I need to remove one of several molecules within a protein dimer, which then goes on to form a multi subunit complex. The goal is to have the complete complex with all proteins lacking this one specific molecule, the whole thing has a defined crystal structure at 2.72 A. The molecule is peripheral, located at the terminal end of the aa seq, and interacts (rather weakly) with at least 2 other similar molecules - possibly this interaction stabilises the tertiary structure (this organisation is very much conserved in nature). I first thought of changing 2 aa's which are supposed to be the binding sites for the molecule of interest, however, I got a suggestion to change one aa's very close to the terminal end to a sth larger, such that there isn't enough space for this one molecule to fit in its regular site.
This rather sums up to what I want to do and what I know
The wet lab stages part is rather straight forward and simple to do. What I fear is that my changes want have the expected effect so I'd like to do some modelling to be sure (I've got no access to the wet labs until autumn anyways, so got a lot of spare time).
My experience with modelling is equal to none so..
What I'm looking for is some tips or directions as to how to get started with modelling towards
1.creating a mutated molecule,
2.checking that the mutation does remove the small molecule from the dimer,
3. that the mutation or removal of the small molecule from the dimer doesn't significantly disturb the tertiary structure, or binding of the 2 other molecules with which it interacts,
4. that the mutated dimer lacking the one molecule will organise into similar looking similar to the one made for the wild type
I would be grateful for any indication of literature on the topics (sth that a beginner grasping the whole concept can assimilate without getting either drunk or jumping from a window at the end of the day), and recommendation of software, preferably something with a free licence (I've been thinking to start working with NMD, as I'm familiar with VMD, do zou think it's a good idea?) with a chance that I could get it run on a cluster somewhere. Some sort of graphic interface would be welcome, I tend to get lost in line command applications.
Thanks for any advice, suggestions and comments as to the "plan"
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