Question: Protein-Protein Interaction After Mutation
5
gravatar for Jean-Paul Abbuehl
5.9 years ago by
EPFL
Jean-Paul Abbuehl50 wrote:

Hi everyone,

I have a simple request: lets say we have 4 proteins. I know from several databases (Stitch, Uniprot, Etc..) that protein A binds directly to 3 different proteins (B, C, D), with experimental evidences.

If protein A has point mutation(s) or INDEL at known position(s), is there a way to predict its impact (Yes/No) on interaction with the other proteins. I am not interested in the function itself, but just the interaction (and maybe the stability of protein A)

Eg. In protein A, G aa replaced by Y aa at position 235 -> protein A cannot bind anymore to protein B, but can still bind proteins C and D.

Ideally I need to implement that locally because I have several proteins to test... (up to 100)

I have the feeling this is a trivial request that should have been already addressed, but I cannot find any hints in the web.

Could you give me some recommendations/papers/links/database where I could start first (instead of reinventing the wheel ahah)

Thank you very much

Best

Jean-Paul

protein mutation • 1.8k views
ADD COMMENTlink modified 4.6 years ago by Hayssam250 • written 5.9 years ago by Jean-Paul Abbuehl50

@Jean-Paul What method did you end up using? Thanks.

ADD REPLYlink written 2.8 years ago by Tommy Carstensen150
2
gravatar for AsoInfo
5.9 years ago by
AsoInfo220
Bonn, Germany
AsoInfo220 wrote:

Firstly perform the macro-molecular docking between the wild-type protein and their corresponding ligands then perform the same process using the mutated protein instead of normal protein. This will help you in judging whether the mutation had effected the binding sites or not.

There are several softwares for docking like Hex, PyMOL (plug-in of autdock), AutoDock (it also gives you the interaction). You will find numerous papers related to macro-molecular docking on the website. There are many online servers also which can help you in this regard like ZDock, RosettaDock. There are also many linux based softwares also which will make your tasks feasible.

ADD COMMENTlink written 5.9 years ago by AsoInfo220

Amazing I'll see what I can do in that direction Thank you

ADD REPLYlink written 5.9 years ago by Jean-Paul Abbuehl50
1
gravatar for Michael Kuhn
5.9 years ago by
Michael Kuhn4.9k
Dresden, Germany
Michael Kuhn4.9k wrote:

No solution, but a paper on this concept: Edgetic perturbation models of human inherited disorders

ADD COMMENTlink written 5.9 years ago by Michael Kuhn4.9k
0
gravatar for Hayssam
4.6 years ago by
Hayssam250
France
Hayssam250 wrote:

Hi,

I found the study of Wang et al. 2011, Three-dimensional reconstruction of protein networks provides insight into human genetic disease quite interesting and scientifically sound. Might be relevant for you too.

ADD COMMENTlink written 4.6 years ago by Hayssam250
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