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Author Topic: Protein Bound DNA via w3DNA  (Read 2080 times)

Offline acolasanti

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Protein Bound DNA via w3DNA
« on: June 04, 2013, 12:30:30 pm »
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I have a question regarding the reconstruction of a protein-bound DNA model from Web 3DNA.
When I use this function to create a complex of a protein bound to a DNA duplex, is the DNA structure (and the protein structure) locally distorted by the interaction?

Offline acolasanti

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Re: Protein Bound DNA via w3DNA
« Reply #1 on: June 04, 2013, 12:31:35 pm »
When using the reconstruction section of the w3DNA website to create protein bound DNA the following method applies

-  DNA base pairs interacting with protein in the original X-ray will adopt the same configuration (pair and step parameters) as those found in the original structure.  Because of this the model must have at a minimum the same number of steps as found in the X-ray structure.

- Extra DNA that you add to the beginning or end of the structure will adopt the configuration (A-, B-) selected on the w3DNA site.

If I did not answer your question please let me know so that I can further assist you.

Thanks,

Andrew

 
« Last Edit: June 04, 2013, 12:37:34 pm by acolasanti »

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.