Today we report in Nature Materials a general strategy for creating proteins that form into precise and pre-specified crystalline structures. The ability to design such biomaterials with high accuracy sets the stage for the development of advanced optical tools, new technologies for chemical separation, and a range of other applications in biotechnology and medicine.
This research was led by Baker Lab postdoctoral scholars Zhe Li, PhD, and Shunzhi Wang, PhD, and former graduate student Una Nattermann, PhD. It included collaborators from Tehran University of Medical Sciences, University of Massachusetts Lowell, Argonne National Laboratory, Lawrence Berkeley National Laboratory, and the Core R&D Labs at the Institute for Protein Design.
“Crystallizing proteins has always been mysterious — you need a lot of work and luck to get these irregular molecules to form into orderly crystalline arrays. Our work shows that it is now possible to design brand new proteins that will form crystals in precise and predictable ways,” explained Li.
To create proteins that assemble into pre-defined three-dimensional arrangements, the team followed a hierarchical design approach. Individual proteins were first programmed to form into smaller, non-crystal oligomers, and these oligomers were then redesigned to form unbounded crystal arrangements with specific crystal spacings. The team used the docking tool RPXDock and traditional Rosetta design.
After purifying their protein components in the lab and then mixing them to enable self-assembly, the team used X-ray scattering and electron microscopy to confirm that the intended crystal spacing and exact protein interfaces were achieved. They observed several protein crystals with the correct structures, with the most accurate deviating less than 0.2 nanometers on average from its design model.
“I’ll never forget the first time we compared high-resolution data from one of our lab-grown crystals to our design model and saw that they matched almost perfectly. Building off this initial success, we used the same underlying principles to design more crystals the very next day,” said Wang.
The team measured several unique properties of the new protein crystals. Some had extremely high solvent content (as high as 90%). One was found to be extremely stable, with little to no observed loss in crystalline structure after being placed in near-boiling water for one hour or autoclaved at high temperatures and pressures for 40 minutes. Other designed crystals were stable up to 65°C or 85°C.
“The ability to program where every atom goes inside robust biomaterials that you can see with the naked eye is a milestone for protein design. We believe this could lead to new tools for materials engineering, biomanufacturing, and therapeutics delivery,” explained Nattermann.
Leveraging the remarkable stability and large open spaces with the crystals, the team experimented with encapsulating gold nanoparticles within the biomaterials and also dehydrating and rehydrating them to change their size. This significantly altered the optical properties of the crystals, suggesting this new class of material may have applications in advanced optics.
This research was supported by The Audacious Project, Howard Hughes Medical Institute, Open Philanthropy Project, Washington Research Foundation, Nordstrom Barrier Fund, Human Frontiers Science Program, Amgen, Novo Nordisk, and the US Department of Energy (DE-SC0018940, DE-SC0019288, DE-AC02-06CH11357, DE-AC02-05CH11231), Defense Advanced Research Projects Agency (HR001117S0003, FA8750-17-C-0219), National Institutes of Health (T32GM007270, P30 GM124165, P30 GM124169-01, U24GM129547), and National Science Foundation (DGE-1762114).