Difference between revisions of "Predicting the Effect of SNPs (PKU)"

From Bioinformatikpedia
Line 32: Line 32:
 
===ARG158GLN===
  
===ARG158GLN===
 
From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.
  
From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.
  +
  +
[[File:Pymol_158_close.png|200px|thumb|right|Close-up of the mutated glutamine at residue 158 in PheOH. The best fitting rotamer was chosen to minimize severe or smaller collisions (red to green discs) with neighbouring residues. This rotamer appears in 1.7% of mutations according to the PyMol rotamer database.]]
  +
  +
[[File:Pymol_158.png|200px|thumb|right|Mutated glutamine at residue 158 in PheOH. The residue is located in a helix region and is statistically less likely in this type of structure than the original arginine.]]
   
 
===GLN172HIS===
  
===GLN172HIS===
   
 
From neutral, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic, ring-structure
  
From neutral, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic, ring-structure
  +
  +
  +
[[File:Pymol_172_close.png|200px|thumb|right|Close-up of the mutated histidine at residue 172 in PheOH. The best fitting rotamer was chosen to minimize severe or smaller collisions (red to green discs) with neighbouring residues. This rotamer appears in 18.9% of mutations according to the PyMol rotamer database.]]
  +
  +
[[File:Pymol_172.png|200px|thumb|right|Mutated histidine at residue 172 in PheOH. The residue is located in a coil region.]]
   
 
===ARG243GLN===
  
===ARG243GLN===
   
 
From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.
  
From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.
  +
  +
[[File:Pymol_243_close.png|200px|thumb|right|Close-up of the mutated histidine at residue 243 in PheOH. The best fitting rotamer was chosen to minimize severe or smaller collisions (red to green discs) with neighbouring residues. This rotamer appears in 17.3% of mutations according to the PyMol rotamer database.]]
  +
  +
[[File:Pymol_243.png|200px|thumb|right|Mutated glutamine at residue 243 in PheOH. The residue is located in a sheet region.]]
   
 
===LEU255SER===
  
===LEU255SER===
Line 60: Line 73:
   
 
From pos. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, slightly hydrophilic, large.
  
From pos. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, slightly hydrophilic, large.
  +
  +
==References==
  +
  +
A helix propensity scale based on experimental studies of peptides and proteins.

Revision as of 17:44, 13 June 2012

Short Introduction

This week's task builds on the data gathered last week. We blindly choose 5 disease causing and 5 harmless SNPs and will try to predict their effect from the sequence change alone. You may find a detailed task description at the usual place and consult our task journal.

Our dataset

we propose the following dataset:

  • GLU76GLY
  • SER87ARG
  • GLN172HIS
  • ARG158GLN
  • ARG243GLN
  • LEU255SER
  • MET276VAL
  • ALA322GLY
  • GLY337VAL
  • ARG408TRP

You could check them, if you like.. I put them together 5 minutes ago and already forgot, which are which. ;-)

Investigated SNPS

GLU76GLY

From neg. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, non-hydrophilic, small.

SER87ARG

From neutral, polar, slightly hydrophilic to pos. charged, polar, strongly hydrophilic.

ARG158GLN

From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.

Close-up of the mutated glutamine at residue 158 in PheOH. The best fitting rotamer was chosen to minimize severe or smaller collisions (red to green discs) with neighbouring residues. This rotamer appears in 1.7% of mutations according to the PyMol rotamer database.
Mutated glutamine at residue 158 in PheOH. The residue is located in a helix region and is statistically less likely in this type of structure than the original arginine.

GLN172HIS

From neutral, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic, ring-structure


Close-up of the mutated histidine at residue 172 in PheOH. The best fitting rotamer was chosen to minimize severe or smaller collisions (red to green discs) with neighbouring residues. This rotamer appears in 18.9% of mutations according to the PyMol rotamer database.
Mutated histidine at residue 172 in PheOH. The residue is located in a coil region.

ARG243GLN

From pos. charged, polar, strongly hydrophilic to neutral, polar, strongly hydrophilic.

Close-up of the mutated histidine at residue 243 in PheOH. The best fitting rotamer was chosen to minimize severe or smaller collisions (red to green discs) with neighbouring residues. This rotamer appears in 17.3% of mutations according to the PyMol rotamer database.
Mutated glutamine at residue 243 in PheOH. The residue is located in a sheet region.

LEU255SER

From neutral, non polar, strongly hydrophobic to neutral, polar, slightly hydrophilic.

MET276VAL

From neutral, non-polar, hydrophobic to neutral, non-polar, strongly hydrophobic.

ALA322GLY

From neutral, non-polar, hydrophobic, small to neutral, non-polar, slightly hydrophilic, small.

GLY337VAL

From neutral, non-polar, slightly hydrophilic, small to neutral, non-polar, strongly hydrophobic, medium sized.

ARG408TRP

From pos. charged, polar, strongly hydrophilic, medium sized to neutral, non-polar, slightly hydrophilic, large.

References

A helix propensity scale based on experimental studies of peptides and proteins.

Retrieved from "https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Predicting_the_Effect_of_SNPs_(PKU)&oldid=22928"