Capping termini - protein modeling

[CoffeeIsTheColour]

Hi,

My question regards peptide caps. I have a few proteins (~25kDa) in which the first and last few residues are truncated. In what circumstances should I cap the protein termini, and apart from stability in small alpha helices, why should we cap protein termini?

Thanx,

[JackBean]

What do you mean by capping the termini?

[CoffeeIsTheColour]

Thanks for the reply...

I'm referring to capping protein residues with NME and ACE residues. I know they are used in when simulating short alpha helices, to introduce an level of stability and to prevent helix fraying...

Perhaps a better way to phrase the question...what is the best way to treat terminal residues in protein modelling and MD. The residues are not the end of sequence but truncated, as obtained from the crystal structure. Such terminal residues in my case include...Thr, Ser, Glu, Gln, Val. Should I have these residues protonated, deprotonated, neutral...

Thanx