NSF Award
2428112
NON-TECHNICAL SUMMARY: <br/><br/>Proteins perform a myriad of functions essential to life, making them subjects of extensive study across the physical and life sciences. Protein organization, either through natural or artificial means, is a way to realize materials with structural and functional diversity. Leveraging their versatility, scientists have shown that proteins can be engineered for specific tasks, including binding events, energy transformations, and more. However, controlling protein-protein interactions remains challenging, partly due to the competing forces between the molecular units that exist in these systems. The goal of this proposed research is to overcome challenges associated with protein-protein interactions by synthesizing designer protein structures with strategically designed modifications. Specifically, this work will combine protein modifications with DNA, an easily tailored molecular unit that can be programmed and synthesized in the lab. This proposal will leverage the distinct attributes of DNA, including its specific bonding, tunable length, inherent flexibility, and tailorable interaction strength, to prepare protein-DNA hybrid structures. By investigating the interplay between proteins and DNA at the molecular level, this research seeks to unravel underlying principles governing biomolecular interactions and assembly processes. Through a systematic approach of exploration and experimentation, the project will elucidate fundamental mechanisms driving the formation of protein-DNA hybrid structures across different dimensions (i.e., one-, two-, or three-dimensions). This pursuit of knowledge will not only enhance our understanding of biological systems but also lay the foundation for developing generalizable design principles applicable to a diverse set of biomaterials. Consequently, the outcomes from this project are expected to expand the boundaries of scientific knowledge and provide insights that could spur innovations in various fields, ranging from biotechnology and medicine to materials engineering. Finally, the project encompasses a comprehensive plan to nurture scientific talent within the United States, providing graduate and undergraduate students and postdoctoral trainees with opportunities for professional skill development, technical expertise, and the expansion of fundamental scientific knowledge through collaborations within Northwestern University and other institutions.<br/><br/>TECHNICAL SUMMARY:<br/> <br/>The proposed research aims to deepen our understanding of how protein organization can be controlled using DNA, leading to the design of novel functional materials such as the formation of larger complexes and assemblies that display a wealth of structural diversity. Although chemically engineered proteins have shown promise in building designer protein architectures, protein-protein interactions are generally complex and difficult to control synthetically, and therefore the design of materials that leverage the inherent functions of natural protein building blocks is challenging. Therefore, the exploration of biochemically disrupting, controlling, and directing protein interactions is worthwhile and could lead to the engineering of materials possessing properties and functions that rival or exceed those observed in nature. This proposal seeks to advance protein-based materials into a new era where designer structures can be made by controlling the linkage of structures into one, two, and three dimensions in an effort to control cooperative function. We hypothesize that new properties, like dynamic or responsive actuation, can be accessed within hybrid DNA-protein supramolecular structure. By realizing such materials, we will gain a greater fundamental understanding of chemical and biological design principles essential to these systems. Therefore, this proposal will address a major challenge pertaining to the realization of dynamic functional biomaterials by developing generalizable bioconjugation strategies and DNA design rules to disrupt and override complex protein-protein interactions. Moreover, these strategies are expected to enable precise structural and functional control with hybrid protein-DNA supramolecular structures. To achieve this, the project is organized into three distinct and synergistic objectives: (1) designing generalizable site-specific DNA functionalization to control proteins in 1D arrays; (2) designing dynamic, DNA-driven, 2D protein lattices; and (3) utilizing DNA interactions to facilitate protein crystallization in 3D. In doing so, this work seeks to advance our overall understanding of protein-based biomaterials and pave the way for accessing new materials with defined cooperative functions. This proposal builds upon knowledge gained from prior work where our research team established routes to direct protein crystallization outcomes via programmable DNA interactions. Broadly, the knowledge gained from these studies will contribute to fundamental knowledge at the intersection of biochemistry, molecular biology, and materials science by investigating hybrid protein-nucleic acid structures to reprogram protein interactions. Finally, the project will provide the expansion of fundamental scientific knowledge to the broader community and will provide graduate, undergraduate, and postdoctoral trainees with opportunities for professional skill development.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
