Re: Modifying a peptide and introducing residues

From: felmerino_at_uchile.cl
Date: Sat Aug 14 2010 - 19:09:37 CDT

Hey,

As i see it you have two simple ways on how to proceed. When you build a psf from pdb filesyou usually use the psfgen package in vmd which
(as charmm does) reads two times your pdb file, one for knowing the sequence of your segment and another to read the known coordinates. You
can specify a new sequence for your segment that includes the ASN insertion that you need and "trick" the program later to use just the coordinates that you think are useful. However the coordinates of the new residues would not be very good at the beginning.

Also vmd has a package for building molecules and one of the options is for peptides. You just need to specify the sequence and it will build it. Later you have to apply the DISU patch to make the disulfide bond and that is all.

I guess that you need to consider the relaxation time that your system have in order to decide which of those strategies to follow.

best

felipe

PS: of course there is a bounch of other programs that can build a peptide.... vmd is just what i suppose is at hand.

----Mensaje original----

De: aditya.sia_at_gmail.com

Fecha: 14-08-2010 13:02

Para: "Jason Richard Mick"<dw2413_at_wayne.edu>

CC: <namd_at_ks.uiuc.edu>, "NAMD list"<namd-l_at_ks.uiuc.edu>

Asunto: Re: namd-l: Modifying a peptide and introducing residues

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.

ThanksAditya

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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