PubMed · 13054697
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K YAMAFUJI. 1953-04-25. Enzymatic transoximation.. https://doi.org/10.1038/171745a0
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MOTIVATION: Predicting enzyme function from its sequence is still an unsolved problem in the life sciences. Moreover, with the explosion of annotated genome data, we are inundated with potential enzymatic sequences that have not yet been biochemically characterized. While it is not possible to assign a not-yet-existing label to such a sequence, there is high value in placing the sequence as accurately as possible in known function space. Doing so can help provide more accurate falsifiable hypotheses for experimentalists wishing to characterize enzymes from specific functional families. RESULTS: Here we present a contrastive learning algorithm for predicting enzyme function from sequence. Our method, EnzPlacer, predicts the third, second, and first EC numbers for a protein whose fourth EC number is not in the training corpus. This novel prediction mechanism accurately places a protein sequence within a narrowed-down functional context, even if the precise function remains unknown. AVAILABILITY AND IMPLEMENTATION: EnzPlacer and data is available at https://github.com/drxiangma/EnzPlacer under a GPL3 license.
An immersible manometric sensor was made by covering the gaseous cavity of a pressure transducer with a 1 microm controlled pore membrane. Transfer of gas across the membrane allowed the pressure transducer to record changes in humidity or dissolved gas when immersed in solution. By immersing the sensor in distilled water, atmospheric humidity could be estimated by the deficit of atmospheric vapor pressure from saturation. In another application of the sensor, CO(2) was monitored continuously. This was not possible in previous closed-reactor type manometric sensors, and may allow the new technology to be used in applications requiring continuous monitoring of a process or stream. By coupling the sensor with enzymes liberating or consuming dissolved gas, different chemicals could be estimated. Urea was estimated by first hydrolyzing it with urease and then measuring the resulting CO(2) gas in solution. Glucose was measured through its enzymatic oxidation by glucose oxidase. The sensitivity to urea over the range 0-2.5 mM was about 1.02 kPa/mM, and the standard error was 0.086 mM. Due to the lower solubility of oxygen, the sensitivity to glucose in a range from 0 to 10 microM was over 100 kPa/mM, with a standard error of only 0.76 microM. This sensitivity was not possible in closed-reactor type manometric sensors due to constraints of dimensioning the head space gas volume for reproducibility and effective mass transfer. The 90% rise times for the sensor ranged from about 1-60 min for the different applications. The dynamic characteristics of the device may be improved by using a membrane with greater porosity, higher rigidity and lower thickness, and by reducing the dimensions of the cavity volume in the sensor through integrated microfabrication of the membrane onto the transducer.
DNA is damaged in vivo by the Fenton reaction mediated by Fe2+ and cellular reductants such as NADH, which reduce Fe3+ to Fe2+ and allow the recycling of iron. To study the response of Escherichia coli to such cycling, the activities of several enzymes involved in nicotinamide nucleotide metabolism were measured following an H2O2 challenge. NADPH-dependent peroxidase, NADH/NADP+ transhydrogenase, and glucose-6-phosphate dehydrogenase were most strongly induced, increasing 2.5-3-fold. In addition, the cellular ratios of NADPH to NADH increased 6- or 92-fold 15 min after exposure to 0.5 or 5 mm H2O2, respectively. In vitro, NADH was oxidized by Fe3+ up to 16-fold faster than NADPH, despite their identical reduction potentials. To understand this rate difference, the interactions of Fe3+ and Ga3+ with NAD(P)H were examined by 1H, 13C, and 31P NMR spectroscopy. Association with NADH occurred primarily with adenine at N7 and the amino group, but for NADPH, strong metal interactions also occurred at the 2'-phosphate group. Interaction of M3+ (Fe3+ or Ga3+) with the adenine ring would bring it into close proximity to the redox-active nicotinamide ring in the folded form of NAD(P)H, but interaction of M3+ with the 2'-phosphate group would avoid this close contact. In addition, as determined by absorbance spectroscopy, the energy of the charge-transfer species was significantly higher for the Fe3+.NADPH complex than for the Fe3+.NADH complex. We therefore suggest that upon exposure to H2O2 the NADH pool is depleted, and NADPH, which is less reactive with Fe3+, functions as the major nicotinamide nucleotide reductant.