[gmx-users] about AFM pulling of one complex of two proteins

Wang Ling wang at bioinformatik.uni-saarland.de
Wed Sep 13 13:54:45 CEST 2006

hi, everyone

     now i am trying to pull one complex apart, which includes two proteins.
but i met one problem, when i fixed the COM of one protein,
pulling the COM of another protein, i found the pulled protein unfolding 
before pulling these two proteins apart, this is not the result i expected.
my objective is to pull these two proteins apart, in order to study the 
interaction between two proteins. while the structures of these two proteins 
themselves don't change too much, could you give me
some suggestions?

   i have read some references about AFM pulling, i found most of the papers
are to pull a small molecule(no complicated secondary structures) from a big
biological molecules, while in my case, the reference group and the pulled
group are both complicated proteins, the interactions within the proteins and
between the proteins are similiar, therefore before pulling the interface
apart, the pulled group unfolding first. so i want to know if AFM pulling in
Gromacs can do this kind of pulling?

Thanks in advance!

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