Designing repeat proteins for biosensors and medical imaging

Parker, Rachael N.; Grove, Tijana Ž.

doi:10.1042/bst20150085

Cited by 8 publications

(7 citation statements)

References 44 publications

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“…Further, they are comparatively easy to design, have highly variable binding surfaces, and can be remarkably stable . Engineered binding scaffolds based on repeat proteins have found applications in biosensing, diagnostics, and therapeutics …”

Section: Engineering Repeat Proteinsmentioning

confidence: 99%

Engineering repeat proteins of the immune system

McCord

Grove

2020

Biopolymers

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Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule.Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.

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Section: Engineering Repeat Proteinsmentioning

confidence: 99%

Engineering repeat proteins of the immune system

McCord

Grove

2020

Biopolymers

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“…[4][5][6] Scaffolds can address these drawbacks because they are typically smaller in size, have increased environmental stability, lack reactive cysteine residues, utilize cost-efficient bacterial overexpression methods, and can be designed for potent binding of a wide variety of ligands. 1 Repeat proteins have emerged as leading candidates in the field of alternative protein scaffolds. 1 These proteins contain repeating structural motifs where the number of amino acids in each repeat varies, usually consisting of 20 to 40 residues.…”

Section: Introductionmentioning

confidence: 99%

“…1 Repeat proteins have emerged as leading candidates in the field of alternative protein scaffolds. 1 These proteins contain repeating structural motifs where the number of amino acids in each repeat varies, usually consisting of 20 to 40 residues. 7 Each of the repeat protein families has a signature structural and sequence motif.…”

Section: Introductionmentioning

confidence: 99%

Designed leucine‐rich repeat proteins bind two muramyl dipeptide ligands

2021

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Designed protein receptors hold diagnostic and therapeutic promise. We now report the design of five consensus leucine‐rich repeat proteins (CLRR4–8) based on the LRR domain of nucleotide‐binding oligomerization domain (NOD)‐like receptors involved in the innate immune system. The CLRRs bind muramyl dipeptide (MDP), a bacterial cell wall component, with micromolar affinity. The overall Kd app values ranged from 1.0 to 57 μM as measured by fluorescence quenching experiments. Biphasic fluorescence quenching curves were observed in all CLRRs, with higher affinity Kd1 values ranging from 0.04 to 4.5 μM, and lower affinity Kd2 values ranging from 3.1 to 227 μM. These biphasic binding curves, along with the docking studies of MDP binding to CLRR4, suggest that at least two MDPs bind to each protein. Previously, only single MDP binding was reported. This high‐capacity binding of MDP promises small, soluble, stable CLRR scaffolds as candidates for the future design of pathogen biosensors.

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“…Engineering of biomolecules to alter or augment their function continues to broaden in scope for both design novelty and the range of applications. Recent advances in medicine[ 1 ], agriculture[ 2 ], carbon capture[ 3 ], biosensors[ 4 ], and advanced materials[ 5 ] are the direct results of success in protein design. The vast majority of such designs have been constructed using the twenty canonical amino acids (CAAs) found in nature.…”

Section: Introductionmentioning

confidence: 99%

A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity

2017

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Redesigning protein surface topology to improve target binding holds great promise in the search for highly selective therapeutics. While significant binding improvements can be achieved using natural amino acids, the introduction of non-canonical residues vastly increases sequence space and thus the chance to significantly out-compete native partners. The potency of protein inhibitors can be further enhanced by synthesising mirror image, D-amino versions. This renders them non-immunogenic and makes them highly resistant to proteolytic degradation. Current experimental design methods often preclude the use of D-amino acids and non-canonical amino acids for a variety of reasons. To address this, we build an in silico pipeline for D-protein designs featuring non-canonical amino acids. For a test scaffold we use an existing D-protein inhibitor of VEGF: D-RFX001. We benchmark the approach by recapitulating previous experimental optimisation with canonical amino acids. Subsequent incorporation of non-canonical amino acids allows designs that are predicted to improve binding affinity by up to -7.18 kcal/mol.

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Designing repeat proteins for biosensors and medical imaging

Cited by 8 publications

References 44 publications

Engineering repeat proteins of the immune system

Engineering repeat proteins of the immune system

Designed leucine‐rich repeat proteins bind two muramyl dipeptide ligands

A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity

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