Protein Crystallization Programmed with DNA

PART 1: NON-TECHNICAL SUMMARY

Proteins are natural, tiny molecular machines – often 10,000 times smaller than the width of a human hair – that play crucial roles in biology. Since their discovery almost 200-years ago, understanding their structures and functions has enabled scientists to learn about the processes that underpin life and solve scientific problems facing humanity.

However, their tiny size makes them incredibly difficult to characterize and understand. One powerful way to determine the structures and functions of proteins is protein crystallography, a technique where X-rays interact with a highly ordered assembly of proteins, known as a single crystal. Unfortunately, obtaining protein single crystals represents a major bottleneck in this process because proteins can interact with each other in many ways that prevent them from forming highly ordered assemblies.

This project aims to overcome this challenge using DNA – the genetic code of life – as a blueprint to define the interactions between proteins and thus control how they arrange into single crystals. Importantly, these single crystals will not only provide insight into the tiny world of proteins but will function as new, synthetic materials in their own right, useful as sustainable catalysts or energy conversion materials.

Using DNA to control protein interactions and arrangement will allow crystals to be assembled by design. This work will help transform protein crystallography from an experiment of chance to an experiment of purpose to solve pressing societal needs in energy, sustainability, and medicine. Researchers at various stages of their careers (from undergraduate students to postdoctoral researchers) will benefit from the training provided by this project, and will disseminate their knowledge and skills in publications, presentations, and by engagement with students from typically underrepresented and marginalized groups through synergistic outreach activities.

PART 2: TECHNICAL SUMMARY

Protein single crystals provide valuable, angstrom-level resolution and structural insight into the macromolecules that engender the infrastructure of life and represent a promising class of biomaterials with cooperative properties and concerted functions. This project seeks to understand the interactions that drive crystallization and discover a means to disrupt, reprogram, and redefine those interactions, using the programmability of DNA.

This challenge will be approached from four complementary perspectives, each of which will yield valuable fundamental insight into protein crystallization: increasing the role of DNA in protein-DNA crystals; investigating how symmetry and valency affect crystallization; defining specific protein interfaces within crystals; and manipulating the conformations of flexible proteins so that they can be controlled and, ultimately, harnessed. These findings will result in design principles that will allow one to exploit the many distinct attributes of DNA, including its specific hybridization, tunable length, inherent flexibility, and tailorable interaction strength, to program the assembly of proteins.

Therefore, achieving these objectives will not only render challenging proteins amenable to crystallographic analysis but also, importantly, open a new class of tailorable, programmed crystalline materials that can harness the intrinsic functionality of proteins. This project will generate new fundamental knowledge of how to control the interplay between DNA-DNA and protein-protein interactions, thereby empowering researchers with tools to engineer the structural outcomes of protein crystallization towards the creation of novel functional biomaterials.

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.