Dear all,
This might be more common question but any input would be greatly
appreciated.
I am looking for some suggestion on selecting correct histidine protonation
state before we run the simulation.
I have tried to use H++ online program to help determine the correct
protonation state of my protein complex at PH 7. All four histidine
residues were assigned as HIP (Both nitrogen protonated) after I ran
through the H++. When I inspect manually, I realize that none of these
histidine residues are/can involve in any possible hydrogen bond
interaction. Actually two of the histidines are at N terminal end which are
just flanking out without possibility of any other interactions within or
between protein. So I am trying to understand why this histidine was
assigned as HIP? I understand we can't always depend on just the program to
assign the protonation state but I just want to make sure I am not missing
any general information here. My understanding is, at neutral PH a neutral
histidine is always more preferred than a charged one (HIP).
My common question here is:
While assigning the protonation state for histidine, what other factors do
we consider other than possibility of hydrogen bonding interactions?
Any other suggestions on other programs to use to help in this kind of
process would be greatly appreciated.
Thank you,
Sincerely,
Jag Silwal
Graduate Student
Chemistry, Michigan State
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Received on Thu Jun 15 2017 - 09:00:02 PDT
