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

Jerome Henin jhenin at vitae.cmm.upenn.edu
Thu Sep 14 02:18:20 CEST 2006

I would say one of these three statements holds (in order of increasing 

1) The force field does not describe the protein dimer accurately enough,
2) Your assumptions on the dissociation mechanism are wrong,
3) You are pulling too fast.


On Wednesday 13 September 2006 07:54, Wang Ling wrote:
> 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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