[gmx-users] non-specific protein-protein interactions

Ben Reynwar ben at reynwar.net
Sat Nov 19 06:30:58 CET 2011

On Fri, Nov 18, 2011 at 8:07 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 19/11/2011 6:42 AM, Ben Reynwar wrote:
>> On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham<Mark.Abraham at anu.edu.au>
>>  wrote:
>>> On 18/11/2011 8:10 AM, Ben Reynwar wrote:
>>>> Dear gromacs list,
>>>> Does anyone know how well current force fields capture the energetics
>>>> of non-specific protein-protein interactions?  I'm simulating a
>>>> protein with an arm that alternates between (apparently) non-specific
>>>> adsorption to the main-body of the protein and free movement in the
>>>> solvent.  Can I place any trust in the results of an MD simulation for
>>>> something like this?  I haven't seen any comparison of experimental
>>>> results with simulation results of the energetics of non-specific
>>>> protein-protein interactions so I'm a little skeptical about it.
>>>> Currently I'm using generalized born implicit solvent, which is
>>>> perhaps a mistake when solvation energies could be critical to the
>>>> results.
>>> I'd be very skeptical unless you can observe many adsorption/desorption
>>> processes and with explicit solvent (though they're probably mutually
>>> exclusive).
>>> Mark
>> I think I asked my question poorly.
>> In a perfect simulation with explicit solvent and infinite sampling,
>> roughly what kind of error might one expect for peptide-peptide
>> interaction energies due to the force field?
>> Presumably there are papers out there that go into this, but I'm not
>> finding them.  If anyone knows of any directions to point me in, I'd
>> really appreciate it.
> I don't recall having ever seen an explicit solvation simulation on even a
> small peptide that claimed exhaustive sampling, never mind a system that
> shows such complex behaviour. It's possible someone has used slow-growth
> methods to grow a small peptide ligand onto the side of a protein, and that
> could give a guide to the accuracy of inter-protein energetics, but I've
> never gone looking for such.
> Mark

Cool.  Thank you.  I think I need to spend some quality time with the
parameterisation literature.

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