I'm trying map-out interaction sites of two protein units sitting on the same protein super-complex. They are well known to interact with each other, but the PDB structures I'm looking at have crystallized these proteins separately. So I'm trying to find a way to load both of them simultaneously in Pymol and then structurally align them as they would sit on the Super-complex and then study their interaction interfaces.
Hi Daniel,
Thanks for your comment, but "super" command seems to be doing the same thing "align" does! The two structures are somewhat superimposed, which is not the case found in its original native crystal structure.
Thanks again,
Dilshan
Hi Dilshan,
I haven't used Pymol for some time. You should be able to rotate and translate the pdb files separately to generate an approximate alignment. See http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
You will probably need to use other molecular modeling tools to produce more refined models of the complex. There are a number of computer programs available for this. For the latest assessments of these methods, have a look at the CAPRI web site http://www.ebi.ac.uk/msd-srv/capri/. In general, "consensus scores" are more predictive than results form any single algorithm. (Protein-protein docking has an extensive history.) If you move forward with this, make sure you some programs that can incorporate experimental restraints (e.g., distance restraints from chemical cross-linking experiments) that you have. Also, unless there are very, very good reason to favor one particular interaction interface model, keep and evaluate alternate models. You may be able to rule-in or rule-out possible models when/if new experimental data become available.
Keith.
Hi Keith,
Thanks for your comprehensive answer! I agree, consensus scores are more predictive than a single algorithm generated model.
Best Regards,
Dilshan
From your question, I assume you do not want to align the two interacting proteins onto each other, but want to place them in the relative orientation in which they would interact. If you know the interaction sites on both proteins, you can try to manually arrange the two proteins in Pymol well enough for illustration purposes, but for a serious analysis you need to go to specialized programs to determine the relative orientation of the interacting proteins:
This is usually done using docking - this article offers a review of different protein-protein docking tools: Article Software for Molecular Docking: A review
. Many of the programs discussed therein are available as web services.- Badges
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