[phenixbb] how to move one domain of a protein in respect to another?

Ed Pozharski epozh001 at umaryland.edu
Wed Feb 9 13:07:06 PST 2011

You mean something like changing the elbow angle between the domains and
further exploring how it affects packing of the oligomer?

Something like this would be relatively simple task in CNS, doing the
rigid body minimization without experimental terms and with fake NOE
restraints to force a certain elbow angle (or simply defining an
additional restraint for however defined elbow angle.  You can then
follow up with simulated annealing to relax the linker region.

All of this assumes, of course, that you are trying to come up with some
way to determine what elbow angle range is permitted by your protein
(without doing the full blown md simulation).  If, on the contrary, you
simply want to get few models with different orientation of subunits,
disregarding their feasibility, then your best approach is to figure out
the rotation axes for the elbow angle and then apply the corresponding
set of transformations.



On Wed, 2011-02-09 at 14:57 -0500, Tatyana Sysoeva wrote:
> Dear all,
> I am working with a protein which form homooligomeric assembly. Each
> subunit of the assembly consists of 2 subdomains. I would like to
> create chimeras with the subdomains moved with respect to each other,
> keeping the linkers.
> I am wondering what would be the easiest way to do this?
> Any suggestions are welcome!
> Sincerely,
> Tanya
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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