Protein Crystallization Programmed with DNA

Project: Research project

Project Details

Description

Overview. Crystallization is a fundamental process observed throughout the physical sciences. Crystallizing proteins is particularly challenging due to their conformational flexibility, large size, and inherent stereopurity but attractive due to the exquisite functionality of many protein building blocks. Single crystals organize proteins in a highly ordered array, not only rendering them amenable to X-ray crystallography for structure determination but also providing long-range order of functional moieties enabling cooperative or concerted functions across the entire material. However, protein crystallization relies on fortuitous interactions between proteins, making it difficult to control protein packing within single crystals or, in some cases, to obtain any protein crystal at all. As such, a fundamental understanding of how to control or overcome these protein-protein interactions is an outstanding grand challenge in the field.
Over the past 20 years, the Mirkin group has pioneered the use of DNA as a programmable interaction to direct the assembly of nanoscale building blocks. This work has led to the development of a series of design rules that enable the prediction and assembly of target crystal phases, made possible due to the ability to tailor the nature of bonding interactions via the inherent programmability of DNA. In the proposed project, we aim to discover how DNA can augment, replace, and eliminate protein-protein interactions and direct crystallization outcomes. This work will exploit the many distinct advantages of DNA including its specific hybridization, tunable length, inherent flexibility, and tailorable interaction strength. The project is organized into four distinct yet synergistic objectives: 1) programming multivalent DNA interactions on proteins by exploiting their native geometry; 2) leveraging symmetry and valency control to enhance protein crystallization; 3) controlling protein orientation via interface design; and 4) pre-organizing conformationally-flexible proteins towards actuatable protein materials.

Intellectual Merit of Proposed Activity. Protein crystallography provides valuable, angstrom-level resolution and structural insight into the macromolecules that engender the infrastructure of life. The proposed work seeks to understand the interactions that drive crystallization and discover a means to disrupt, reprogram, and redefine those interactions, using the programmability of DNA. Achieving the objectives herein 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. The proposed research will approach this challenge from four complementary perspectives, each of which will yield valuable fundamental insights 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. Together the proposed project will develop a fundamental understanding of how to control the interplay between DNA-DNA and protein-protein interactions. This knowledge will empower researchers with tools to precisely engineer the structural outcomes of protein crystallization towards the creation of novel functional biomaterials.

Broader Impacts of Proposed Activity. The proposed research will provide the sci
StatusActive
Effective start/end date6/1/215/31/24

Funding

  • National Science Foundation (DMR-2104353)

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