Regarding obtaining dimer form
Dear modeller users,
I am modelling a protein which is of homodimer in nature and this protein matched with the same family protein which is also of homodimer.
But matching with the only one chain(of two chains).So , i got a model in a monomer form.How i have to use the modeller to get the replicate of other monomer so my model will be of homodimer in nature.Please suggest me ideas to overcome this problem.Thanks in advance.Expecting reply from your people.
******************************** R.Senthil kumar Junior Research Fellow(JRF), C/O Dr.Akash Ranjan, Computational & Functional Genomics(CFG), Centre for DNA Fingerprinting & Diagnostics(CDFD), ECIL road, Nacharam, Hyderabad - 500 076. India.
E-mail:skumar@www.cdfd.org.in senkumar7@yahoo.com
Ph.no:040-7151344-EXTN(1304)--->Lab (2300)--->Hostel
********************************
Hi,
It is not clear to me from your question whether the template structure is actually in the dimeric form. Assuming it is, modeling a dimer is very easy with MODELLER. All you need to do is align the sequences of both monomers with the sequences of the corresponding monomers in the template structure.
Your alignment would look like this:
>P1;template structure:template:1:A:200:B::::: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB* >P1;target sequence::::::::: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX/YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY*
where the slash ('/') indicates the end of a chain. A, B are the two chains in the template. X, Y are the two copies of the target sequence.
You would use exactly the same procedure for a heterodimer. Since you have a homodimer you may also want to consider adding symmetry restraints during model building. For an example on this check the following list message:
http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/archives/modeller_us...
I hope this helps.
Best,
-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/
R Senthil Kumar wrote:
> Dear modeller users, > > I am modelling a protein which is of homodimer in nature and this protein > matched with the same family protein which is also of homodimer. > > But matching with the only one chain(of two chains).So , i got a model in > a monomer form.How i have to use the modeller to get the replicate of > other monomer so my model will be of homodimer in nature.Please suggest me > ideas to overcome this problem.Thanks in advance.Expecting reply from your > people. > > ******************************** > R.Senthil kumar > Junior Research Fellow(JRF), > C/O Dr.Akash Ranjan, > Computational & Functional Genomics(CFG), > Centre for DNA Fingerprinting & Diagnostics(CDFD), > ECIL road, Nacharam, > Hyderabad - 500 076. > India. > > E-mail:skumar@www.cdfd.org.in > senkumar7@yahoo.com > > Ph.no:040-7151344-EXTN(1304)--->Lab > (2300)--->Hostel > > ******************************** > > > >
Dear friends,
Thank you very much for your replies.First i will tell my problem clearly.
I am having a protein of 274 amino acids.When i searched for the template for this protein it picked up the template which is of homodimer in nature. i.e, it is having
aaaaaaaaaaaaaa/aaaaaaaaaaaaaaaaa(two chains).My protein is also belong to the same family of template.In this family homodimer is of active form.
My protein matching with only to the first chain.
If i go ahead with this alignment i will get my peotein in monomeric form.
My question is
1.Whether i can go ahead and get my protein in monomeric form and after that i can do any trick to convert it into homodimer form-->how to do this.
2.else in the alignment itself can i do any trick so that i can get homodimer model of my protein--->how to do this. or in the script file.
If you tell me it will be of very helpful to me.Expecting reply from you.
from, Senthil kumar.R
participants (2)
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R Senthil Kumar -
Roberto Sanchez