Hello everyone,
A while ago I was working with single-point mutations in protein structures. At the time, I needed to open PDB files and replace a single amino acid using a Python script.
I tried to do this using Biopython's Bio.PDB package, but I got stuck trying to accomplish this using BIO.PDB objects.
Finally, I implemented the mutations by simply opening the PDB file with the open() function; I have erased the lines referring to the atoms in the side chain of the residue in question; I calculated the coordinates of the new atoms based on the main chain (which has not changed); and I recorded the new lines in a new PDB file (then, I used another tool to minimize the atoms' positions but these details are not so important here).
That worked!
Still, I had the feeling that this wasn't the most robust way to solve the problem.
Has anyone tried to do something like this using Biopython?
Hi,
Point mutations
A special case arises when disorder is due to a point mutation, i.e. when two or more point mutants of a polypeptide are present in the crystal. An example of this can be found in PDB structure 1EN2.
Since these residues belong to a different residue type (e.g. let’s say Ser 60 and Cys 60) they should not be stored in a single Residue object as in the common case. In this case, each residue is represented by one Residue object, and both Residue objects are stored in a single DisorderedResidue object (see Fig. 11.1).
The DisorderedResidue object forwards all uncaught methods to the selected Residue object (by default the last Residue object added), and thus behaves like an ordinary residue. Each Residue object in a DisorderedResidue object can be uniquely identified by its residue name. In the above example, residue Ser 60 would have id “SER” in the DisorderedResidue object, while residue Cys 60 would have id “CYS”. The user can select the active Residue object in a DisorderedResidue object via this id.
Example: suppose that a chain has a point mutation at position 10, consisting of a Ser and a Cys residue. Make sure that residue 10 of this chain behaves as the Cys residue.
>>> residue = chain[10]
>>> residue.disordered_select("CYS")
In addition, you can get a list of all Atom objects (ie. all DisorderedAtom objects are ’unpacked’ to their individual Atom objects) using the get_unpacked_list method of a (Disordered)Residue object.
And read more here: http://biopython.org/DIST/docs/tutorial/Tutorial.html
Dear Diego Mariano
These links and tutorials might be an asset, have a look:
1. https://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf
2. https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
3. http://biopython.org/DIST/docs/tutorial/Tutorial.html
4. https://www.researchgate.net/post/How_do_you_change_a_single_amino_acid_in_a_pdb-file
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8002403/
Kind Regards
Qamar Ul Islam
Diego Mariano can you share the script which you have written to do point mutation using biopython.
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