Protein-based nanostructure

Marlon D. Jerez

November 7, 2017

1 Introduction: Definition
The complexity and sophistication of protein-based structures and materials in nature hints
to the great potential of designed protein-based materials and nanostructures. Amino acid
sequences encode the complex structures and functions of proteins, thus, the manipulation
of protein sequence can generate structural and functional building blocks, and encode the
formation of supramolecular protein assemblies. Therefore, if it possible to manipulate protein
structure and function, it would be possible to generate sophisticated nanotools. In this sense,
the application of protein to assemble new nanostructures has been recently explored.
Self-assembling and nanostructure patterning based on different biomolecules have been
widely explored recently, being most of the works based on the assembly of nucleic acids. DNA
provides a good control over the assembly. However, DNA cannot provide the functional and
structural diversity of proteins.
One of the main limitations for rational protein design is the lack of a deep understanding
about how protein sequence-structure-function relate. The three dimensional structure of pro-
teins is defined by their primary sequence and is directly related to its function. Thus,manipulation
of the protein structure through changes in its primary sequence can generate different nanos-
tructures and functionalities. Most of the nanostructures are based on a particular type of
proteins, which are the repeat proteins. Due to their modular nature, these proteins are better
suited to be used as building blocks than other protein scaffolds [7].
Repeat proteins are non-globular structures that are involved in essential cellular processes
acting typically as scaffolds for the mediation of proteinprotein interactions [1]. There are
a variety of repeat protein families composed of units with different structures, being alpha
helical, beta-strand or a mixture of the two secondary structure elements. Some of the most
abundant and well studied classes of repeat proteins are formed by the repetition of simple

1
building blocks, such as; tetratricopeptide repeats (TPR), ankyrin repeats (ANK), leucine rich
repeats (LRR), armadillo repeats (ARM), and transcription activator-like (TALE) [3].

2 Structures and applications

Considering the main features of repeat proteins previously described, it is evident that they
are ideally suited for nanobioengineering. Each repeat unit can be used as a building block
with individually engineered properties (stability, function, and interactions between modules)
in order to generate designed proteins and higher order assemblies. Because repeat proteins
are simplified systems, it is possible to control how protein sequence-structure-function relate
in these type of proteins [4].
The tetratricopeptide repeat (TPR) is an example of the wide range of possibilities that
repeat proteins give to the field of protein assemblies. TPR consists of 34 amino acid sequence
that folds in helix-turn-helix motif [2]. To create new TPR proteins that capture the sequence-
structure relationship of the TPR fold, a consensus TPR (CTPR) sequence was designed by
the Regan Laboratory from the statistical analysis of natural TPRs.
The modular structure of the CTPR repeat proteins and the basic understanding of their
sequence-structure relationships opens the possibility to modulate the interaction between the
units. Thus, it is possible the formation of different protein assemblies in a controlled manner
through a hierarchical self-assembly including nanofibers, nanotubes, and nano-structured thin
films.

2.1 Nanofibers

Protein nanofibers are generated using the intrinsic head-to-tail interactions and a simple disul-
fide bond staple to fix those interactions between molecules. By combining the head-to-tail
interactions observed in the CTPR crystals with the introduction of specific reactives into the
CTPR units, linear higher order structures have been assembled [6].

2.2 Nanotubes

CTPR protein nanotubes formed by the introduction of a second interacting interface that
provides an extra dimension to the final structure by allowing two superhelical CTPR molecules
to assemble [5].

2
2.3 Nano-structured thin films

One advantage of using CTPR proteins for the generation of highly ordered materials and
devices is the fact that these proteins can maintain their structure in the solid state. Nano-
structured protein thin films are generated using the intrinsic head-to-tail and side-to-side
assembly properties of CTPRs through specific noncovalent interaction

References
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