Re: Modifying a peptide and introducing residues

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Sat Aug 14 2010 - 12:02:19 CDT

Thanks Jason,

Is there a way I can built a linear chain of residues using some peptide
builder and then introduce a disulphide bond between the two cysteine
residues in the sequence and then energy minimize and equilibrate the
structure? Would it be an easier way to achieve what I want. Could you
elaborate a way that could be done if it is possible as I`m quite a novice
here.

Thanks
Aditya

On Sat, Aug 14, 2010 at 7:07 PM, Jason Richard Mick <dw2413_at_wayne.edu>wrote:

> Hi Aditya,
> You should look at how patch residues (PRES) are applied to serine and
> other amino acid residues in the latest version of CHARMM. A patch lets you
> add a small modification on to amino acids (see phosphorylated serine, for
> example). This would be the easiest and most efficient route to accomplish
> what you are asking.
>
> As for the Asn residue, that's a bit more challenging. What you will
> likely have to do is figure out how much space the Asn is going to occupy
> and then shift the coordinates of the previous residues accordingly,
> inserting the new residue in your PDB file, while making sure your R-chain
> isn't overlapping the rest of residues. Molecular modelling tools like
> Gaussian View (if you have access to it) may even allow you to directly do
> this, without even editing the PDB file by hand or by script.
>
> Good luck!
>
> Cheers,
> Jason
>
> ------------------------------
> *From: *"Aditya Ranganathan" <aditya.sia_at_gmail.com>
> *To: *namd_at_ks.uiuc.edu, "NAMD list" <namd-l_at_ks.uiuc.edu>
> *Sent: *Saturday, August 14, 2010 6:57:28 AM
> *Subject: *namd-l: Modifying a peptide and introducing residues
>
>
> Hello All,
>
> I`m at the moment looking at starting a simulation with somatostatin which
> is 14-residues long and has the following sequence:.*
> Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys.*
> However, the only coordinates available on PDB and structures resolved are
> of synthetic constructs of somatostatin analogues which have modified
> residues or nontypical residues. Is there a method by which I could change
> those non-typical residues like D-TRYPTOPHAN or 3-IODO-TYROSINE or 4-[(ISOPROPYLAMINO)METHYL]PHENYLALANINE
> to the ones which are present in the actual peptide.
> Also, the coordinates of analogue structure in PDB does not have the Asn
> residue which is present in somatostatin peptide at the 5th position between
> the Lys and Phe residues.
> Is there a way I could add the missing residue to the available PDB file? I
> would also like to notify that the peptide forms a ring like structure or
> cyclic structure between the Cys at the 3rd position and Cys at the last
> position.
>
> Please help me out with this as I need it urgently as a part of my project.
>
> Thanks,
>
> Srivastav Ranganathan
> Junior Research Assistant and Masters Student,
> IIT-Bombay, Mumbai,
> India
>

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