Hi,
I wish to apply in silico methods for analysing the activity of a protein. the protein is actually an enzyme that destroys gram positive cell walls. I wish to model the effect of various ligands on the activity of the enzyme. However, there is no structure of gram positive cell walls in any database. Previous publication used N-acetyl glucosamine - pentapeptide for their in silico analysis. I couldn't find any structure file for the same. Please tell me how can I create a structure of N- acetyl glucosamine - pentapeptide for insilco analysis? Thank you.
It all depends on what software you have available. I tend to use the old graphics program O from Uppsala Software "Factory". The PDB (www.rcsb.org) has several N-acetylglucosamine containing ligands bound to proteins that you can find by Advanced Search at the PDB site using the Chemical components / ligands key (search: N-acetylglucosamine) though as you say, none of the ones have NAG attached to a peptide. For starters, you can just find the files containing NAG ligands and editing /copying the appropriate atoms from the text file leaving out the unnecessary atoms. For the peptide, the graphics program O has a way to go from sequence to a chain, but at this point, there are enough protein structures in the PDB that you can also probably find something close to your pentapeptide in an existing structure. First do a BLAST search to find proteins that may contain a similar peptide; find an appropriate PDB file for the BLAST hit; and then extract the peptide by editing it from of the PDB text file. Then you can use whatever graphics software to get the NAG and peptide close enough and at about the right orientation to start fixing it up with appropriate energetics software. If you ever have a new ligand there are ways to go from a ChemDraw Drawing to coordinate files. (e.g. "Copy as SMILES" option allows you to paste into a .smi text file and there is software available to convert the SMI file to a pdb coordinate file: Google search smi to pdb) It all depends if you have ChemDraw or some other graphics program and molecular energetics/mechanics programs to fix-up the initial structures. Some advanced versions of ChemDraw also give you PDB files directly.
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