Dear Carlos
Thanks for the reply but I need to know that is it correct to compare
the binding free energy of two protein of the same family but different
in number of total residues as well as number of positively charged
residue.
With regards
On 2016-03-28 2:36 pm, Carlos Simmerling wrote:
> in principle, binding affinity is connected to free energy through the
> usual transformation between free energy and equilibrium constant, where
> delta G = -RTlnK. You do need to make sure to understand how the Kd was
> measured, though, and often people are really measuring other quantities
> such as Ki or even IC50. If you really know the equilibrium constant then
> the conversion is straightforward. having said this, though, be aware that
> in MM-PBSA you are normally not calculating the absolute binding affinity.
> There are many approximations involved as well, especially or large
> molecules such as proteins and DNA, and for highly charged interfaces like
> these problems have, and the potential for involvement of structured water
> or even ions. It does sound like your results are opposite of the expected
> trend, but I don't find it surprising. I suggest doing some reading about
> free energy calculations, there have been a number of good reviews lately,
> and also some new methods for calculating absolute binding free energies
> (it's rather costly compared to MM-PBSA though). For the system you're
> studying, look for other published studies that successfully use MMPBSA to
> calculate protein-DNA binding affinities. I expect it's very challenging.
>
> On Mon, Mar 28, 2016 at 2:55 PM, Sangita Kachhap <sangita.imtech.res.in>
> wrote:
>
>> Dear All I am working on understsnding the mechanism of protein-DNA ternary complex formation. One protein has more banding affinity (kd value) to target DNA than second protein. When I was calculating the free energy of binding of indivisual protein to target DNA, protein having less affinity to target DNA showing more negative binding free energy than protein having more affinity but showing less negative binding free energy. I want to know that, is it correct way to relate kd value with MMPBSA calculated binding free energy? ---------------------------------------------- Sangita Kachhap Senior Research Fellow C/O Dr. Balvinder Singh Bioinformatics centre CSIR-Institute of Microbial Technology Chandigarh, Sector-39A, INDIA ---------------------------------------------- _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber [1]
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--
----------------------------------------------
Sangita Kachhap
Senior Research Fellow
C/O Dr. Balvinder Singh
Bioinformatics centre
CSIR-Institute of Microbial Technology
Chandigarh, Sector-39A, INDIA
----------------------------------------------
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Received on Thu Mar 31 2016 - 22:00:05 PDT
