De novo design of functional proteins: Toward artificial hydrogenases

Abstract

Over the last 25 years, de novo design has proven to be a valid approach to generate novel, well-folded proteins, and most recently, functional proteins. In response to societal needs, this approach is been used increasingly to design functional proteins developed with an eye toward sustainable fuel production. This review surveys recent examples of bioinspired de novo designed peptide based catalysts, focusing in particular on artificial hydrogenases.

Photo‐Driven Hydrogen Evolution by an Artificial Hydrogenase Utilizing the Biotin‐Streptavidin Technology

“…Their oxygen sensitivity and production costs call for the development of artificial hydrogenases. Several artificial hydrogenases rely on the incorporation of artificial metal cofactors in host proteins (cytochrome c , rubredoxin, ferredoxin) or linking to a polypeptide . In the past decade, the biotin‐streptavidin technology has found widespread use for the assembly of artificial metalloenzymes (ArM) .…”

Modulation of cluster incorporation specificity in a de novo iron‐sulfur cluster binding peptide

“…Iron‐sulfur clusters are one of the primitive prosthetic groups found in extant proteins; their chemical properties, such as oxygen sensitivity often paired with low redox potentials, suggest that they originally emerged in a prephotosynthetic world . Because of their ancient origins, [FeS] clusters are widespread in nature and exhibit a wide variety of functions, ranging from electron transfer conduits within complex proteins, diffusible electron shuttles e.g., in ferredoxins, regulation of iron levels, redox sensors, and catalysts in multielectron redox reactions . These functions are carried out by various types of clusters, including [2Fe‐2S], [3Fe‐4S], [4Fe‐4S] and higher order clusters .…”

“…De novo design offers an alternative approach to investigate these factors in simplified model proteins, and it has been used extensively over the last two decades . Recently, our group and others have developed methods to engineer iron‐sulfur binding sites in coiled coils . Using an internally domain‐swapped, dimeric three‐helix bundle as starting point we designed two proteins, DSD‐bis[4Fe‐4S] and DSD‐Fdm, and we showed that a single binding site engineered in the hydrophobic core can be replicated on each half of the protein by symmetry.…”

“…1,2 Because of their ancient origins, [FeS] clusters are widespread in nature and exhibit a wide variety of functions, ranging from electron transfer conduits within complex proteins, diffusible electron shuttles e.g., in ferredoxins, regulation of iron levels, redox sensors, and catalysts in multielectron redox reactions. [3][4][5] These functions are carried out by various types of clusters, including [2Fe-2S], [3Fe-4S], [4Fe-4S] and higher order clusters. 6 Generally, the clusters are incorporated into the protein scaffold via coordination of the iron atoms by cysteine side chains; more infrequently, other amino acids such as histidines are utilized, or nonproteinogenic thiol ligands e.g., in the [2Fe-2S] cluster of hydrogenases.…”

“…[20][21][22][23][24][25][26][27] Recently, our group and others have developed methods to engineer iron-sulfur binding sites in coiled coils. 4,[28][29][30][31][32][33][34] Using an internally domain-swapped, dimeric three-helix bundle as starting point we designed two proteins, DSD-bis[4Fe-4S] and DSD-Fdm, and we showed that a single binding site engineered in the hydrophobic core can be replicated on each half of the protein by symmetry. We were able to modulate the distance between the two sites by altering the number of heptad repeats separating the sites along the longitudinal axis of the protein.…”