Exploring the Impact of Altered Backbone Composition on Protein Folding and Function

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PROJECT SUMMARY Proteins drive essential functions of life as well as aberrant functions in disease, making the development artificial molecules that mimic proteins a significant challenge in biomedical research. The problem of protein mimicry is rooted in the hierarchy that defines protein structure, where covalent connectivity gives rise to local folding motifs, unimolecular arrangements of such motifs, and multi-chain assemblies. The construction of sequence-specific oligomers with artificial backbones and defined folding propensities is a powerful approach to peptide and protein mimetics. Most precedent with such scaffolds has focused on isolated secondary structure. Creating more complex tertiary folding patterns presents a formidable challenge, as it requires the design of both backbone connectivity and side-chain sequence that will result in multiple biomimetic secondary structures that pack in a defined way in a single chain. Addressing this challenge has the potential to advance artificial protein-like chains toward the functional versatility of biomacromolecules. A unifying theme underlying research in the PI’s laboratory is the design, synthesis, and application of molecules that are inspired by proteins but expand beyond natural constraints of covalent connectivity. A major goal in this work, supported in prior awards from NIGMS, has been the development of strategies for producing protein tertiary structure mimetics from artificial bio-inspired backbones. The central hypothesis guiding this effort is that any protein can be treated as a chemical entity with two orthogonal sequences: one of side-chain functional groups and a second of backbone units that display those functional groups. Systematic engineering of backbone composition in a prototype sequence from nature can yield a heterogeneous-backbone analogue with similar fold and function. In work to date, design rules have been conceived for the construction of such agents, the impacts of altered composition on folding examined, and the functional potential of these molecules explored. The present application seeks to advance this program through continued effort across four complementary research areas. From a practical standpoint, artificial backbone composition can impart useful properties, such as enhanced biostability, and tune biological activity. In fundamental terms, changing backbone characteristics in ways not possible with traditional mutagenesis can further understanding of natural biomacromolecules. An important aspect of the concept underlying the research is that it addresses the problem of tertiary structure mimicry by an approach that is generalizable, as natural sequences serve as the starting point for design of their own mimics. Further, while the molecules are synthetic, the design principles are applicable in the context of new emerging approaches to biological production of protein-like artificial chains.