View source for Mapping HSQC Chemical Shift Changes To Protein Structures

==Mapping HSQC Chemical Shift Changes To Protein Structures==


'''NOTE:''' You must first have your chemical shift assignments completed and a full structure or homology model before running this.

'''NOTE:''' For some homology models it will take more massaging of the “mapping_chem_shifts.awk” file for this to work; if there are any questions ask for help.

1.Open Linux or IRIX running environment

2.Move structure or homology model file ('''model.pdb''') and “mapping_chem_shifts.awk” file into the same directory

3.Identify the chemical shift changes in your HSQC ('''NOTE:''' it helps to sort by residue number)

4.Open with vi editor the “mapping_chem_shifts.awk” file

5.In the “mapping_chem_shifts.awk” file you will see a list of if statements (see example).  These are saying if the residue number in the pdb file matches the residue changing in the HSQC; insert a 10 to the 11<sup> th </sup> column.  For most .pdb files the residue number is in the 6<sup> th </sup> column of the file.  Append “mapping_chem_shifts.awk” so that all residues which correspond to a change in chemical shift ($6==37) add “10” to this 11th column or in other words residue 37 changed in the HSQC so it get a 10.   

6.The VMD Explorer reads the numbering scheme as gradient of changes (10=change, 0=no change, or –10=opposite change).  Therefore, there must be a -10 somewhere in the .pdb file.  Find a residue distant from the bulk of changes and add the -10 to this residue ($6==120). 
 
Example: Modifying mapping_chem_shifts.awk

if ($6==37) $11 =10.0

if ($6==45) $11 =10.0

if ($6==46) $11 =10.0

if ($6==66) $11 =10.0

if ($6==120)$11 =-10.00

7.After making the necessary modifications save and exit the awk script 

8.Run “mapping_chem_shifts.awk” (awk –f mapping_chem_shifts.awk model.pdb >> '''out.pdb''') ('''NOTE:''' this will run the awk script on your structure file and output a new pdb file.)

9.Open the newly created pdb file ('''out.pdb''') with VMD Explore ('''NOTE:''' ask how to run VMD if you need help) 

10.Generate a surface model or MS/MS model for the file and color by occupancy.  For all residues labeled with a “10” in the new .pdb file (out.pdb) the color will change to blue.  The blue regions of the protein indicate where the changes in the HSQC have taken place.   ('''A'''=root protein structure '''B'''=mapped changes in HSQC mapped to protein surface blue=10 red=-10)

[[Image:protocol mapping chemical shift changes to protein structures.png]]

[[Category:Protein_Software]]