From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking

Small-molecule stabilization of protein-protein interactions (PPIs) is a promising strategy in chemical biology and drug discovery. However, the systematic discovery of PPI stabilizers remains a largely unmet challenge. Herein we report a fragment-linking approach targeting the interface of 14-3-3 and a peptide derived from the estrogen receptor alpha (ERα) protein. Two classes of fragments—a covalent and a noncovalent fragment—were co-crystallized and subsequently linked, resulting in a noncovalent hybrid molecule in which the original fragment interactions were largely conserved. Supported by 20 crystal structures, this initial hybrid molecule was further optimized, resulting in selective, 25-fold stabilization of the 14-3-3/ERα interaction. The high-resolution structures of both the single fragments, their co-crystal structures and those of the linked fragments document a feasible strategy to develop orthosteric PPI stabilizers by linking to an initial tethered fragment.</p

Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4230).Also part of the Lecture Notes in Bioinformatics book sub series (volume 4230).International audienceWe propose to model the dynamics of gene regulatory networks as concurrent processes in the stochastic pi calculus. As a first case study, we show how to express the control of transcription initiation at the lambda switch, a prototypical example where cooperative enhancement is crucial. This requires concurrent programming techniques that are new to systems biology, and necessitates stochastic parameters that we derive from the literature. We test all components of our model by exhaustive stochastic simulations. A comparison with previous results reported in the literature, experimental and simulation based, confirms the appropriateness of our modeling approach

Approximation Algorithms for Min-Max Path Cover Problems with Service Handling Time

20th International Symposium on Algorithms and Computation (ISAAC 2009), Honolulu, Hawaii, USA, December 16-18, 2009This paper presents improved approximation algorithms and inapproximability results for min-max path cover problems with service handling time, which have wide applications in practice when the latest service completion time for customers is critical. We study three variants of this problem, where paths must start (i) from a given depot, (ii) from any depot of a given set, and (iii) from any vertex of the given graph, respectively. For these three variants, we are able to achieve approximation ratios of 3, (4 + ε), and (5 + ε), respectively, for any ε> 0. We have further shown that approximation ratios less than 4/3, 3/2, and 3/2 are impossible for them, respectively, unless NP = P.Department of Logistics and Maritime StudiesRefereed conference pape

From Your Nose to Your Toes: A Review of Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic‒Associated Pernio.

Despite thousands of reported patients with pandemic-associated pernio, low rates of seroconversion and PCR positivity have defied causative linkage to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pernio in uninfected children is associated with monogenic disorders of excessive IFN-1 immunity, whereas severe COVID-19 pneumonia can result from insufficient IFN-1. Moreover, SARS-CoV-2 spike protein and robust IFN-1 response are seen in the skin of patients with pandemic-associated pernio, suggesting an excessive innate immune skin response to SARS-CoV-2. Understanding the pathophysiology of this phenomenon may elucidate the host mechanisms that drive a resilient immune response to SARS-CoV-2 and could produce relevant therapeutic targets

Evolution of Mercury’s Earliest Atmosphere

MESSENGER observations suggest a magma ocean formed on proto-Mercury, during which evaporation of metals and outgassing of C- and H-bearing volatiles produced an early atmosphere. Atmospheric escape subsequently occurred by plasma heating, photoevaporation, Jeans escape, and photoionization. To quantify atmospheric loss, we combine constraints on the lifetime of surficial melt, melt composition, and atmospheric composition. Consideration of two initial Mercury sizes and four magma ocean compositions determines the atmospheric speciation at a given surface temperature. A coupled interior–atmosphere model determines the cooling rate and therefore the lifetime of surficial melt. Combining the melt lifetime and escape flux calculations provides estimates for the total mass loss from early Mercury. Loss rates by Jeans escape are negligible. Plasma heating and photoionization are limited by homopause diffusion rates of ∼106 kg s−1. Loss by photoevaporation depends on the timing of Mercury formation and assumed heating efficiency and ranges from ∼106.6 to ∼109.6 kg s−1. The material for photoevaporation is sourced from below the homopause and is therefore energy limited rather than diffusion limited. The timescale for efficient interior–atmosphere chemical exchange is less than 10,000 yr. Therefore, escape processes only account for an equivalent loss of less than 2.3 km of crust (0.3% of Mercury's mass). Accordingly, ≤0.02% of the total mass of H2O and Na is lost. Therefore, cumulative loss cannot significantly modify Mercury's bulk mantle composition during the magma ocean stage. Mercury's high core:mantle ratio and volatile-rich surface may instead reflect chemical variations in its building blocks resulting from its solar-proximal accretion environment

Hydrogen-peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

To understand how sulphate-reducing bacteria respond to oxidative stresses, the responses of Desulfovibrio vulgaris Hildenborough to H{sub 2}O{sub 2}-induced stresses were investigated with transcriptomic, proteomic and genetic approaches. H{sub 2}O{sub 2} and induced chemical species (e.g. polysulfide, ROS) and redox potential shift increased the expressions of the genes involved in detoxification, thioredoxin-dependent reduction system, protein and DNA repair, and decreased those involved in sulfate reduction, lactate oxidation and protein synthesis. A gene coexpression network analysis revealed complicated network interactions among differentially expressed genes, and suggested possible importance of several hypothetical genes in H{sub 2}O{sub 2} stress. Also, most of the genes in PerR and Fur regulons were highly induced, and the abundance of a Fur regulon protein increased. Mutant analysis suggested that PerR and Fur are functionally overlapped in response to stresses induced by H{sub 2}O{sub 2} and reaction products, and the upregulation of thioredoxin-dependent reduction genes was independent of PerR or Fur. It appears that induction of those stress response genes could contribute to the increased resistance of deletion mutants to H{sub 2}O{sub 2}-induced stresses. In addition, a conceptual cellular model of D. vulgaris responses to H{sub 2}O{sub 2} stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H{sub 2}O{sub 2}-induced stresses

Distinctive Oxidative Stress Responses to Hydrogen Peroxide in Sulfate Reducing Bacteria Desulfovibrio vulgaris Hildenborough

Response of Desulfovibrio vulgaris Hildenborough to hydrogen peroxide (H2O2, 1 mM) was investigated with transcriptomic, proteomic and genetic approaches. Microarray data demonstrated that gene expression was extensively affected by H2O2 with the response peaking at 120 min after H2O2 treatment. Genes affected include those involved with energy production, sulfate reduction, ribosomal structure and translation, H2O2 scavenging, posttranslational modification and DNA repair as evidenced by gene coexpression networks generated via a random matrix-theory based approach. Data from this study support the hypothesis that both PerR and Fur play important roles in H2O2-induced oxidative stress response. First, both PerR and Fur regulon genes were significantly up-regulated. Second, predicted PerR regulon genes ahpC and rbr2 were derepressedin Delta PerR and Delta Fur mutants and induction of neither gene was observed in both Delta PerR and Delta Fur when challenged with peroxide, suggesting possible overlap of these regulons. Third, both Delta PerR and Delta Fur appeared to be more tolerant of H2O2 as measured by optical density. Forth, proteomics data suggested de-repression of Fur during the oxidative stress response. In terms of the intracellular enzymatic H2O2 scavenging, gene expression data suggested that Rdl and Rbr2 may play major roles in the detoxification of H2O2. In addition, induction of thioredoxin reductase and thioredoxin appeared to be independent of PerR and Fur. Considering all data together, D. vulgaris employed a distinctive stress resistance mechanism to defend against increased cellular H2O2, and the temporal gene expression changes were consistent with the slowdown of cell growth at the onset of oxidative stress