Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains

Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K(d) correlate with changes in k(off).     

Determination of technetium-99 in environmental samples: A review

Due to the lack of a stable technetium isotope, and the high mobility and long half-life, ⁹⁹Tc is considered to be one of the most important radionuclides in safety assessment of environmental radioactivity as well as nuclear waste management. ⁹⁹Tc is also an important tracer for oceanographic research due to the high technetium solubility in seawater as TcO₄⁻. A number of analytical methods, using chemical separation combined with radiometric and mass spectrometric measurement techniques, have been developed over the past decades for determination of ⁹⁹Tc in different environmental samples. This article summarizes and compares recently reported chemical separation procedures and measurement methods for determination of ⁹⁹Tc. Due to the extremely low concentration of ⁹⁹Tc in environmental samples, the sample preparation, pre-concentration, chemical separation and purification for removal of the interferences for detection of ⁹⁹Tc are the most important issues governing the accurate determination of ⁹⁹Tc. These aspects are discussed in detail in this article. Meanwhile, the different measurement techniques for ⁹⁹Tc are also compared with respect to advantages and drawbacks. Novel automated analytical methods for rapid determination of ⁹⁹Tc using solid extraction or ion exchange chromatography for separation of ⁹⁹Tc, employing flow injection or sequential injection approaches are also discussed.     

Robust registration of point sets using iteratively reweighted least squares

Registration of point sets is done by finding a rotation and translation that produces a best fit between a set of data points and a set of model points. We use robust M-estimation techniques to limit the influence of outliers, more specifically a modified version of the iterative closest point algorithm where we use iteratively re-weighed least squares to incorporate the robustness. We prove convergence with respect to the value of the objective function for this algorithm. A comparison is also done of different criterion functions to figure out their abilities to do appropriate point set fits, when the sets of data points contains outliers. The robust methods prove to be superior to least squares minimization in this setting.     

Rotational image deblurring with sparse matrices

We describe iterative deblurring algorithms that can handle blur caused by a rotation along an arbitrary axis (including the common case of pure rotation). Our algorithms use a sparse-matrix representation of the blurring operation, which allows us to easily handle several different boundary conditions. We also include robust stopping rules for the iterations. The performance of our algorithms is illustrated with examples.     

On certain functional equation related to two-sided centralizers

Let m ≥ 0, n ≥ 0 be fixed integers with m + n ≠ 0 and let R be a prime ring with char(R) = 0 or m + n + 1 ≤ char(R) ≠ 2. Suppose that there exists an additive mapping T : R → R satisfying the relation 2T(x ^m+n+1) = x ^m T(x) x ⁿ  + x ⁿ T(x)x ^m for all ${x\in R}$ . In this case T is a two-sided centralizer.     

Decay heat studies for nuclear energy

The energy associated with the decay of fission products plays an important role in the estimation of the amount of heat released by nuclear fuel in reactors. In this article we present results of the study of the beta decay of some refractory isotopes that were considered important contributors to the decay heat in reactors. The measurements were performed at the IGISOL facility of the University of Jyväskylä, Finland. In these studies we have combined for the first time a Penning trap (JYFLTRAP), which was used as a high resolution isobaric separator, with a total absorption spectrometer. The results of the measurements as well as their consequences for decay heat summation calculations are discussed.     

A semisynthetic glutathione peroxidase with high catalytic efficiency. Selenoglutathione transferase

Glutathione peroxidase (GPX) protects cells against oxidative damage by catalyzing the reduction of hydroperoxides by glutathione (GSH). GPX therefore has potential therapeutic value as an antioxidant, but its pharmacological development has been limited because GPX uses a selenocysteine as its catalytic group and it is difficult to generate selenium-containing proteins with traditional recombinant DNA technology. Here, we show that naturally occurring proteins can be modified to generate GPX activity. The rat theta-class glutathione transferase T2-2 (rGST T2-2) presents an ideal scaffold for the design of a novel GPX catalyst because it already binds GSH and contains a serine close to the substrate binding site, which can be chemically modified to bind selenium. The modified Se-rGST T2-2 efficiently catalyzes the reduction of hydrogen peroxide, and the GPX activity surpasses the activities of some natural GPXs.     

Shifted-basis technique improves accuracy of peak position determination in Fourier transform mass spectrometry

The present paper suggests a new algorithm for estimation of peak positions in FTMS spectra. It is shown theoretically and experimentally that the new technique yields superior results compared to the currently applied techniques, when the noise level is high and/or the peaks are located close to each other. Cases are presented where the deviation from the true mass could be mistaken for space charge effect, while the shift is in fact solely due to the shortcomings of the current techniques and can be corrected by applying the shifted-basis technique. In two out of three cases, this technique gave more accurate (>5 times) result compared to the conventional analysis. In the third case, where the signal was high compared to the noise, the results were comparable. The new technique can be used to achieve better mass accuracy for noisy and not well resolved spectra, and to further investigate the features of the space charge effect.     

Mechanistic studies of multipole storage assisted dissociation

The degree and onset of fragmentation in multipole storage assisted dissociation (MSAD) have been investigated as functions of several hexapole parameters. Strict studies of hexapole charge density (number of ions injected) and hexapole storage time were made possible by placing a pulsed shutter in front of the entrance to the mass spectrometer. The results obtained show that the charge density is the most critical parameter, but also dependencies on storage time, radio-frequency (rf) -amplitude, and pressure are seen. From these data, and from simulations of the ion trajectories inside the hexapole, a mechanism for MSAD, similar to the ones for sustained off-resonance irradiation (SORI), and for low energy collisionally induced dissociation in the collision multipole of a triple quadrupole mass spectrometer, is proposed. It is believed that, at higher charge densities, ions are pushed to larger hexapole radii where the electric potential created by the rf field is higher, forcing the ions to oscillate radially to higher amplitudes and thereby reach higher (but still relatively low) kinetic energies. Multiple collisions with residual gas molecules at these elevated energies then heat up the molecules to their dissociation threshold. Further support for this mechanism is obtained from a comparison of MSAD and SORI spectra which are almost identical in appearance.     

Synthesis and characterization of arc deposited magnetic (Cr,Mn)2AlC MAX phase films

(Cr_1–xMn_x)₂AlC MAX phase thin films were synthesized by cathodic arc deposition. Scanning transmission electron microscopy including local energy dispersive X‐ray spectroscopy analysis of the as‐deposited films reveals a Mn incorporation of as much as 10 at% in the structure, corresponding to x = 0.2. Magnetic properties were characterized with vibrating sample magnetometry, revealing a magnetic response up to at least room temperature. We thus verify previous theoretical predictions of an antiferromagnetic or ferromagnetic ground state for Cr₂AlC upon alloying with Mn. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)