[gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)

[Gerrit Groenhof]

Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each 
other. The bonds prevent these atoms to get apart too far, so 1-4 won't 
destabilize the overall structure. The SR part is negative, thus keeping 
your protein together.

Gerrit


>
> Message: 3
> Date: Fri, 6 Mar 2009 19:43:19 +0900
> From: Seungpyo Hong <sp1020 at gmail.com>
> Subject: [gmx-users] Positive energy for Coulumb term. Does this mean
> 	Coulumb 	interaction destabilizes protein?
> To: gmx-users at gromacs.org
> Message-ID:
> 	<bd5475eb0903060243q7a553766r70664758fa47f88c at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear GMX-Users,
>
> As I analyze energy terms of proteins, I found something looks weird.
> I thought that fullly folded proteins are stabilized by Coulomb interaction
> (such as hydrogen bonds).
> However, what I found embarasses me.
>
> The Coulomb interaction seems to destabilize the protein structure as its
> energy is positive.
>
> Coul-SR + Coul-14 = 32 > 0
> Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0
>
>
> Energy                      Average       RMSD     Fluct.      Drift
> Tot-Drift
> -------------------------------------------------------------------------------
> Coul-SR:Protein-Protein    -11.6253    365.244    357.507  -0.735925
> -259.047
> LJ-SR:Protein-Protein      -6.51389    204.554    203.627   0.191426
> 67.3824
> Coul-14:Protein-Protein     38.5848    1212.26    1196.75    1.90253
> 669.696
> LJ-14:Protein-Protein       3.58465    112.688    112.645 -0.0303438
> -10.6811
> Coul-SR:Protein-Non-Protein   -14.1247    443.927    437.195   -0.75795
> -266.8
> LJ-SR:Protein-Non-Protein   -1.51471    47.6924    46.2568   -0.11429
> -40.2302
>
>
> I thought of the total charge of the protein; but it is only +2.
> And, the structure is quite stable through the simulation. (RMSD: 0.17)
>
> I am quite confusing about the effect of Coulumb interaction on the
> stability of the protein.
> I feel like I am missing very important concept about the stability of
> protein or the energy term used here.
> Can anyone help me to understand the effect of Coulumb interaction in the
> stability of the protein?
>
> Any opinion or comment would be great help for me.
>
> Thank you very much!
>
> Sincerely,
> Seungpyo Hong
>
>