Parker,
You probably could- I personally haven't ever used alanine scanning, but it
looks like it does the same thing that decomposition does.
Best,
Kenneth
On Thu, Jun 18, 2015 at 4:50 PM, Parker de Waal <Parker.deWaal.vai.org
<javascript:_e(%7B%7D,'cvml','Parker.deWaal.vai.org');>> wrote:
> Thanks Kenneth,
>
> I'm wondering if I can do a simple MMPBSA alanine scanning on my system to
> determine the relative energy contribution. That might be simplest.
>
> Cheers,
> Parker
> ________________________________________
> From: Kenneth Huang [kennethneltharion.gmail.com
> <javascript:_e(%7B%7D,'cvml','kennethneltharion.gmail.com');>]
> Sent: Thursday, June 18, 2015 12:06 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Energy contribution of phosphorylated residues
>
> Parker,
>
> I think so- someone might be able to give a more detailed answer than me,
> but if you have MMPBSA decompose the binding energy by a per residue basis,
> you'll be able to estimate their relative contributions. That said, you'll
> may want to have it decompose all residues if you can, and run the
> hetrodimer without the phosphoserine present so you can have a point of
> comparison to see how it contributes.
>
> A more general example off the top of my head is
>
> http://secure-web.cisco.com/1WuEgyCE-SeskdSR04Ibjl35BvHExN1lUdYT7EMCYXVV-mXGTYDPhGbXOy5_QEr7JZIAqkbPPkPWasCMxdewm-9MtaHHhwoKPcLPzfq7tITPD4KfoUDjbJf2IpyD3XjpuOECUxen4alYnUu_Jl15yEQ4Dp5R9DZucMPgp8GJqRn8iV_CaUUGORvx_ylZUGtna-jaf0PxhuJhBuJh-4Qk5CjL1XS1huISe_p0U34aJAHpkc2sJ_xO1S8Wiqi7dplgE/http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F11054292-
> it is fairly dated and there's
> probably much more recent work done since that would be worth looking into.
>
> Best,
>
> Kenneth
>
> On Thu, Jun 18, 2015 at 9:57 AM, Parker de Waal <Parker.deWaal.vai.org
> <javascript:_e(%7B%7D,'cvml','Parker.deWaal.vai.org');>>
> wrote:
>
> > Hi Everyone,
> >
> > I'm currently working with a heterodimer protein complex in which one
> > protein is phosphorylated and this interaction has been shown in vitro to
> > be required for dimer formation.
> >
> > Using MM/PBSA, would it be possible to perform an energy deconvolution to
> > determine the energy contribution of the phosphoserine and the two salt
> > bridges it is forming?
> >
> > I am familiar with protein-ligand calculations, but in this case it is
> > protein-protein.
> >
> > Any advice would be greatly appreciated.
> >
> > Best,
> > Parker
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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here could not dream of heaven?
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Ask yourselves, all of you, what power would hell have if those imprisoned
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Received on Thu Jun 18 2015 - 14:30:04 PDT
