Computational design of a protein crystal

Abstract

Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a "honeycomb-like" structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify "designable" structures from minima in the sequencestructure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.M olecular design provides powerful tools for exploring how molecular properties dictate macroscopic structure and function. One of the most precise forms of self-organization, crystallization achieves orientation and symmetry across many length scales and can be leveraged to engineer materials with well-defined molecular order (1). In addition to their central role in structure determination, molecular crystals have many applications, including nanoparticle templating (2, 3), nonlinear optical devices (4), molecular scaffolding (5), and porous frameworks (6). A predictive understanding of how to achieve self-assembled macroscale structure and desired properties remains challenging, however, particularly when large, conformationally flexible molecules are employed.Small synthetic molecules have been designed that display complementary functional groups in a manner consistent with a chosen crystal structure. Intermolecular contacts are often patterned using strong, directional interactions (e.g., hydrogen bonding, metalcoordination, and electrostatic interactions) (7). The constituent molecules, however, are typically small and synthetic, thus limiting size, shape, and functionality. Hence, simultaneously achieving functional properties and the presentation of complementary intermolecular interactions that confer a targeted crystal structure can be difficult. Commonly, weak intermolecular forces stabilize crystalline ordering, and as a result, quantitative, predictive approaches to crystal de...

A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals

“…Although effective methodologies have been developed for facilitating protein crystallization, 7,8 successes in obtaining 3D protein crystals by design have been rare. [9][10][11] In contrast, the ability to rationally engineer crystalline materials from small organic and inorganic building blocks, though still challenging, is considerably more advanced. 1,[12][13][14] A prominent class of these crystalline materials is metal-organic frameworks (MOFs), which have attracted much attention due their applications in separation, storage, and catalysis, etc.…”

Soft matter perspective on protein crystal assembly

“…Studying the structure of transient complexes in solution [149] may not only help identify potential crystal contacts, but also competing interactions that can hinder crystal assembly. The design of proteins that easily crystallize could also be used to validate and further enrich the microscopic insights obtained from the direct studies of protein-protein interactions [150].…”

Flexible, symmetry-directed approach to assembling protein cages

“…An important realization was that a large number of complex symmetries could be generated from only two distinct symmetry elements (for a protein, these must be rotational symmetries specified by its quaternary structure), provided the orientation of the symmetry axes with respect to each other could be carefully controlled. These principles have now been quite widely applied to design both protein cages and protein networks (16)(17)(18)(19)(20)(21)(22). The principal challenge to researchers has been to design new interactions between the protein subunits that promote assembly in the desired geometry, and, in particular, to align the angle between symmetry axes correctly.…”