Research Project 1: Design New Recognition Elements
RESEARCH Lead:
Dr. Robert Pantazes
Auburn University
FOCUS:
Developing engineering principles for designing protein interactions, allowing for the development of a near-infinite variety of on-demand direct analyte recognition elements for sensors.
Major Industry Challenge:
Biosensors require recognition elements (REs) that bind to target analytes and induce a signal at desired conditions. Current experimental approaches are not guaranteed to produce proteins with the necessary properties, and typically require a long time and incur high costs. With protein structure prediction recently solved or nearly-solved by AlphaFold27, engineering principles are now needed to computationally design proteins REs to bind with desired affinities at specified conditions (e.g. temperatures, pressures, pHs).
Hypothesis:
Protein binding is dominated by hotspot residues28–30 that are preorganized prior to binding.31,32 This concept can be integrated into novel and existing protein design algorithms, enabling on-demand design of REs with needed properties in minutes to hours on a personal computer.
Major Outcomes:
Algorithms for designing a variety of protein REs will be developed. The algorithms will be able to design REs of various sizes with a range of affinities at specified environmental conditions (e.g. temperature, pressure, pH). The algorithms will be considered successful when at least 50% of their predictions have the desired properties.