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 -- -------------------------------------------------- '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 spho...@kaist.ac.kr sp1...@gmail.com
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