Problem with NH RDCs in orienting multi-domain protein
2012-01-13 08:52:56 GMT
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.
Sai Chaitanya Chiliveri
Centre for Cellular and Molecular Biology (CCMB).
Uppal Road, Hyderabad-007, A.P, INDIA.
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