Description
A tool to help iGEM teams to optimize residue replacement in proteins, to allow for protein immobilization to the hardware.
Background: Why Do We Want to Optimize Residue Replacement?
When attempting to attach a protein or polypeptide to a surface, it is important to be able to recognize and replace an amino acid residue that would allow for attachment without compromising function. To do this, one must consider the localization of the residue near the surface of the protein, its distance from the active site, its involvement in a secondary structure (either an alpha helix or a beta sheet), and its conservation in homologous protein sequences. Though much of this information can easily be accessed for proteins whose crystal structure and method of acting has already been determined, like proteins that could be found in PDB databases, proteins synthesized for a specific purpose require one to use various complex calculations and methods to predict the information listed above. These complicated steps often have to be performed manually, which can introduce several errors into the calculations that might result in incorrect predictions. Various online servers can also be used to automate some steps, but these servers are often difficult to combine with one another.
Due to these difficulties, MutaGuide was developed to automate the process of obtaining secondary structure and surface area predictions and combining this with homology analysis to output optimal residues to replace.
How It Works
- Determines conservation of target residue across all protein homologues, based on output from PHYRE2 webserver.
- Obtains predictions for secondary structure and relative solvent accessibility (RSA) from SABLE 2.0 webserver.
- Scores occurrences of target residue in the input sequence based on conservation from step 1, and secondary structure and RSA prediction (if user indicates preference for residues with high RSA) from step 2.
- Outputs results with residues ordered from their scores.
For more information on Phyre2, please click here.
For more information on SABLE 2.0, please click here.