Designing and Engineering Self-Assembling Systems to Control Quaternary Structures Open Access

Gonzalez de la Nuez, Ayda (Spring 2021)

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Supramolecular assemblies that form high-ordered structures from monomers are ubiquitous. Protein and peptide-based nanomaterials are emerging as a promising array of tools in biotechnology due to their biocompatibility, stability, and ability to spontaneously self-assemble into a set of monodispersed structures or experience polymorphism. Self-assembly of these nanomaterials have unique physical and mechanical properties that often dictates the size, morphologies, and functionality. These nanomaterials are particularly attractive due to their critical roles associated with life processes and function. However, the properties that dictate how monomers assemble into specific high-ordered structures are still unknown. The ability to control and rationally design materials that self-assemble is helpful when trying to control the morphology, which has potential uses in biotechnological applications.

Hence, this thesis focuses on understanding the design rules and properties that dictate the self-assembly of two different systems: Encapsulins and peptide-based assemblies. The first chapter focuses on protein-based nanocompartments, encapsulins, which typically support the cell during metabolic processes. We aim to elucidate the principles that dictate the size and symmetry which encapsulins adopt when assembled. Structural analysis suggests that the E-loop, one of the motifs found within the monomer of the encapsulin, is responsible for conformational changes, which give rise to distinct quaternary structures. To probe the E-loop’s structural role, we employ protein engineering to modify a native T-1 symmetry encapsulin to adopt the quaternary structure of a T-3 symmetry encapsulin.

Moreover, the second chapter centers on rationally designing de novo peptides that assemble into high-ordered structures in order to understand them and precisely control their architecture. Here, we design and characterize the supramolecular assembly of b-sheet peptides, which have been previously used to understand the pathological formation of amyloids. To study the effects of sequence to structure relationship of b-sheet forming proteins, we aimed to survey the landscape of how amino acid identity affects the supramolecular assembly of b-sheet peptides. The results of these projects will lay the initial groundwork to improve our comprehension of the roles that are critical in peptide-based self-assembly. Understanding these properties will offer us a manual for the rational design and control of self-assembling nanomaterials, improving the usefulness of biotechnological applications, including controlled drug delivery and release, nanoreactors, conducting polymers, and potentially shed light into amyloid formation.

Table of Contents


Chapter 1 Introduction to Encapsulins

1.1 Investigating the principles which drive the self-assembly of TmE

1.2 The encapsulin monomer

1.3 Results and Discussion

1.4 Conclusion

1.5 Materials and Methods

1.6 References

Chapter 2 Introduction to Nanotubes

2.1 Insight into the peptide motifs

2.2 Sequence Design

2.3 Results and Discussion

2.4 Conclusion

2.5 Materials and Methods

2.6 References

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