Showing papers by "James E. Penner-Hahn published in 2021"
TL;DR: In this article, the same binding site was designed within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs and showed that a simple CuHis3 binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils.
Abstract: Copper nitrite reductase (CuNiR) is a copper enzyme that converts nitrite to nitric oxide and is an important part of the global nitrogen cycle in bacteria. The relatively simple CuHis3 binding site of the CuNiR active site has made it an enticing target for small molecule modeling and de novo protein design studies. We have previously reported symmetric CuNiR models within parallel three stranded coiled coil systems, with activities that span a range of three orders of magnitude. In this report, we investigate the same CuHis3 binding site within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs. We determine that a simple CuHis3 binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils. Incorporating more complex designs or repositioning this binding site can decrease this activity as much as 15 times. Comparing these constructs, we reaffirm a previous result in which a blue shift in the 1s to 4p transition energy determined by Cu(I) X-ray absorption spectroscopy is correlated with an enhanced activity within imidazole-based constructs. With this step and recent successful electron transfer site designs within this scaffold, we are one step closer to a fully functional de novo designed nitrite reductase.
3 citations
TL;DR: In this article, the authors demonstrate that ORF1p binds Pb(II) and demonstrate that exposure to heavy metals such as lead could influence the structural parameters of ORF 1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.
Abstract: The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of ORF1p was recently solved and showed the presence of tris-cysteine layers in the interior of the coiled-coil that could function as metal binding sites. Here, we demonstrate that ORF1p binds Pb(II). We designed a model peptide, GRCSL16CL23C, to mimic two of the ORF1p Cys3 layers and crystallized the peptide both as the apo-form and in the presence of Pb(II). Structural comparison of the ORF1p with apo-(GRCSL16CL23C)3 shows very similar Cys3 layers, preorganized for Pb(II) binding. We propose that exposure to heavy metals, such as lead, could influence directly the structural parameters of ORF1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.
2 citations
TL;DR: Malasi et al. as mentioned in this paper reported the synthesis and detailed characterization of Fe 2.75Dy-oxide thin films prepared on various substrates using electron beam co-evaporation.
Abstract: Recently, amorphous/disordered oxide thin films made from Fe and lanthanides like Dy and Tb have been reported to have a rich set of magnetic, optical, and electronic properties, as well as room-temperature magneto-electric coupling with multiferroics [A. Malasi et al., Sci. Rep. 5, 18157 (2015); H. Taz et al., Sci. Rep. 6, 27869 (2016); and H. Taz et al., Sci. Rep. 10, 1–10 (2020)]. Here, we report the synthesis and detailed characterization of Fe 2.75Dy-oxide thin films prepared on various substrates using electron beam co-evaporation. The structure, chemistry, electric, magnetic, and optical properties were studied for the as-prepared and annealed (373 K, in air, 1 h) films of thickness 40 nm. High resolution transmission electron microscopy and electron diffraction study showed that the films were amorphous in both the as-prepared and annealed states. The electron energy-loss spectroscopy studies quantified that metal oxygen stoichiometry changed from Fe 2.75Dy-O 1.5 to Fe 2.75Dy-O 1.7 upon annealing. Synchrotron-based x-ray absorption spectroscopy investigation confirmed that the as-prepared films were highly disordered with predominantly metallic Fe and Dy states that became slightly oxidized with annealing in air. The as-prepared amorphous films demonstrated significantly high value of ordinary ( ∼ 10 cm 2/V s) and anomalous ( ∼ 10 2 cm 2/V s) Hall mobility and high electrical conductivity of ∼ 10 3 S/cm at room temperature. The cryogenic magnetic property measurement shows two-step magnetization below 200 K, suggesting exchange-spring magnetic interaction. The nature of the field cooled and zero-field cooled curves suggested a spin-glass like transition between 78 K and 80 K, with a characteristic broad peak. The Tauc plot analysis from optical transmission spectra confirms the existence of an optical bandgap of ∼ 2.42 eV that increased slightly to ∼ 2.48 eV upon annealing. This rich set of transport, optical, and magnetic properties in these thin films is very exciting and points to potential applicability in low-cost multifunctional devices requiring a combination of transparent, semiconducting, and magnetic responses, such as in spintronics.