Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups.

The 14-3-3 protein family, one of the first discovered phosphoserine/phosphothreonine binding proteins, has attracted interest not only because of its important role in the cell regulatory processes but also due to its enormous number of interactions with other proteins. Here, we use a computational approach to predict the binding sites of the designed hybrid compound featuring aggregation-induced emission luminophores as a potential supramolecular ligand for 14-3-3ζ in the presence and absence of C-Raf peptides. Our results suggest that the area above and below the central pore of the dimeric 14-3-3ζ protein is the most probable binding site for the ligand. Moreover, we predict that the position of the ligand is sensitive to the presence of phosphorylated C-Raf peptides. With a series of experiments, we confirmed the computational prediction of two C 2 related, dominating binding sites on 14-3-3ζ that may bind to two of the supramolecular ligand molecules.

Dual activity inhibition of threonine aspartase 1 by a single bisphosphate ligand.

Therapy resistance remains a challenge for the clinics. Here, dual-active chemicals that simultaneously inhibit independent functions in disease-relevant proteins are desired though highly challenging. As a model, we here addressed the unique protease threonine aspartase 1, involved in various cancers. We hypothesized that targeting basic residues in its bipartite nuclear localization signal (NLS) by precise bisphosphate ligands inhibits additional steps required for protease activity. We report the bisphosphate anionic bivalent inhibitor 11d, selectively binding to the basic NLS cluster (220KKRR223) with high affinity (K D = 300 nM), thereby disrupting its interaction and function with Importin α (IC50 = 6 µM). Cell-free assays revealed that 11d additionally affected the protease's catalytic substrate trans-cleavage activity. Importantly, functional assays comprehensively demonstrated that 11d inhibited threonine aspartase 1 also in living tumor cells. We demonstrate for the first time that intracellular interference with independent key functions in a disease-relevant protein by an inhibitor binding to a single site is possible.

Thermal conductivity of the cell membrane in the presence of cholesterol and amyloid precursor protein.

The cell membrane is responsible for the transportation of heat between inside and outside the cell. Whether the thermal properties of the cell membrane are affected by the cholesterol concentration or the membrane proteins has not been investigated so far. Although the experimental measurement of the membrane thermal conductivity was not available until very recently, computational methods have been widely used for this purpose. In this study, we carry out molecular dynamics simulations to investigate the relation between the concentration of cholesterol and the thermal conductivity of a model membrane. Our results suggest an increase in the membrane thermal conductivity upon increasing the concentration of cholesterol in the membrane. Moreover, we find that the asymmetric distribution of cholesterol in the two membrane leaflets decreases thermal conductivity. We also find a rectification effect when heat flows in opposite directions through a model membrane decorated with the amyloid precursor protein. The results of this study apply to the advancement of selective treatment methods, as well as the development of new materials such as biological rectifiers.

Photocount statistics of ultra-weak photon emission from germinating mung bean.

Ultra-weak photon emission (UPE) is an endogenous bioluminescence phenomenon present in all biological samples with an active oxidative metabolism, even without an external pre-illumination. To verify the potential of UPE for non-invasive monitoring of metabolism and growth in germinating plants, the aim of this study was to investigate the UPE from a model system - germinating mung bean seedlings (Vigna radiata) - and analyze the statistical properties of UPE during the growth in two different conditions of imbibition (pure water and 1% sucrose). We found that in all days and in both conditions, photocount distributions of UPE time series follow the negative binomial distribution whose parameters changed during the growth due to the increasing ratio of signal-to-detector dark count. Correspondingly for both groups, the mean values of UPE increased during the seedlings growth, while the values of Fano factor show a decreasing trend towards 1 during the 6day period. While our results do not show any significant difference in hypocotyl length and weight gain between the two groups of mung seedlings, there is an indication of a tiny suppressing effect of sucrose on UPE intensity. We believe that UPE can be exploited for a sensitive non-invasive analysis of oxidative metabolism during the plant development and growth with potential applications in agricultural research.