My software notes

July 19, 2012

[Xplor-NIH] modified residues (protein)

Filed under: xplor/xplor-nih/cns — kpwu @ 1:02 am
Tags: , , ,

I searched the Xplor-NIH mailing list to know how many modified amino acids are supported in Xplor-NIH.

So far, I can see N-terminal acetylation and spin labeled (MTSL) cysteine are documented in the mailing list. I wonder to know if acetylated lysine, phosphorylated serine, threonine and methylation are also supported in Xplor-NIH.

Here is the example of N-terminal acetylation and MTSL-labeled cysteine:

code: ACE = N-terminal acetylation. Xplor-NIH set it as an individual residue
CYSP = spin labeled cysteine.

Steps to do:

  1.  edit your sequence file: (3-letter code, residues are separated by space), add ACE as the first residue and change the desire CYS to CSYP
  2. in typical xplor-nih anneal.py (see such example scripts in xplor-nih home/eginputs), around line 35-45, change to:
    # generate PSF data from sequence and initialize the correct parameters.
    #
    from psfGen import seqToPSF
    #seqToPSF(open(‘xyza.seq’).read())
    seqToPSF(“xyza.seq”, seqType=’prot’, startResid=0)

    –> The original script was marked off and a similar script was shown here. I also alter the number start residue to “0”.  That will be easier for me while doing NOESY assignment without shifting my residue numbers

  3. Then, run “xplor -py anneal.py” to check if the generated template PDB have correct residue numbers and the modified amino acids.

Here is the snapshot of my generated template PDB. (ACE as residue 0, CYSP as residue 2)

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2 Comments »

  1. As a fellow structural biologist – love your blog, you’ve provided a lot of helpful info here.
    Esp your script from 2006 for calculating intra/inter residual NOEs – saved me a ton of time!
    Best,
    Aravinda

    Comment by Aravinda — July 30, 2012 @ 6:53 pm | Reply

    • Thanks, Aravinda. I am glad that my little script is helpful to your work.

      Comment by kpwu — July 30, 2012 @ 11:00 pm | Reply


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