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  1. Abstract

    Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway inEscherichia coliwhich can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106variants per iteration, the growth selection discovers aLactobacillus pentosusNADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.

  2. The rare-earth tritellurides (RTe 3 ) are a distinct class of 2D layered materials that recently gained significant attention due to hosting such quantum collective phenomena as superconductivity or charge density waves (CDWs). Many members of this van der Waals (vdW) family crystals exhibit CDW behavior at room temperature, i.e. , RTe 3 compound where R = La, Ce, Pr, Nd, Sm, Gd, and Tb. Here, our systematic studies establish the CDW properties of RTe 3 when the vdW spacing/interaction strength between adjacent RTe 3 layers is engineered under extreme hydrostatic pressures. Using a non-destructive spectroscopy technique, pressure-dependent Raman studies first establish the pressure coefficients of phonon and CDW amplitude modes for a variety of RTe 3 materials, including LaTe 3 , CeTe 3 , PrTe 3 , NdTe 3 , SmTe 3 , GdTe 3 , and TbTe 3 . Results further show that the CDW phase is eventually suppressed at high pressures when the interlayer spacing is reduced and interaction strength is increased. Comparison between different RTe 3 materials shows that LaTe 3 with the largest thermodynamic equilibrium interlayer spacing (smallest chemical pressure) exhibits the most stable CDW phases at high pressures. In contrast, CDW phases in latemore »RTe 3 systems with the largest internal chemical pressures are suppressed easily with applied pressure. Overall results provide comprehensive insights into the CDW response of the entire RTe 3 series under extreme pressures, offering an understanding of CDW formation/engineering in a unique class of vdW RTe 3 material systems.« less
    Free, publicly-accessible full text available August 25, 2023
  3. Free, publicly-accessible full text available May 3, 2023
  4. Abstract

    Noncanonical redox cofactors are attractive low-cost alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) in biotransformation. However, engineering enzymes to utilize them is challenging. Here, we present a high-throughput directed evolution platform which couples cell growth to the in vivo cycling of a noncanonical cofactor, nicotinamide mononucleotide (NMN+). We achieve this by engineering the life-essential glutathione reductase inEscherichia colito exclusively rely on the reduced NMN+(NMNH). Using this system, we develop a phosphite dehydrogenase (PTDH) to cycle NMN+with ~147-fold improved catalytic efficiency, which translates to an industrially viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations. Moreover, the PTDH variants also exhibit improved activity with another structurally deviant noncanonical cofactor, 1-benzylnicotinamide (BNA+), showcasing their broad applications. Structural modeling prediction reveals a general design principle where the mutations and the smaller, noncanonical cofactors together mimic the steric interactions of the larger, natural cofactors NAD(P)+.

  5. Free, publicly-accessible full text available June 22, 2023
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