Dear Alex,
some time ago I created a consistent parameter set for crosslinking
peptide chains via non-main chain peptide (isopeptide) bonds between
Glu/Gln or Asp/Asn and Lys.
The approach also works for mixed peptide bonds between mid-chain
residues' sidechains and peptide termini, of course. Unfortunately, the
parameter set still awaits its publication ...
But if you are interested in the parameter set, please contact me off
the list. Maybe it is exactly what you need.
Best regards,
Anselm
On 08/25/2020 02:24 PM, alex rayevsky wrote:
> Hello!
> I'm trying to investigate a polyglutamilation effect in tubulins (
> https://en.wikipedia.org/wiki/Polyglutamylation or
> https://www.nature.com/articles/s41594-020-0462-0#Sec25 ), which seems to
> be a slightly tricky task.
> First of all I've to generate a non-terminal glutamine which is a part of
> the chain (for example, chain A), but its terminal gamma carboxyl group
> forms a peptide bond with glutmaine tag (in attachment). I think, that I
> can build such strange amino acid, forming three peptide bonds at once,
> with R.E.D.III or something else. Thus, it should look like a simple
> in-chain glutamine with a replaced gamma-carboxyl oxygen by amide group of
> the connected glutamine. This is already difficult manipulation, but the
> number of the added glutamines can vary.
> Another way to generate a new topology based on GAFF force field
> parameters library. As we can replace carboxyl group with amide group of
> asparagine and calculate the difference in charges with gaussian/gamess.
> Is it real or not?
> Then I thought about the possibility of binding together of two separate
> chains (like cys-cys) - namely, one chain contains a modified glutamine
> residue, and all substituted in gamma position glutamines belong to another
> chain. Is it possible or not? Of course charge distribution should be
> correctly tuned up to reflect natural behaviour of the construction.
>
> Is it possible or not? Do You have any suggestions?
> Thank You!
> [image: glu.png]
>
>
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Received on Tue Aug 25 2020 - 08:30:02 PDT
