Difference between revisions of "Wikiomics:Site Directed Mutagenesis"

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The idea here is to create a flow of work to simulate the point mutation of a single amino acid in a protein.  
 
The idea here is to create a flow of work to simulate the point mutation of a single amino acid in a protein.  
  
#First step is to choose your target.  (This is up to you).
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#First step is to choose your target.  (This is up to you.)
 
#Finding the nucleic sequence ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi ENTREZ])
 
#Finding the nucleic sequence ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi ENTREZ])
 
#What type of mutation will be introduced ? (substitution / deletion / addition)  
 
#What type of mutation will be introduced ? (substitution / deletion / addition)  
 
#Can we find the wanted mutation in other related proteins ? (Blast)
 
#Can we find the wanted mutation in other related proteins ? (Blast)
 
#How conserved is the protein we wish to mutate ?
 
#How conserved is the protein we wish to mutate ?
#Does the w.t. protein has a known 3D structure ?  (Check [http://www.rcsb.org/pdb/ PDB])  
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#Does the w.t. protein have a known 3D structure ?  (Check [http://www.rcsb.org/pdb/ PDB])  
##if not check out [http://speedy.embl-heidelberg.de/gtsp/flowchart2.html  STRUCTURE PREDICTION FLOWCHART]
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##If not, check out [http://speedy.embl-heidelberg.de/gtsp/flowchart2.html  STRUCTURE PREDICTION FLOWCHART]
 
#What are the known domains inside our protein ?  
 
#What are the known domains inside our protein ?  
 
## see [[Wikiomics:Searching for 3D functional sites in a protein structure]]
 
## see [[Wikiomics:Searching for 3D functional sites in a protein structure]]
 
## Where is the Active Site ? ([http://bioinfo2.weizmann.ac.il/~pietro/SARIG/V3/index.html SARIG])
 
## Where is the Active Site ? ([http://bioinfo2.weizmann.ac.il/~pietro/SARIG/V3/index.html SARIG])
 
## What is the location of the mutation? (surface / inside the protein)  
 
## What is the location of the mutation? (surface / inside the protein)  
#What impact does the mutation have on the protein (no backbone changes yet)
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#What impact does the mutation have on the protein? (no backbone changes yet)
 
#If the protein is a multiple subunit protein - what are the subunit interaction residues ? (CSU)
 
#If the protein is a multiple subunit protein - what are the subunit interaction residues ? (CSU)
  
 
[[Category:Protocol]] [[Category:In silico]] [[Category:Cloning]]
 
[[Category:Protocol]] [[Category:In silico]] [[Category:Cloning]]

Revision as of 19:37, 5 March 2010

This page is beta. please feel free to update it.

The idea here is to create a flow of work to simulate the point mutation of a single amino acid in a protein.

  1. First step is to choose your target. (This is up to you.)
  2. Finding the nucleic sequence (ENTREZ)
  3. What type of mutation will be introduced ? (substitution / deletion / addition)
  4. Can we find the wanted mutation in other related proteins ? (Blast)
  5. How conserved is the protein we wish to mutate ?
  6. Does the w.t. protein have a known 3D structure ? (Check PDB)
    1. If not, check out STRUCTURE PREDICTION FLOWCHART
  7. What are the known domains inside our protein ?
    1. see Wikiomics:Searching for 3D functional sites in a protein structure
    2. Where is the Active Site ? (SARIG)
    3. What is the location of the mutation? (surface / inside the protein)
  8. What impact does the mutation have on the protein? (no backbone changes yet)
  9. If the protein is a multiple subunit protein - what are the subunit interaction residues ? (CSU)