +
! Frequent Amino Acid
 +
! Amount of Frequent Amino Acids
 +
! Chain Length
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! Ratio
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|-
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| 1ETF
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| Arginine
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| 11
 +
| 23
 +
| 0.48
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|-
 +
| 1IWQ
 +
| Lysine
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| 7
 +
| 19
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| 0.37
 +
|-
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| 1PJN
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| Lysine
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| 8
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| 21
 +
| 0.38
 +
|}
==References==
==References==

Revision as of 13:24, 2 July 2013

CEST Based Marker Proteins

To create bacteria with the ability to generate contrast on a CEST MRI scan, polypeptides that have that ability had to be found. Various solutions based on short Lysine, Arganine, Threonine or Serine rich sequences were proposed.McMahonDIACESTM.T. McMahon, New "Multicolor" Polypeptide Diamagnetic Chemical Exchange Saturation Transfer (DIACEST) Contrast Agents for MRI. Magnetic Resonance in Medicine 60, 803-812 (2008) However, it is hard to predict how well these sequences will express in bacteria and whether they are sufficiently stable in vivo. To avoid these problems a new approach was taken. The suitability as a CEST based marker was estimated for proteins of which the structure is already clarified.

Scanning for Candidates

For good CEST contrast a protein should have a high Lysine or Arganine content.McMahonDIACESTGiladArtificialGeneA.A. Gilad, Artificial reporter gene providing MRI contrast based on proton exchange.. Nature biotechnology 25.2, 217-219 (2007) To find these suitable proteins the [http://www.pdb.org RCSB Protein Data Bank] was queried for all entries containing proteins. This was done using the SEARCH Web Service of PDB.org, for the XML query used see query.xml. A Python program was written to analyse the obtained amino acid sequences and calculate the ratio of Lysine or Arginine to the total chain length (see PDB.py and queryPDB.py). The results are visualized in and .

TU-Eindhoven Images LysineRatio.png
lysineRatioPlot Plot of the Lysine ratio and Length of a broad range of proteins from PDB.org. Red dots represent potentially interesting proteins.
TU-Eindhoven Images ArginineRatio.png
arginineRatioPlot Plot of the Arginine ratio and Length of a broad range of proteins from PDB.org. Red dots represent potentially interesting proteins.
Using this data a selection of interesting proteins was made for further analysis. The selection is shown below:

PDB ID Frequent Amino Acid Amount of Frequent Amino Acids Chain Length Ratio
1ETF Arginine 11 23 0.48
1IWQ Lysine 7 19 0.37
1PJN Lysine 8 21 0.38

References

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