Protonation states of N and C terminal of the protein

User discussions
1

GROMACS version: 5.1.4
GROMACS modification: No
Hello respected community members. I am a beginner in Gromacs. While using the -ter flag in pdb2gmx command gromacs asks to set the protonation/deprotonation state of N and C termini. Can any experienced person please share a reliable server/tool which can be used for this purpose. I am using the H++ server but it appears that the N and C terminal pKa values given by H++ are not that reliable. Please guide me. Thanks in advance.

2

The N- and C-terminal pKa values do not vary much because these residues are typically solvent-exposed and therefore similar across species. The N-terminal amino group has a pKa around 8 and the C-terminal carboxylic acid has a pKa around 3.

3

Thanks a lot Dr. Lemkul for replying to my question. So can we take these values (N terminal - pka 8, C terminal - pKa 3) for all the proteins irrespective of the overall protonation state of the protein? Thanks in advance

4

Generally, yes. Shifts in pKa arise from the presence of chemically interesting microenvironments, which usually aren’t relevant for solvent-exposed termini. Values may shift slightly due to the chemical nature of the side chain of each residue, but not enough that it will impact how you protonate the molecule at a given pH value.