[gmx-users] problem with a complex cofactor

[Justin Lemkul]

On 3/6/13 6:29 AM, Anna Marabotti wrote:
> Dear gmx-users,
>
> I'm working on a protein of the family of green fluorescent proteins, which has
> a cofactor formed by the rearrangement of three residues that cyclized forming a
> complex heterocyclic fluorescent probe. This probe is covalently bound to the
> protein and is part of the backbone; in the PDB file it is marked as HETATM in
> the middle of the protein sequence which is: ...S61-H62-V63-CFY66-H68...
>
> I really do not know how to deal with the topology of this residue and with the
> fact that the protein sequence is interrupted. I don't know if I have to manage
> this residue as a new residue to be added in the force field; please take into
> account that this residue is bound to V63 and H68 with covalent bonds similar,
> but not strictly identical, to peptide bonds. I found in the gmx-users archive a
> suggestion about how to manage the topology of a Lysine bound to pyridoxal
> phosphate, but that situation is different from mine, since Lysine is a
> "regular" residue "regularly" forming peptide bonds with its adjacent residues,
> and which is attached to PLP with its terminal side chain NZ atom, whereas in my
> case a heterocyclic molecules is forming peptide-like bonds with adjacent
> residues. Moreover, mine is not the case of a N-ter or a C-ter residue somehow
> modified: this heterocyclic compound is in the middle of protein sequence.
>
> Can somebody suggest me a strategy on how to proceed?
>

Weird bonds can be assigned with specbond.dat, but you may be able to do 
everything within the .rtp file, anyway, since you're still dealing with a 
linear polypeptide.  Usually specbond.dat is only necessary for branch points or 
other complex structures.  Please note that we have discussed the GFP 
chromophore at length several times, even recently, so there is bound to be 
relevant information in the list archive.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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