Proteins, in one form or another, are involved in all processes sustaining life and can be used to control cellular function (e.g. pharmaceuticals) or be used outside of cells to impart advanced function to materials (e.g. detectors to identify bacteria or catalyzing reactions in an industrial setting). Before using proteins outside of their native environment, steps must be taken to stabilize the molecule to prevent degradation. Attaching the protein to a solid substrate or adding polymer chains to the molecule can overcome degrading effects, but such methods are not always effective because of the many different options available for such alterations. This research uses recently-developed computational models together with state-of-the-art experimental methods to identify and target the most stabilizing locations on proteins. This knowledge will then be used to create a process for rapid development of biomaterials with specific function.
The potential benefits to society of successfully achieving the goals of this research are huge and improve many fields including sustainable chemical processing, national competitiveness, defense, and medical care. An example in the medical field is improved and cost-effective prescription drugs. Many newly-developed pharmaceuticals are protein based, but their efficacy is limited because they are quickly degraded in the body. Attaching polymers to the proteins at the correct location (that would be provided by this research) would increase the time that the drug remains in the body and reduce healthcare costs by decreasing the amount of protein needed for a treatment. Another example from the defense field is hazard detection. Many potential threats to homeland security come from weaponized chemicals or biological agents (e.g. mustard, anthrax, ebola, etc.). Attaching proteins to solid substrates, at the location that preserves function, paves the way for the development of chip-based detectors that can be placed in vulnerable areas such as mail processing centers, airports, sports venues, etc. or could be sewed into the uniforms of soldiers. Other benefits to society include creating hands-on modules to teach biomaterials in K-12 classrooms and increased participation in pre-freshman activities.
Incorporating unnatural amino acids (UAAs) into proteins, in place of their natural counterparts, can be used to tether polymers to proteins or attach the protein to a surface at any location desired. The challenge is to select the correct location that preserves function because such substitution can destabilize the protein and no method currently exists to predict the ultimate behavior. A combinatorial approach cannot be used in most instances due to costs and time, so the objective of this research is to create an integrated computational and experimental technology that rapidly predicts and validates the optimal residues on a protein to be used in a novel biomaterial. The work will proceed by first determining the effects of UAA incorporation on function because such is not fully understood. Once this is accomplished, efforts will be done to optimize polymer-protein interactions for stability, active site accessibility, etc. The final stage of the project will be to produce biocatalysts and smart surfaces by optimizing protein-surface interactions. The key to accomplishing the computational work is to build on the PI's expertise in coarse-grain protein modelling by developing such a model for UAAs. This model will be parameterized and validated against experimental data produced with the co-PI's novel method of UAA incorporation and biofunctionalization called PRECISE (Protein Residue-Explicit Covalent Immobilization for Stability Enhancement). This work will train two graduate students and two to four undergraduate students on proper application of the scientific method using state-of-the-art techniques in an interdisciplinary, experimental/computational team environment.
