Re: Changing the Secondary Structure of a Protein

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Sun Dec 28 2008 - 16:33:28 CST

Hello Mike, given the residue numbers you gave, I think I know which
protein you're talking about, because I faced a similar problem with
it. If that is the case, there is a more recent NMR structure (1X02)
that may be a better starting point than changing manually the older
X-ray one.

Bests
Giacomo

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
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---- ----

On Sun, Dec 28, 2008 at 8:18 AM, MIke S <vmd.namd_at_gmail.com> wrote:
> Hello,
>
> I would like to modify the secondary structure of my protein prior to
> running a simulation in NAMD.
>
> Currently when I load the (crystallographic) PDB in VMD certain residues
> (78-81) are helical. However, I would like to change these residues to be
> turns or coils since NMR data show that these residues are not in
> fact helical (ie. the conditions used in the crystallographic study promoted
> helical formation in this region of the protein).
>
> I've glanced at some of the previous messages posted on VMD with regards to
> STRIDE and making changes to secondary structure. I've tried the suggestion
> in this post
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/0849.html which
> worked, however when I tried to save the corresponding PDB file the changes
> to the secondary structure weren't preserved. Obviously, using the
> 'structure' command only changes the graphic image of the protein in the VMD
> display...and my knowledge of STRIDE is slim. I was hoping to save a PDB
> file with the corresponding structural changes and follow that up with a run
> of psfgen to generate the necessary PSF and PDB files for my NAMD
> simulations.
>
> How can I make the necessary changes to the protein structure and save this
> to a file? I assume I will need to manipulate some of the data listed in
> the PDB or PSF files. In fact, I've played around with the HELIX string in
> the PDB file and modifyed the residues listed in the HELIX string of
> interest, but it didn't work - at least when I checked the structure on VMD
> the residues were still helical. Also, if I need to manipulate the
> dihedral angles for example, how do I know which phi and psi values to use
> for a coil or turn?
>
> Some side notes:
> There aren't any NMR PDB files of the full protein that I'm aware of. In
> addition to the above residues there are other residues that would need
> structural changes. I've used the program SwissPDB Viewer to add missing
> residues (1-4) and for some reason these residues are helical even though
> they should be coiled. (For those familiar with SwissPDB: I've tried to
> change the secondary structure using the control panel in SwissPDB
> before importing to VMD, but the structure remains helical). Btw, I'm using
> the latest versions of VMD and NAMD.
>
> I hope someone can offer some assistance.
>
> Happy Holidays,
>
> Mike
>
> (PS. I also posted this on the NAMD mailing list)
>
>
>
>
>

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