Amanda Loshbaugh

Building homes

Computational Protein Design

Computational Protein Design

Computational Protein Design

Computational Protein Design

- Engineered modular sensor-reporters for previously undetectable small molecules - Developed and optimized protein complementation assays in an in vitro transcription translation platform. These assays characterized dimerization-based sensors in which a computationally-designed de novo ligand binding site mediates dimerization of the protein heterodimer. - Development and benchmark comparison of flexible-backbone design methods on binding interactions - Developed a computational design protocol within the Rosetta molecular modeling suite that couples fragment kinematic closure backbone moves and sidechain moves in a single design step. Found that this new protocol outperforms existing Rosetta protocols on benchmarks of small-molecule binding sites and protein-protein interactions.

Development of a novel computational method for predicting protease peptide substrate specificity

Transplant chromophore from fluorescent protein into unrelated scaffolds using Rosetta.

Use known molecular determinants of recombination to develop an algorithm to alter the sequence of live attenuated Poliovirus vaccine to minimize recombination.

Computationally designed and experimentally characterized optimizing mutations of engineered protein PA-Rac (photo-activatable Light-Oxygen-Voltage domain fused to Rac GTPase), a protein tool that enables laser-mediated control of motility or other responses in living cells.

Engineered the interaction interface between two proteins, BRCA1 and an E2 ubiquitin-conjugating enzyme, to track BRCA1’s downstream signals and their relationship to breast cancer susceptibility.