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Re: Regarding obtaining dimer form



You got only one match in your sequence search because you ran a search for only one chain.
But because your template and target are HOMOdimer use as alignment file in your .top script this kind of alignment:

>P1;Template
StructureX:::::::
AAAAAAAAAAAAAAA/AAAAAAAAAAAAAAA
>P1;Target
Sequence::::::
BBBBBBBBBBBBBB/BBBBBBBBBBBBBBBB

good luck,
Eric

--------------------------------------------------------
Eric Feyfant, Ph.D.
Department of Biological Chemistry
WYETH Research
85 bolton St.
Cambridge ,MA 02140

tel: (617) 665 8987
fax:(617) 665 8993
email: 

>>> R Senthil Kumar <> 11/29 7:11 PM >>>

 Dear Eric,

  Thank you very much for your reply.Eric 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.

If you tell me it will be of very helpful to me.Expecting reply from you.

                                             from,
                                        Senthil kumar.R

  
     R.Senthil Kumar,
     Junior Research Fellow(JRF),
     c/o Dr.Akash Ranjan,
     Computational & Functional Genomics Group,
     Centre For DNA Fingerprinting(CDFD),
     Hyderabad-500 076
     
     Ph:040-7151344-Extn(Lab:1304)
                        (Hostel:2300)
     E-mail: 

                                              
                                              
                                               
                                              
                                              
                                              
                                              
                                              
                                                
                                              
                                              
                                              
                                              
                                              
                                              
                                              
 

On Wed, 28 Nov 2001, Eric Feyfant wrote:

> Dear Senthil;
> 
> I don't understand something you said:
> 
> you have an homodimer to model: seq: AAAAAAAAAAAAAAA/AAAAAAAAAAAA
> You got a template that is an other homodimer so with sequence like: BBBBBBBBBBBB/BBBBBBBBBBBBB (/ separate the 2 chains).
> Now you say that you got a match for only one chain????
> 
> if you can align 1 chain you should be able to align the 2nd chain since in the homodimer the 2 chains are identical?
> So the alignment should look like : 
> 
> AAAAAAAAAAAAAA/AAAAAAAAAAAAAA
> BBBBBBBBBBBBBB/BBBBBBBBBBBBBB
> 
> Now if you know the binding site between the 2 chains are different (not only in sequence but also the binding site location) the situation is more complicate and I will suggest you to use biological data and do the docking manually or using docking software like ftdock where you can specify known interaction.
> 
> For any further question, I will be happy to help you.
> 
> Eric 
> 
> --------------------------------------------------------
> Eric Feyfant, Ph.D.
> Department of Biological Chemistry
> WYETH Research
> 85 bolton St.
> Cambridge ,MA 02140
> 
> tel: (617) 665 8987
> fax:(617) 665 8993
> email:  
> 
> >>> R Senthil Kumar <> 11/28 9:06 PM >>>
> 
> 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: 
>                   
>  
>           Ph.no:040-7151344-EXTN(1304)--->Lab
>                                 (2300)--->Hostel    
>           
>        ********************************
> 
>