Mimicking nature with protein scaffolds

Daniel Evanko

doi:10.1038/nmeth0506-334b

Customized signaling with reconfigurable protein scaffolds

Nature Biotechnology ◽

10.1038/nbt0508-526 ◽

2008 ◽

Vol 26 (5) ◽

pp. 526-528 ◽

Cited By ~ 2

Author(s):

Patrick Guye ◽

Ron Weiss

Keyword(s):

Protein Scaffolds

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Break the template boundary: Test of different protein scaffolds by genetic code expansion resulted in NADPH-dependent secondary amine catalysis

10.21203/rs.3.rs-468406/v2 ◽

2021 ◽

Author(s):

Thomas Williams ◽

Yu-Hsuan Tsai ◽

Louis Luk

Keyword(s):

Genetic Code ◽

Secondary Amine ◽

Transfer Hydrogenation ◽

Protein Scaffolds ◽

Artificial Enzyme ◽

Enzyme Design ◽

Catalytically Active ◽

Amine Catalysis ◽

Genetic Code Expansion ◽

Distinctive Role

Abstract Here, incorporation of secondary amine by genetic code expansion was used to expand the potential protein templates for artificial enzyme design. Pyrrolysine analogue containing a D-proline could be stably incorporated into proteins, including the multidrug-binding LmrR and nucleotide-binding dihydrofolate reductase (DHFR). Both modified scaffolds were catalytically active, mediating transfer hydrogenation with a relaxed substrate scope. The protein templates played a distinctive role in that, while the LmrR variants were confined to the biomimetic BNAH as the hydride source, the optimal DHFR variant favorably used the pro-R hydride from NADPH for reactions. Due to the cofactor compatibility, the DHFR secondary amine catalysis could also be coupled to an enzymatic recycling scheme. This work has illustrated the unique advantages of using proteins as hosts, and thus the presented concept is expected to find uses in enabling tailored secondary amine catalysis.

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A Model for Shaping Membrane Sheets by Protein Scaffolds

Biophysical Journal ◽

10.1016/j.bpj.2015.06.001 ◽

2015 ◽

Vol 109 (3) ◽

pp. 564-573 ◽

Cited By ~ 14

Author(s):

Yonatan Schweitzer ◽

Tom Shemesh ◽

Michael M. Kozlov

Keyword(s):

Protein Scaffolds

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Intracellular targeting with engineered proteins

F1000Research ◽

10.12688/f1000research.8915.1 ◽

2016 ◽

Vol 5 ◽

pp. 1947 ◽

Cited By ~ 13

Author(s):

Shane Miersch ◽

Sachdev S. Sidhu

Keyword(s):

Protein Engineering ◽

Coming Of Age ◽

Target Space ◽

Protein Scaffolds ◽

Intracellular Space ◽

Intracellular Targeting ◽

Alternative Protein ◽

Clinical Advantage ◽

Daunting Challenge ◽

Complex Architecture

If the isolation, production, and clinical use of insulin marked the inception of the age of biologics as therapeutics, the convergence of molecular biology and combinatorial engineering techniques marked its coming of age. The first wave of recombinant protein-based drugs in the 1980s demonstrated emphatically that proteins could be engineered, formulated, and employed for clinical advantage. Yet despite the successes of protein-based drugs such as antibodies, enzymes, and cytokines, the druggable target space for biologics is currently restricted to targets outside the cell. Insofar as estimates place the number of proteins either secreted or with extracellular domains in the range of 8000 to 9000, this represents only one-third of the proteome and circumscribes the pathways that can be targeted for therapeutic intervention. Clearly, a major objective for this field to reach maturity is to access, interrogate, and modulate the majority of proteins found inside the cell. However, owing to the large size, complex architecture, and general cellular impermeability of existing protein-based drugs, this poses a daunting challenge. In recent years, though, advances on the two related fronts of protein engineering and drug delivery are beginning to bring this goal within reach. First, prompted by the restrictions that limit the applicability of antibodies, intense efforts have been applied to identifying and engineering smaller alternative protein scaffolds for the modulation of intracellular targets. In parallel, innovative solutions for delivering proteins to the intracellular space while maintaining their stability and functional activity have begun to yield successes. This review provides an overview of bioactive intrabodies and alternative protein scaffolds amenable to engineering for intracellular targeting and also outlines advances in protein engineering and formulation for delivery of functional proteins to the interior of the cell to achieve therapeutic action.

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