Dear all,
I'm using steered MD to pull apart the counterparts of protein-protein
complexes. In some cases independently of the group of atoms definition,
to which the forces are applied, I get rather a partial unfolding of one
of the counterpart than pulling two proteins from each other. This
problem has been described and analyzed in the paper of Cuendet and
Michielin for TCR-pMHC complex (Biophysical Journal 2008, p.3575-3590).
The way the authors solved the problem for this system was applying
additional restraints to each conterpart perpendicular to the axis of
pulling these counterparts. Since these constraining forces are
perpendicular to the pulling force, they are expected not to contribute
to the work of the pulling force. My question is: is there any standard
way to apply these "individual" restraints (as the authors define these
restraints for each counterpart) in AMBER? I haven't managed to find
anything relevant in the lierature. If not, what could be a solution?
Would it be correct/possible to restrain the distances, let's say,
between all C-alpha atoms and one of the atoms close to the center of
mass but for each counterpart separately and then pull? In this case the
atoms with restraints is going to content N1+N2-2 distance restraints,
where N1 and N2 are the numbers of residues (C-alphas) for the pulled
proteins 1 and 2.
Thanks in advance!
Cheers,
Sergey
--
Sergey A. Samsonov
Postdoctoral researcher
Structural Bioinformatics
Biotechnology Center
Tatzberg 47-51
01307 Dresden, Germany
Tel: (+49) 351 463 400 83
Fax: (+49) 351 463 402 87
E-mail: sergey.samsonov.biotec.tu-dresden.de
Webpage: www.biotec.tu-dresden.de
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Received on Fri Sep 09 2011 - 08:00:02 PDT
