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Sai Chaitanya Chiliveri | 13 Jan 2012 09:52
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Problem with NH RDCs in orienting multi-domain protein

Hi.

This is Chaitanya from Centre for Cellular and Molecular Biology, Hyderabad, INDIA.
I am facing a weird problem in orienting multiple-domain protein using N-H RDCs.

I have a system with two domains and a flexible linker connecting them (of around 40 aa length), there are absolutely no interdomain NOEs. When I calculated some 100 structures including N-H RDCs of the individual domains, top 30 structures show similar orientation of the domains. I wonder when I use only one set of RDCs (NH RDCs with no interdomain contacts), how the top 30 structures can attain one possible orientation. I am using a script similar to anneal.inp from protG folder of Xplor-NIH.2.27.

Regards,
Chaitanya.
--
Sai Chaitanya Chiliveri
Ph.D Student
Centre for Cellular and Molecular Biology (CCMB).
Uppal Road, Hyderabad-007, A.P, INDIA.

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Anna Kuznetsova | 25 Jan 2012 00:29
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how can I modify cysteines in my peptide pdb with IAP nitroxide spin label

Dear XPLOR users,


I need to modify cysteines in my peptide pdb with IAP nitroxide spin label. I have generated so far conventional .psf  and  extended .pdb  files for my peptide to start minimization of structure with constraints. Making non conventional  .psf  and .pdb files  as well  as modifying folded (not extended)  structure in pdb by adding spin label or other things seems quite challenging to me. I have seen examples on making .psf and extended .pdb files with N-terminus and proline modifications to initiate structure calculation, but I can not figure out how to modify already existing pdb file with folded peptide in it...

I also do not know where can I get IAP spin label  parameter file to merge it with my peptide pdb using some kind of python interface script.

Any script, parameter file or advice would help me a lot!

Thank you very much for help

--
Best regards,
Anna Kuznetsova
Joanna R. Long research group
University of Florida
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Charles Schwieters | 25 Jan 2012 04:38

Re: how can I modify cysteines in my peptide pdb with IAP nitroxide spin label


Hello Anna--

> 
> I need to modify cysteines in my peptide pdb with IAP nitroxide spin label. I
> have generated so far conventional .psf  and  extended .pdb  files for my
> peptide to start minimization of structure with constraints. Making non
> conventional  .psf  and .pdb files  as well  as modifying folded (not
> extended)  structure in pdb by adding spin label or other things seems quite
> challenging to me. I have seen examples on making .psf and extended .pdb
> files with N-terminus and proline modifications to initiate structure
> calculation, but I can not figure out how to modify already existing pdb file
> with folded peptide in it...
> 
> I also do not know where can I get IAP spin label  parameter file to merge it
> with my peptide pdb using some kind of python interface script.
> 

Of course, the easiest way is to get the topology and parameter files
from someone who has already created them. Anyone?

In the absence of existing files, I can help you generate these if you
send the exact structure to me.

best regards--
Charles


--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt


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