Protonation state decisions
Protonation states
The protonation states of several amino acids and the termini of a protein
are unknown in general.
Pdb files normally do not contain the relevant hydrogen atoms.
It is up to the user to decide how to treat these chemical groups.
- Easy: Let mmtsb decide the
states with default decisions.
Defaults are:
- All Histidines (HIS) are protonated on delta carbon (HSD)
- Acidic residues are unprotonated (ASP, GLU, C-terminus)
- All Histidines (HIS) are protonated on delta carbon (HSD)
- More Effort: Analyze the energetics of the possible protonation states.
- Most Effort: analyze the physical and chemical environment of the
chemical groups in question. One would determine from pH
and the proximity and types of other chemical groups
what the likely protonation state would be using chemical
insight. Often this method will include visual and analytical
inspection of the region surrounding chemical groups in question and
of the energetics of the possible states.
Protonation tutorial
(download gzipped tar file)
In this tutorial, the protonation states are examined to make
a decision about which states to use.
For the purpose of the tutorial, only the histidines are examined. THere
are two histidines, residues 6 and 29 in this structure (1fsc.pdb).
First: Default protonation states are used and energy determined.
Second: Energy of all hsd structure is determined.
Third: Energy for each state in which only one histidine is in
epsilon-protonated state (hse).
From the results, it can be seen that the best protonation state is with:
Residue 6 HSD
Residue 29 HSE
The next tutorials will use this result in convpdb.pl to
construct the correct protonation state.
One can download the script, change to
to be executable, and execute it
OR
enter each command individually from the shell prompt.