[gmx-users] Positive energy for Coulumb term. Does this mean Coulumb interaction destabilizes protein?

Seungpyo Hong sp1020 at gmail.com
Fri Mar 6 11:43:19 CET 2009

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
Coul-SR:Protein-Protein    -11.6253    365.244    357.507  -0.735925
LJ-SR:Protein-Protein      -6.51389    204.554    203.627   0.191426
Coul-14:Protein-Protein     38.5848    1212.26    1196.75    1.90253
LJ-14:Protein-Protein       3.58465    112.688    112.645 -0.0303438
Coul-SR:Protein-Non-Protein   -14.1247    443.927    437.195   -0.75795
LJ-SR:Protein-Non-Protein   -1.51471    47.6924    46.2568   -0.11429

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!

Seungpyo Hong

'God used beautiful mathematics in creating the world.'
-Paul Dirac
'At the same time, he allowed interaction among objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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