Re: regarding protein-protein interaction

From: Marcin Krol (
Date: Fri Jun 05 2009 - 03:23:13 CDT

Dear Prasun

In general solvated MD is not the best tool to study protein-protein
interactions. In principle you should observe that two proteins start to
interact, but this may happen on the timescale much longer than
accessible in the simulation. I suppose it takes a lot of time to
reorient water molecules, waters also shield interactions between
proteins, and so on...
So if you want to simulate binding between two proteins you need to drag
them to each other eg. using a restraint between their centres of mass.
But you need to have them properly aligned, facing their interfaces;
they won't rotate in water to align interfaces unless you force them to
do so by restraints
Have a look at Alexander Heifetz, Sandeep Pal^ * , Graham R. Smith
'Protein-protein docking: Progress in CAPRI rounds 6-12 using a
combination of methods: The introduction of steered solvated molecular
dynamics' Proteins 69(4):816-822, 2007

Good luck
> Dear all
> I am trying to study protein-protein interaction using NAMD & CHARMM
> forcefield.
> Steps I am following are:
> 1. two proteins are placed at a distance of 10 angstrom to each other
> 2. minimized in vacuum
> 3. solvated in water and ionized
> 4. Minimization was done again
> 5. I have done the equlibration also
> 6. while doing dynamics ,volume is getting decreased and at last
> simulation is stopped saying fatal error related to the volume
> and asking to increase the margin.
> 7. what should I do for it????????
> 8. I have studied that two proteins are interacting to each
> other(its proved in wetlab)
> 9. while doing dynamics the two proteins are not seems to coming
> towards each other
> 10. I want to know whether I should "*tclforces on*" or not.......
> Thanx in advance
> with regards
> Prasun kumar

Dr Marcin Krol
Zaklad Bioinformatyki i Telemedycyny
Collegium Medicum Uniwersytet Jagiellonski

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