Development of a new protocol for computatinal site-directed mutagenesis

Mutagenesis, the technique of mutating individual amino acids on proteins and peptides, is an important part of protein engineering and analysis. By changing residues and measuring the effect of the mutation on the properties of the protein such as its structure and interaction, a deeper understanding can be gained, which can be used to design new, better biomolecules. However, when performed experimentally, mutagenesis can be expensive, time-consuming and a rate-limiting step in research. Computational tools can be used to aid within this context, but a review of existing methods revealed gaps in the current literature. The Parasol Protocol was developed in order to address these issues and provide a new method that would be suitable for virtual scans and which relied on molecular dynamics. The Parasol Protocol is a tool which utilises the AMBER package framework to mutate at will between any pair of natural amino acids, incorporating a wide range of possible different functional groups and transformations. It is cheap, quick and easy to use while still allowing a high degree of control. After the development, work focused on validating the protocol by applying it to various test cases. Experimentally observed interactions and structures were compared with those obtained via computational simulations, performed using the Parasol Protocol. Our understanding of those systems has deepened thanks to these studies and in some cases it had remarkable agreement with laboratory results, indicating predictive power. We think that the Parasol Protocol has performed well so far and could become a standard method used in molecular dynamics and protein design.Open Acces