Title: Using molecular modeling to assess structural conservation of KP4-Like proteins and their potential as antifungals
Project Team: Paul Rowley, Jonathan Barnes
Start Date: May 2022
KP4 protein has been used as a potent antifungal drug to reduce the spoilage of commodity crops. While the potential of KP4 has not been fully realized due to its narrow spectrum of activity, there are at least 500 more KP4-like (KP4L) homologs that we have identified that are encoded by fungal genomes. The central hypothesis is that these proteins represent an untapped resource of novel antifungal proteins that could be leveraged against important fungal diseases. To that end, we propose to initiate a molecular modeling project to determine if the low sequence homology of KP4L proteins to KP4 translates into structural conservation. This work will complement empirical studies that are underway in the Rowley lab. We anticipate that this project will be completed and published before the end of 2022.
Molecular dynamic simulations previously collected by Dr. Jagdish Patel from a prior MAG demonstrated that three KP4L proteins adopt a stable structure similar to the structural model of KP4 that was determined by X-ray crystallography. This MAG would follow up this work by using AlphaFold2 and molecular dynamics simulations to predict the structure of 20 KP4L proteins that represent the known diversity of these proteins. Furthermore, the application of in silico mutagenesis by FoldX will enable us to draw conclusions about the structural plasticity of these proteins and their ability to tolerate mutations. In silico mutagenesis will be complemented by site-saturated empirical mutagenesis to determine the accuracy of the computational models and to identify amino acids that are critical for the toxicity of KP4L proteins.