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]
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>
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
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 18 2015 - 14:00:02 PDT
