[gmx-users] problem with a complex cofactor

[Anna Marabotti]

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?

Thanks in advance and best regards

Anna

-- 
______________________________________________
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabotti at unisa.it
Skype: annam1972

"When a man with a gun meets a man with a pen, the man with the gun is a dead man"
(Roberto Benigni, about Roberto Saviano)