Dear GMX-Users, <br><br>As I analyze energy terms of proteins, I found something looks weird. <br>I thought that fullly folded proteins are stabilized by Coulomb interaction (such as hydrogen bonds). <br>However, what I found embarasses me. <br>
<br>The Coulomb interaction seems to destabilize the protein structure as its energy is positive. <br><br>Coul-SR + Coul-14 = 32 > 0 <br>Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0 <br><br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>Coul-SR:Protein-Protein -11.6253 365.244 357.507 -0.735925 -259.047<br>LJ-SR:Protein-Protein -6.51389 204.554 203.627 0.191426 67.3824<br>
Coul-14:Protein-Protein 38.5848 1212.26 1196.75 1.90253 669.696<br>LJ-14:Protein-Protein 3.58465 112.688 112.645 -0.0303438 -10.6811<br>Coul-SR:Protein-Non-Protein -14.1247 443.927 437.195 -0.75795 -266.8<br>
LJ-SR:Protein-Non-Protein -1.51471 47.6924 46.2568 -0.11429 -40.2302<br><br><br>I thought of the total charge of the protein; but it is only +2. <br>And, the structure is quite stable through the simulation. (RMSD: 0.17)<br>
<br>I am quite confusing about the effect of Coulumb interaction on the stability of the protein. <br>I feel like I am missing very important concept about the stability of protein or the energy term used here. <br>Can anyone help me to understand the effect of Coulumb interaction in the stability of the protein?<br>
<br>Any opinion or comment would be great help for me. <br clear="all"><br>Thank you very much!<br><br>Sincerely, <br>Seungpyo Hong <br><br>-- <br>--------------------------------------------------<br>'God used beautiful mathematics in creating the world.'<br>
-Paul Dirac <br>'At the same time, he allowed interaction among objects.'<br>-Seungpyo Hong <br><br>Seungpyo Hong <br>Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>Tel. (82)-18-372-2468<br>
<a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a><br>