Protein structure,amino acid composition and sequence determine proteome vulnerability to oxidation‐induced damage

Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential. The radiation‐resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ‐irradiation in Escherichia coli and D. radiodurans at multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS resistance of the D. radiodurans proteome. Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans. Our findings substantiate that protein‐intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.     

Acute Infantile Liver Failure Due to Mutations in the TRMU Gene

Acute liver failure in infancy accompanied by lactic acidemia was previously shown to result from mtDNA depletion. We report on 13 unrelated infants who presented with acute liver failure and lactic acidemia with normal mtDNA content. Four died during the acute episodes, and the survivors never had a recurrence. The longest follow-up period was 14 years. Using homozygosity mapping, we identified mutations in the TRMU gene, which encodes a mitochondria-specific tRNA-modifying enzyme, tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase. Accordingly, the 2-thiouridylation levels of the mitochondrial tRNAs were markedly reduced. Given that sulfur is a TRMU substrate and its availability is limited during the neonatal period, we propose that there is a window of time whereby patients with TRMU mutations are at increased risk of developing liver failure.     

Conjugate and Other Distributional Methods in Configural Frequency Analysis

Configural Frequency Analysis (CFA) is being increasingly used by psychologists and other researchers to test for the presence of combinations of categorical variables which occur more frequently or less frequently than expected under a particular model of chance. Configurations which occur more frequently than chance are known as “Types”-Configurations which are conspicuous by their absence or rarity are known as “Antitypes”. Most configural frequency test theory consists of binomial tests applied to the cells of a cross-tabulation table. The wide variety of statistical tests described in papers and books on CFA are approximations to the binomial test, due to the computational intensity associated with performing binomial tests directly (VON EYE, 1990b). This paper advocates direct computation of binomial probabilities instead of the usual approximations used in CFA. Mathematical relationships of the binomial distribution with the F and incomplete beta distributions are described which enable the researcher to efficiently compute binomial probabilities using functions available in common statistical software. The classical inference approach adopted by traditional CFA makes it difficult to make conclusions regarding the likely prevalence rates of types or antitypes in the reference population. It is also not possible to exploit additional information about the sample which, while not known precisely, is known with a degree of confidence and can aid in the identification of types and antitypes. A Bayesian conjugate distributions approach based on the incomplete beta distribution is proposed. Bayesian extensions of this model to both classical CFA and a sequential CFA analysis advanced by KIESER and VICTOR (1991) are described.     

The effect of angiotensin II on myosin heavy chain expression in cultured myocardial cells

Summary Angiotensin II (AII), the principal mediator of the renin-angiotensin system, is an important regulator of vascular and cardiac homeostasis. AII has also been shown to be a regulator of cardiac hypertrophy and of the corresponding changes in amount and composition of certain tissue proteins. We examined the trophic effects of AII on cultured myocytes derived from neonatal rat ventricles and followed, by Northern blot analysis and polyacrylamide gel electrophoresis, the expression of α- and β-myosin heavy chain iso-mRNAs and isoproteins. Our findings show that a single administration of AII is sufficient to induce a trophic response in cultured beating myocytes and to enhance the expression of β-myosin heavy chain iso-mRNA and isoprotein, having no effect on α-myosin heavy chain. Induction of α-myosin heavy chain expression by thyroid hormone before AII was administered showed that AII could not potentiate a shift from α- to β-myosin heavy chain predominance. We suggest that the potency of AII to regulate the expression of myosin heavy chain isogenes is restricted to the β isoform and is overridden by thyroid hormone.     

The AC conductivity of human sweat ducts as the dominant factor in the sub-THz reflection coefficient of skin

The helical nature of human sweat ducts, combined with the morphological and dielectric properties of skin, suggests electromagnetic activity in the sub-THz frequency band. A detailed electromagnetic simulation model of the skin, with embedded sweat ducts, was created. The model includes realistic dielectric properties based on the measured water content of each layer of skin, derived from Raman Spectroscopy. The model was verified by comparing it to measurements of the reflection coefficient of the palms of 13 volunteers in the frequency band 350–410 GHz. They were subjected to a measurement protocol intended to induce mental stress, thereby also activating the sweat glands. The Galvanic Skin Response was concurrently measured. Using the simulation model the optimal ac-conductivity for each measurement was found. The range of variation for all subjects was found to be from 100 S/m to a maximum value of 6000 S/m with averages of 1000 S/m. These are one order of magnitude increase from the accepted values for water at these frequencies (~100 s/m at 100 GHz). Considering the known biochemical mechanism for inducing perspiration, we conclude that these ac-conductivity levels are probably valid, even though the real time measurements of sweat ac-conductivity levels inside the duct are inaccessible.     

Hormone-dependent transformation and nuclear localisation of 1,25-dihydroxyvitamin D3 receptors from human breast cancer cell lines and chick duodenum

Recent studies on the 1,25-dihydroxyvitamin D3 (calcitriol) receptor have shown association of unoccupied receptor with isolated nuclei, thus suggesting that hormone is not required for transformation and nuclear localisation of this receptor. In the present work calcitriol receptors from cultured breast cancer cells were studied for evidence of hormone-dependent activation and compared to those from chick duodenum. Unlike other steroid receptors changes in receptor mobility on ion exchange and gel filtration were not found for occupied and unoccupied receptors. Furthermore no changes in affinity were observed on DNA-cellulose with both hormone-bound and unoccupied receptor having equally high affinity, eluting at 0.25 M KCI. However, a substantial hormone-dependent increase in receptor affinity for nuclei was seen. Thus calcitriol receptors do appear to undergo hormone-dependent transformation which is detected by their increased affinity for nuclei, without any accompanying gross changes in charge density, size or affinity for DNA-cellulose. Previously, we have reported that fractionation of T-47D cells in a low salt buffer resulted in recovery of unoccupied receptors in the cytosol, whereas occupied receptors were associated with purified nuclei. The data presented in this paper and our previous work suggest that calcitriol receptors do undergo a hormone-dependent increase in their affinity for nuclei. Furthermore in all this work calcitriol receptors from cultured human breast cancer cells displayed identical physicochemical characteristics to those of chick duodenal receptors.     

In vitro enzyme evolution: the screening challenge of isolating the one in a million

The generation of large mutant libraries for in vitro enzyme evolution presents the challenge of effectively screening libraries of 10⁴–10⁷ mutants on the basis of simultaneously assaying their biocatalytic activity. In this review, we highlight the main steps involved in this process, describe the alternative approaches to address this challenge, survey the state-of-the-art technology and assess achievements already made. It is anticipated that, as a result of the expected accomplishment of further improvements in high-throughput screening that will allow routine screening of whole libraries, the number of useful new and improved enzymes derived through in vitro enzyme evolution will expand rapidly in the near future.