An RNA aptamer that shifts the reduction potential of metabolic cofactors

Abstract

The discovery of ribozymes has inspired exploration of RNA’s potential to serve as primordial catalysts in a hypothesized RNA world. Modern oxidoreductase enzymes employ differential binding between reduced and oxidized forms of redox cofactors to alter cofactor reduction potential and enhance the enzyme’s catalytic capabilities. The utility of differential affinity has been underexplored as a chemical strategy for RNA. Here we show an RNA aptamer that preferentially binds oxidized forms of flavin over reduced forms and markedly shifts flavin reduction potential by −40 mV, similar to shifts for oxidoreductases. Nuclear magnetic resonance structural analysis revealed π–π and donor atom–π interactions between the aptamer and flavin that cause unfavorable contacts with the electron-rich reduced form, suggesting a mechanism by which the local environment of the RNA-binding pocket drives the observed shift in cofactor reduction potential. It seems likely that primordial RNAs could have used similar strategies in RNA world metabolisms.

Anchoring a Structurally Editable Proximal Cofactor‐like Module to Construct an Artificial Dual‐center Peroxygenase

“…Crystallographic studies revealed that exogenous DFSM molecules were tightly bound to the P450 scaffold to create a bis‐center precatalytic state of artificial peroxygenase. The binding affinity of DFSM ( K d of approximately 10 −8 M) was close to that of some natural organic cofactors for their host enzymes, such as FMN or FAD, noncovalently bound to flavoenzymes ( K d <10 −10 M) [30–32] . The high affinity ensures that DFSM can generate P450 peroxygenase activity with a low stoichiometric load, similar to a natural cofactor.…”

“…The binding affinity of DFSM (K d of approximately 10 À 8 M) was close to that of some natural organic cofactors for their host enzymes, such as FMN or FAD, noncovalently bound to flavoenzymes (K d < 10 À 10 M). [30][31][32] The high affinity ensures…”

“…The dissociation constant (K d ) of the typical DFSM for P450BM3, N-(ω-imidazol-1-yl hexanoyl)-L-phenylalanine (Im-C6-Phe), is approximately 10 À 4 M, [29] which is significantly higher than those of native catalytic factors of the host protein, such as flavin mono-nucleotide (FMN) or flavin adenine dinucleotide (FAD), non-covalently bounded to flavoenzymes (K d < 10 À 10 M, Figure 1E). [30][31][32] We therefore hypothesized that construction of an efficient and native-like enzyme driven by an artificial cofactor requires a high-affinity DFSM to allow stoichiometric complex formation between the host enzyme and its organic cofactor.…”

Emergent functional behaviors of ribozymes in oxychlorine brines indicate Mars could host a unique niche for molecular evolution

“…A rich suite of chemical transformations is made possible through the agency of cofactors bound to protein enzymes, and our results extend the transformations possible with ribozyme-cofactor complexes. This adds to the growing lines of evidence that as-yet-discovered RNA-cofactor pairs could catalyze a wider range of chemistries than currently known 52,53 .…”

Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications

“…It is possible that flavin was among the first cofactors used by RNAs to perform complex chemistries, following the RNA world hypothesis. This is hinted by the recent discovery of an RNA aptamer that modulates flavin’s reduction potential . Since ribozymes with SAM-dependent methylation activity , were recently discovered, it is tempting to speculate that ancient ribozymes might have used a flavin carbinolamine (similar to TrmFO and ThyX) for methylation during the early phases of life on Earth.…”