Repeat protein engineering: creating functional nanostructures/biomaterials from modular building blocks

Abstract

There is enormous interest in molecular self-assembly and the development of biological systems to form smart nanostructures for biotechnology (so-called 'bottom-up fabrications'). Repeat proteins are ideal choices for development of such systems as they: (i) possess a relatively simple relationship between sequence, structure and function; (ii) are modular and non-globular in structure; (iii) act as diverse scaffolds for the mediation of a diverse range of protein-protein interactions; and (iv) have been extensively studied and successfully engineered and designed. In the present review, we summarize recent advances in the use of engineered repeat proteins in the self-assembly of novel materials, nanostructures and biosensors. In particular, we show that repeat proteins are excellent monomeric programmable building blocks that can be triggered to associate into a range of morphologies and can readily be engineered as stimuli-responsive biofunctional materials.

Biomolecular templating of functional hybrid nanostructures using repeat protein scaffolds

“…Repeat proteins are ideally suited for engineering biomolecular templating platforms because their structures are modular and their stabilities predictable [16,21]. Repeat proteins are formed by a variable number of tandem repeats composed of an 18-47 amino-acid structural unit.…”

“…The newest and most promising approaches for design of protein-based platforms for biomolecular templating rely on the use of modular building blocks with simple intermolecular interactions that allow for a better control of the assembly [16,17]. Simple building blocks with welldescribed intermolecular interactions, such as coiled-coils and amyloid peptides, allow relatively simple assembly of different nanomaterials [7,18] and even 3D structures [19].…”

PyFolding: An open-source software package for graphing, simulation and analysis of the biophysical properties of proteins

“…In particular, we have incorporated the ability to fit and simulate equilibrium unfolding experiments with user defined protein topologies, using a matrix formulation of the 1-D heteropolymer Ising model. This aspect of PyFolding will be of particular interest to groups working on protein folds composed of repetitive motifs such as Ankyrin repeats and TPRs, given that these proteins are increasingly being used as novel antibody therapeutics (38)(39)(40)(41) and biomaterials (42)(43)(44)(45)(46)(47). Further, as analysis can be performed in Jupyter notebooks, it enables novice researchers to easily use the software and for groups to share data and methods.…”

Computational design of a leucine-rich repeat protein with a predefined geometry

“…In a folded protein, a distinct chemical environment of individual methyl groups leads to different chemical shifts resulting in a dispersion of signals. We expressed gdLRR-2-A-cap and, as a reference, the unfolded gdLRR-3-A-cap (see below) with [1][2][3][4][5][6][7][8][9][10][11][12][13] C]-glucose as the sole carbon source. Expression results in specific labeling of isolated sites, including methyl groups (29).…”

“…Their extended shapes result in proteins with extraordinarily large binding surfaces, which makes them ideal scaffolds for protein binding. Analogous to antibodies, repeat proteins can be divided into framework residues, which encode stability and structure, and variable positions, which are responsible for protein recognition (7). A striking difference from antibodies is that the global structure can vary considerably between repeat proteins, even within a family.…”