Respected All,
As through site-directed mutagensis, the catalytic activity of an enzyme is increase by analyzing there variants. But its time consuming and unpredictable when you are mutating the residues.I want to increase the activity of an enzyme by mutating there residues firstly through computational and bioinformatics analysis, then followed by experimentally among the best variants.
So by which principle i can chose to select among the active residue (interacting residue or nearby residue in the active site?) to mutate it ? Secondly how i can analysis through computationally that this variants will be have good activity as compared to wild type?. Can someone provide articles related to this work?
Thanks in advance.
The enzyme's activity can be increased by in silico analysis, here is the paper which may help you to achieve your goal:
http://www.ncbi.nlm.nih.gov/pubmed/26207800
As Indu has mentioned about her paper ...that might be a starting for you....However in summary you have to first figure out what are the hotspot residues (residues which are participating in catalysis). You can start with the information available with the wild type PDB. Then you need to decide some biophysical properties which you want to concentrate, when you will carry out insilco mutation. Since, every site-directed mutation might not affect them quantitatively. For this you can use Swiss-PDBviewer, it gives option of mutation with different rotamer of each amino acids (it also shows the steric bumps or so). Then it has feature of calculating energy terms using gromos-96 frocefield. This software is totally free, you can download under free GNU license. Then you can use any autodock tool to know how effective those mutations are?
