how to move one domain of a protein in respect to another?
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
Hi Tatyana, without knowing much details about how you want to move the domains I guess these tools may be handy: phenix.pdbtools model.pdb rotate="10 20 30" translate="3 5 7" and phenix.superpose_pdbs pdb_file_fixed.pdb pdb_file_moving.pdb and may be phenix.pdbtools model.pdb --geometry-regularization Pavel. On 2/9/11 11:57 AM, 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
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. Cheers, Ed. 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- 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 /
Hi, this will be trivial to do in the next available PHENIX nightly build: http://www.phenix-online.org/download/nightly_builds.cgi Examples: phenix.pdbtools model.pdb rotate_about_axis.axis="chain A and resseq 1:123 and (name CA or name CB)" rotate_about_axis.atom_selection="chain A and resseq 1" rotate_about_axis.angle=35 where rotate_about_axis.axis defines the rotation axis (must be two points in space); rotate_about_axis.atom_selection defines the atoms that will be rotated about the axis; rotate_about_axis.angle defines rotation angle in degrees. Instead of specifying atom selection string in rotate_about_axis.axis, you can give it coordinates of two points: phenix.pdbtools model.pdb rotate_about_axis.axis="1.234 2.345 4.567 -2.321 3.765 0.001" rotate_about_axis.atom_selection="chain A and resseq 1:123" rotate_about_axis.angle=35 Let me know if there are any problems or questions. phenix.pdbtools available in PHENIX GUI too. Pavel. On 2/9/11 11:57 AM, 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
participants (3)
-
Ed Pozharski -
Pavel Afonine -
Tatyana Sysoeva