Wikiomics:Site Directed Mutagenesis

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(added tags)
Current revision (22:38, 5 March 2010) (view source)
m
 
(One intermediate revision not shown.)
Line 1: Line 1:
-
This page is beta. please feel free to update it.
+
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.  
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).  
+
#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])  
+
#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]
+
##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)
+
#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]]

Current revision

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)
Personal tools