Re: [AMBER] Calculation of dG for dimeric system

From: Enrico Martinez via AMBER <>
Date: Fri, 6 Jan 2023 17:08:40 +0100

Thank you very much David!
Actually I need very approximate values in order that I could
understand if the dimer formation would be favorable or not for a
given combination of monomers..

BTW could I use in principle MMPBSA protocol for any prot-prot
interactions e.g. in the case of binding a small peptide to a bigger
receptor ?
Many thanks in advance

Il giorno ven 6 gen 2023 alle ore 15:53 David A Case
<> ha scritto:
> On Fri, Jan 06, 2023, Enrico Martinez via AMBER wrote:
> >I am dealing with the modeling of a dimeric protein (in the assembled
> >state) in water composed of two monomers of 300 amino acids. Which
> >protocol may be useful to calculate dG for this macromolecular complex
> >(if it's even possible .. ) ? Is it possible to use techniques like
> >MMGBSA or thermodynamic integration?
> What "dG" are you trying to calculate? If it is the protein dimerization
> free energy, that could be a major task. First, do you have evidence that
> the monomer is folded?
> If so, you could compute the buried surface area in the complex and multiply
> by 5 cal/A^2. Then you would be done(!)
> If you really want to learn the ins and outs of protein-protein free energy
> calculations, take a look at this paper:
> %A J.C. Gumbart
> %A B. Roux
> %A C. Chipot
> %T Efficient Determination of Protein-Protein Standard Binding Free Energies from First Principles
> %J J. Chem. Theory Comput.
> %V 9
> %P 3789-3798
> %D 2013
> This illustrates some about how big a task this is likely to be. Think
> about how you plan to use the result -- how accurate an answer do you need?
> ....dac

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Received on Fri Jan 06 2023 - 08:30:03 PST
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