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When running molecular simulations, what is the consequence of not capping the n- and c-terminus?

I have been following gromacs tutorials and haven't come across any that deal with capping the termini, so is it important?

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Interesting question. I have to admit, that I haven't really come across it, but for the moment it seems to me that this mechanism is used mainly to protect short alpha helices and stabilize them. See this articles: "Helix stop signals in proteins and peptides: the capping box." and this one: "Helix capping." A lot of research is done in combination with actin filaments, where the capping plays an important role in stabilizing the filament strands - either prohibiting the addition of new monomers and on the other hand preventing the removal of elements from the polymer strand. This review gives an overview:"F-actin capping proteins." This research article might also be interesting when doing simulations:"N- and C-capping preferences for all 20 amino acids in alpha-helical peptides." As always, if you have some problems with access to the articles, let me know.

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As I explain in my answer, I don't think 'capping' in this context is the same concept as 'helix capping.' – Ryan Dec 31 '13 at 5:55

Capping the termini neutralizes their amine or carboxylic acid moieties. If this was recapitulated in the biological context, it could be important for an accurate MD simulation to neutralize those charges. Termini are mobile enough without extra charges in the mix!

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