Research Project 1: Design New Recognition Elements

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Dr. Robert Pantazes 
Auburn University


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).


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.

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