Computational approaches for protein elucidation
Determining the structure and sequence of proteins is an important part of understanding the protein's biological properties
and potential utility as a drug. Designing predetermined crystal structures, however, can be subtle given the complexity of
proteins and the noncovalent interactions that govern crystallization (1). Researchers at the University of Pennsylvania recently
reported on a computational approach for the design or proteins that self-assemble in three dimensions to yield macroscopic
"People have designed crystals out of smaller, much less complex molecules than proteins, but protein design is much more
subtle," said Jeffrey G. Saven, associate professor of chemistry and biological and theoretical physical chemistry at the
University of Pennsylvania, in a university press release. Saven conducted the research and recently reported on its results
(1). Protein crystals are attractive as a nano-scale building material because their properties, particularly their exterior
surfaces, are highly customizable, according to the university release.
The researchers targeted a crystal built using a relatively small protein containing a sequence of 26 amino acid positions.
The researchers assigned specific amino acids to eight of the positions, but with 18 different types of amino acid to choose
from for each of the remaining 18 slots, the algorithm addressed well more than 1022 potential combinations. The researchers
accounted for other characteristics, such as the spacing between proteins and their orientation with respect to one another,
increasing the variables being considered, according to the release.
"We worked on synthesizing both of those steps, doing the characterization of structure and the sequence at the same time,"
said Saven said in the university release. "As we move through this process, we eliminate things that will never work, such
as proteins where atoms overlap in space or where amino acids don't fit into a given site. At the same time, we identify proteins
that, as you vary the structure, are likely to yield a crystal."
Specifically, the research used a three-helix coiled-coil protein designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which had a "honeycomb-like" structure and
hexameric channels that spanned the crystal (1). The approach involved creating an ensemble of crystalline structures consistent
with the targeted symmetry, characterizing this ensemble to identify "designable" structures from minima in the sequence–structure
energy landscape and designing sequences for these structures, and experimentally characterizing candidate proteins. 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.
The target crystal the researchers produced is a proof of concept. "There's still much we don't know about the interactions
that govern crystallization," Saven said, in the university release. "With this technique, we can explore what those interactions
are or how we might take an existing protein and engineer those interactions so we get much better structures."
1. J.G. Saven et al, PNAS, 109 (19), 7304–7309 (2012).