Peptidyl-Resin Substrates as a Tool in the Analysis of Caspase Activity

Caspases, proteolytic enzymes belonging to the group of cysteine proteases, play a crucial role in apoptosis. Understanding their activity and substrate specificity is extremely important. Fluorescence-based approaches, including fluorogenic substrates, are generally used to confirm cleavage preferences. Here we present a new method of substrate specificity and activity analysis based on the application of fix-charge tagged peptides located on the resin. The proteolysis of peptide bond on the resin, occurring even with low efficiency, results in the formation of N-terminal fragments of model peptide containing ionization enhancers in the form of quaternary ammonium groups, allowing for ultrasensitive and reliable analysis by LC-MS/MS. The possibility of application of the proposed solution was tested through the analysis of substrate specificity and activity of caspase 3 or 7. The obtained results confirm the known substrate specificity of executioner caspases. Our solution also allowed us to observe that caspases can hydrolyze peptides shorter than those presented to date in the scientific literature.     

THE E⇌Z ISOMERIZATION OF 1-METHYLSULFANYLPROPENOIC N-ARYLTHIOAMIDES

Abstract

1-Methylsulfanylpropenoic N-arylthioamides 2 were shown to undergo the two way F/Z isomerization triggered by heat, light and the oxygen and sulfur nucleophiles.     

On the global existence of solutions to an aggregation model

In this paper we consider a reaction-diffusion-chemotaxis aggregation model of Keller-Segel type with a nonlinear, degenerate diffusion. Assuming that the diffusion function f(n) takes values sufficiently large, i.e. takes values greater than the values of a power function with sufficiently high power (f(n)?δnp for all n>0, where δ>0 is a constant), we prove global-in-time existence of weak solutions. Since one of the main features of Keller-Segel type models is the possibility of blow-up of solutions in finite time, we will derive the uniform-in-time boundedness, which prevents the explosion of solutions. The uniqueness of solutions is proved provided that some higher regularity condition on solutions is known a priori. Finally, computational simulation results showing the effect of three different types of diffusion function are presented.     

α-Phosphoryl Cyclopentanones as Possible Intermediates in the Total Synthesis of Sarkomycin

Abstract

In an effort to synthesize sarkomycin 1 trans-2-diphenylphosphinoyl-3-tris (methylthio) methyl-cyclopentanone 7 and trans-2-diphenylphosphinoyl-3-carbo-methoxy-cyclopentanone 8 were prepared. The Horner-Wittig reaction of the latter with formaldehyde failed. (±)-Sarkonycin 1 was prepared by a sequence of reactions starting from diethyl 2-oxopropanephosphonate. The key steps in this synthesis involve the intramolecular carbenoid cyclization of 1-diazo-2-oxopropanephosphonate 10 and the Horner-Wittig reaction of 2-diethoxyphosphoryl-3-carboxy-cyclopentanone 12 with formaldehyde.     

Chemoproteomic Evaluation of the Polyacetylene Callyspongynic Acid

Polyacetylenes are a class of alkyne‐containing natural products. Although potent bioactivities and thus possible applications as chemical probes have already been reported for some polyacetylenes, insights into the biological activities or molecular mode of action are still rather limited in most cases. To overcome this limitation, we describe the application of the polyacetylene callyspongynic acid in the development of an experimental roadmap for characterizing potential protein targets of alkyne‐containing natural products. To this end, we undertook the first chemical synthesis of callyspongynic acid. We then used in situ chemical proteomics methods to demonstrate extensive callyspongynic acid‐mediated chemical tagging of endoplasmic reticulum‐associated lipid‐metabolizing and modifying enzymes. We anticipate that an elucidation of protein targets of natural products may serve as an effective guide to the development of subsequent biological assays that aim to identify chemical phenotypes and bioactivities.     

Separation of image-distortion sources and magnetic-field measurement in scanning electron microscope (SEM)

The electron-microscope image distortion generated by electromagnetic interference (EMI) is an important problem for accurate imaging in scanning electron microscopy (SEM). Available commercial solutions to this problem utilize sophisticated hardware for EMI detection and compensation. Their efficiency depends on the complexity of distortions influence on SEM system. Selection of a proper method for reduction of the distortions is crucial. The current investigations allowed for a separation of the distortions impact on several components of SEM system. A sum of signals from distortion sources causes wavy deformations of specimen shapes in SEM images. The separation of various reasons of the distortion is based on measurements of the periodic deformations of the images for different electron beam energies and working distances between the microscope final aperture and the specimen. Using the SEM images, a direct influence of alternating magnetic field on the electron beam was distinguished. Distortions of electric signals in the scanning block of SEM were also separated. The presented method separates the direct magnetic field influence on the electron beam below the SEM final aperture (in the chamber) from its influence above this aperture (in the electron column). It also allows for the measurement of magnetic field present inside the SEM chamber. The current investigations gave practical guidelines for selecting the most efficient solution for reduction of the distortions.     

Device-Independent Certification of Maximal Randomness from Pure Entangled Two-Qutrit States Using Non-Projective Measurements

While it has recently been demonstrated how to certify the maximal amount of randomness from any pure two-qubit entangled state in a device-independent way, the problem of optimal randomness certification from entangled states of higher local dimension remains open. Here we introduce a method for device-independent certification of the maximal possible amount of 2log23 random bits using pure bipartite entangled two-qutrit states and extremal nine-outcome general non-projective measurements. To this aim, we exploit a device-independent method for certification of the full Weyl–Heisenberg basis in three-dimensional Hilbert spaces together with a one-sided device-independent method for certification of two-qutrit partially entangled states.