Abstract

Due to their remarkably high structural stability, proteins from extremophiles are particularly useful in numerous biological applications. Their utility as alternative protein scaffolds could be especially valuable in small antibody mimetic engineering. These artificial binding proteins occupy a specific niche between antibodies and low molecular weight substances, paving the way for development of innovative approaches in therapeutics, diagnostics, and reagent use. Here, the 50S ribosomal RNA-binding protein L35Ae from the extremophilic archaea Pyrococcus horikoshii has been probed for its potential to serve as a backbone in alternative scaffold engineering. The recombinant wild type L35Ae has a native-like secondary structure, extreme thermal stability (mid-transition temperature of 90°C) and a moderate resistance to the denaturation by guanidine hydrochloride (half-transition at 2.6 M). Chemical crosslinking and dynamic light scattering data revealed that the wild type L35Ae protein has a propensity for multimerization and aggregation correlating with its non-specific binding to a model cell surface of HEK293 cells, as evidenced by flow cytometry. To suppress these negative features, a 10-amino acid mutant (called L35Ae 10X) was designed, which lacks the interaction with HEK293 cells, is less susceptible to aggregation, and maintains native-like secondary structure and thermal stability. However, L35Ae 10X also shows lowered resistance to guanidine hydrochloride (half-transition at 2.0M) and is more prone to oligomerization. This investigation of an extremophile protein’s scaffolding potential demonstrates that lowered resistance to charged chemical denaturants and increased propensity to multimerization may limit the utility of extremophile proteins as alternative scaffolds.

Highlights

  • Protein engineering for selective target recognition has numerous applications in research, diagnostics and therapeutics [1,2,3,4,5,6,7,8,9,10,11,12]

  • The far-UV circular dichroism (CD) analysis revealed that recombinant wild type (rWT) L35Ae was mostly βpleated with a β-sheet content of 40% (Table 2)

  • The mean extent of protein oligomerization is calculated as a ratio of mean apparent molecular weight of a protein (MW) and the molecular weight of its monomer (MWm, 10,988 Da for rWT L35Ae and 10,862 Da for L35Ae 10X)

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Summary

Introduction

Protein engineering for selective target recognition has numerous applications in research, diagnostics and therapeutics [1,2,3,4,5,6,7,8,9,10,11,12]. Animal-sourced and bioengineered antibodies have been successfully used for these purposes for decades [6,7,8,9], the application of antibodies is often complicated by their relatively large molecular sizes, complex multi-subunit structure, limited stability, and abundance of post-translational modifications requiring the use of eukaryotic expression systems, which together lead to technical challenges and high production costs To overcome these limitations, alternative/artificial binding proteins (ABPs) have been developed [1,2,3,4,5,6, 10,11,12]. Artificial binding proteins occupy a specific niche in between antibodies and low molecular weight drugs/substances, which paves the way for development of innovative approaches for therapy, diagnostics, and reagents use

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