Computational Toolkit to Discover Peptides that Self-assemble into User-selected Structures

2020-01-29T21:57:39Z (GMT) by Carol Hall
Many peptides are known to adopt beta-strand conformations and assemble spontaneously into a variety of nanostructures with applications in a variety of fields. The goal of this project is to develop an open software toolkit that enables the identification of peptide sequences that are capable of assembling into user-selected beta-sheet-based structures. Users will be able to screen potentially thousands of peptide sequences that assemble spontaneously into the structure of their choosing, and rank order their stability. Discontinuous molecular dynamics (DMD) simulation software along with the PRIME20 force field will also made available to enable analysis of the designed structures’ assembly kinetics. To establish efficacy and a basis for future improvement of computational tools, selected designs will be validated experimentally using biophysical characterization techniques and solid-state nuclear magnetic resonance (ssNMR) spectroscopy. Our software tool, “Peptide Assembly Designer”, PepAD, will be a “plugin” on the NSF-sponsored Molecular Simulation and Design Framework (MoSDeF).