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We describe the de novo design of an allosterically regulated protein, which comprises two tightly coupled domains. One domain is based on the DF (Due Ferri in Italian or two-iron in English) family of de novo proteins, which have a diiron cofactor that catalyzes a phenol oxidase reaction, while the second domain is based on PS1 (Porphyrin-binding Sequence), which binds a synthetic Zn-porphyrin (ZnP). The binding of ZnP to the original PS1 protein induces changes in structure and dynamics, which we expected to influence the catalytic rate of a fused DF domain when appropriately coupled. Both DF and PS1 are four-helix bundles, but they have distinct bundle architectures. To achieve tight coupling between the domains, they were connected by four helical linkers using a computational method to discover the most designable connections capable of spanning the two architectures. The resulting protein, DFP1 (Due Ferri Porphyrin), bound the two cofactors in the expected manner. The crystal structure of fully reconstituted DFP1 was also in excellent agreement with the design, and it showed the ZnP cofactor bound over 12 Å from the dimetal center. Next, a substrate-binding cleft leading to the diiron center was introduced into DFP1. The resulting protein acts as an allosterically modulated phenol oxidase. Its Michaelis–Menten parameters were strongly affected by the binding of ZnP, resulting in a fourfold tighter K m and a 7-fold decrease in k cat . These studies establish the feasibility of designing allosterically regulated catalytic proteins, entirely from scratch. 

Efficient photosynthetic energy conversion requires quantitative, light-driven formation of high-energy, charge-separated states. However, energies of high-lying excited states are rarely extracted, in part because the congested density of states in the excited-state manifold leads to rapid deactivation. Conventional photosystem designs promote electron transfer (ET) by polarizing excited donor electron density toward the acceptor (“one-way” ET), a form of positive design. Curiously, negative design strategies that explicitly avoid unwanted side reactions have been underexplored. We report here that electronic polarization of a molecular chromophore can be used as both a positive and negative design element in a light-driven reaction. Intriguingly, prudent engineering of polarized excited states can steer a “U-turn” ET—where the excited electron density of the donor is initially pushed away from the acceptor—to outcompete a conventional one-way ET scheme. We directly compare one-way vs. U-turn ET strategies via a linked donor–acceptor (DA) assembly in which selective optical excitation produces donor excited states polarized either toward or away from the acceptor. Ultrafast spectroscopy of DA pinpoints the importance of realizing donor singlet and triplet excited states that have opposite electronic polarizations to shut down intersystem crossing. These results demonstrate that oppositely polarized electronically excited states can be employed to steer photoexcited states toward useful, high-energy products by routing these excited states away from states that are photosynthetic dead ends. 

The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure—a van der Mer (vdM)—that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug–protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.

 

The direction of electron flow in molecular optoelectronic devices is dictated by charge transfer between a molecular excited state and an underlying conductor or semiconductor. For those devices, controlling the direction and reversibility of electron flow is a major challenge. We describe here a novel, single-molecule photodiode. It is based on an internally conjugated, bi-chromophoric dyad with chemically linked (porphyrinato)zinc(II) and bis(terpyridyl)ruthenium(II) groups. On nanocrystalline, degenerately doped indium tin oxide electrodes, the dyad exhibits distinct frequency-dependent, charge-transfer characters. Variations in the light source between red (~ 1.9 eV) and blue (~ 2.7 eV) light excitation for the integrated photodiode result in switching of photocurrents between cathodic and anodic. The origin of the excitation frequency-dependent photocurrents lies in the electronic structure of the chromophore excited states, as shown by the results of theoretical calculations, laser flash photolysis and steady-state spectrophotometric measurements.