Re: Protonation

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sun Aug 29 2010 - 06:20:03 CDT

Andres,

Try to use PROPKA (http://propka.ki.ku.dk/ this is "empirical
algorithm") to estimate aminoacids pKa, which dependent on surroundings,
than ascribe protonation state of each aa in your peptide at pH 5.0.
Also, recently paper on novel pKa estimation for protein pKa appears:
Milletti, Francesca; Storchi, Loriano; Cruciani, Gabriele. Predicting
protein pKa by environment similarity. Proteins: Structure, Function,
and Bioinformatics (2009), 76(2), 484-495. So, try to ask developers
for evaluation.

Branko

On 8/29/2010 4:11 AM, Andres Morales N wrote:
>
> Dear VMD users
>
>
> I need to make simulations of a system at low pH . I found that I
> should protonate some amino acids to simulate this pH condition.
> Particularly, I need to equilibrate the loop36 of hemagglutinin at pH
> of 5.0. The amino acid sequence of this polypeptide is : ARG VAL ILE
> GLU LYS THR ASN GLU LYS PHE HIS GLN ILE GLU LYS GLU PHE SER GLU VAL
> GLU GLY ARG ILE GLN ASP LEU GLU LYS TYR VAL GLU ASP THR LYS ILE
>
> I know that I should do the protonation in HIS, but I do not know if I
> should it with other amino acids. (I work with the polypeptide in a
> water sphere).
>
> I wait that someone can help me with this.
>
> Thanks for your help.
>
> Andres Morales N.
>
> Biophysics and Molecular Modeling Group
> Physics Department
> Escuela Politécnica Nacional, Quito - Ecuador
> Ladrón de Guevara E11-253.
> Casilla 17-01-1253
> http://www.ciencias.epn.edu.ec/~biomod/
> <http://www.ciencias.epn.edu.ec/%7Ebiomod/>
>
>
>
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