Hi Ben. I'm interested in using a crystal structure deposited in the PDB (structure A). However, there are two important loops missing. There is another homologous structure B from another source organism, where those loops are well defined inside electron density. I like to use the experimental data from this template B to model the missing loops in the structure A. I've tried to model the entire sequence of protein A using the B structure as a template, then cut and paste the generated loops from the model and put into the structure A. However, it did not work because many steric collisions occurred between the side chains of those loops and protein A. Carrying out loop modeling (loop.py) correct the clashes, but gives results extremely different from observed in template B. How do I model the missing loops directly in the structure A? Is it possible?
I appreciate any suggestion.
Regards
Flavio
------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br
On 4/5/14, 8:05 AM, flavio seixas wrote: > I'm interested in using a crystal structure deposited in the PDB > (structure A). However, there are two important loops missing. > There is another homologous structure B from another source organism, > where those loops are well defined inside electron density. I like to > use the experimental data from this template B to model the missing > loops in the structure A.
Why not just model using both structures as templates? If you're worried that structure B will "mess up" the model in the non-loop regions, align it just with A in those regions and just with B in the loop regions.
Ben Webb, Modeller Caretaker
Hi, Thank you for the reply
I have already considered that option. However, generating models aligned with structure A does not make a model identic to structure A. In another words, I do not want to lose the experimental information that structure A brings, just want to build the missing regions in crystallographic structure A, as it appears in structure B.
Is it possible?
Regards,
Flavio
------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br On Monday, April 7, 2014 10:34 PM, Modeller Caretaker modeller-care@salilab.org wrote:
On 4/5/14, 8:05 AM, flavio seixas wrote:
> I'm interested in using a crystal structure deposited in the PDB > (structure A). However, there are two important loops missing. > There is another homologous structure B from another source organism, > where those loops are well defined inside electron density. I like to > use the experimental data from this template B to model the missing > loops in the structure A.
Why not just model using both structures as templates? If you're worried that structure B will "mess up" the model in the non-loop regions, align it just with A in those regions and just with B in the loop regions.
Ben Webb, Modeller Caretaker
On 4/8/14, 9:27 AM, flavio seixas wrote: > I have already considered that option. > However, generating models aligned with structure A does not make a > model identic to structure A. In another words, I do not want to lose > the experimental information that structure A brings
In that case, simply select only the loops for refinement: http://salilab.org/modeller/9.13/manual/node23.html
Ben Webb, Modeller Caretaker
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flavio seixas -
Modeller Caretaker