I work with gromacs code on the protein carbon nanotubes interaction. I saw that when the protein becomes unfolded, the number of hydrogen bonds (in protein itself, not with water molecules) increases. What is it's reason?, why?
thanks for attention.
Nanotubes are certainly not a native environment for protein molecules. When not functionalized, they do not form hydrogen bonds with other molecules. Let us assume that you start with a folded protein with coordinates taken from experimental data. If you add nanotubes, you probably create a steric hindrance resulting in a decrease of the number of hydrogen bonds between the protein and water molecules. This could be the first reason why the number of intramolecular ("intraprotein") H-bonds increases. The other reason is the unfolding itself: the folded native structure is often less stable than a structure resulting from denaturation. The presence of nanotubes may force the native structure to collapse into a more stable structure that contains more H-bonds. Let me know the result when you finish with the analysis.
I observed that sort of case in REMD simulation with a beta-sheet proteins. The number of h-bonds increased in molten state of protein, when I calculated hydrogen bonds itself using gromacs command g_hbond. I suggest to use VMD to calculate hydrogen bonds. You have to just employ the following values for VMD: Cutoff angle - 30, Cutoff radius - 0.35.
- Badges
- Science topic