Cherra, Salvatore

Research Activities

Our aim is to investigate the structural and functional aspects of PXF-1, a Rap-GEF protein associated with neurological diseases. Loss-of-function mutations in PXF-1 have been linked to synaptic signal intensity reduction, suggesting involvement in cholinergic signaling regulation. The project entails predicting the structure of PXF-1 using AlphaFold2 and evaluating the stability effects of point mutations via Rosetta's ddG comparison.

List of Projects

PXF-1 structure prediction with AlphaFold 2 - Bridget Carroll, Qi Qiao, Caitline Phan, Khine Aung, Julie Watkins

We will use AlphaFold2 to predict the structure of PXF-1 WT and P1023S based on the FASTA file. The results will be the top 5 possible structures (PDB files with coordinates) for each protein, and the confidence score (pLDDT) for each amino acid. VMD software will be used for the PXF-1 WT and P1023S structure visualization and comparison.

PXF-1 P1023S mutant stability prediction with Rosetta ddG - Bridget Carroll, Qi Qiao, Caitline Phan, Khine Aung, Julie Watkins

We will use Rosetta ddG to predict how a single-point mutation will affect protein stability. The structures of PXF-1 WT and P1023S that are generated from AlphaFold2 will be used as the input for DDG calculations.

Computational Methods

We will use AlphaFold2 to predict the structure of PXF-1 WT and P1023S based on the FASTA file. The results will be the top 5 possible structures (PDB files with coordinates) for each protein, and the confidence score (pLDDT) for each amino acid. The structures of PXF-1 WT and P1023S that are generated from AlphaFold2 will be used as the input for DDG calculations.

List of Software

AlphaFold2
Rosetta

UKY Collaborators

Bridget Carroll, Qi Qiao, Caitline Phan, Khine Aung, Julie Watkins