Re: [AMBER] Selecting histidine Protonation state for simulation

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Thu, 15 Jun 2017 18:30:36 -0500

Molprobity is a good online server for protonation and flipping of his and flipping of asn and gln, and you can, using their kinemages, visualize the results.

The best one that I have encountered is ProToss. http://www.zbh.uni-hamburg.de/forschung/amd/software/protoss.html,
which takes into account ligands (and their tautomers) AND waters of crystallization to maximize hydrogen bonding, and it’s very fast, just a few seconds.
Of course, no “automatic” way is always perfect, especially when there are six different ways to protonate/orient each histidine!

Good luck,

Dean 
-- 
Dean Cuebas 
Associate Professor of Chemistry 
Department of Chemistry
 
Missouri State University 
901 S. National Ave. 
Springfield, MO 65897 
Phone: 417-836-8567 | Fax: 417-836-5507 
deancuebas.missouristate.edu
On 6/15/17, 10:43 AM, "Jag Silwal" <jagsilwal.gmail.com> wrote:
    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 - 17:00:03 PDT
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