Phase separation of p53 precedes aggregation and is affected by oncogenic mutations and ligands

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF). The mechanism of the formation of the aggregates in the nucleus remains uncertain. The present study demonstrated that the DNA-binding domain of p53 (p53C) underwent phase separation (PS) on the pathway to aggregation under various conditions. p53C phase separated in the presence of the crowding agent polyethylene glycol (PEG). Similarly, mutant p53C (M237I and R249S) underwent PS; however, the process evolved to a solid-like phase transition faster than that in the case of wild-type p53C. The data obtained by microscopy of live cells indicated that transfection of mutant full-length p53 into the cells tended to result in PS and phase transition (PT) in the nuclear compartments, which are likely the cause of the GoF effects. Fluorescence recovery after photobleaching (FRAP) experiments revealed liquid characteristics of the condensates in the nucleus. Mutant p53 tended to undergo gel- and solid-like phase transitions in the nucleus and in nuclear bodies demonstrated by slow and incomplete recovery of fluorescence after photobleaching. Polyanions, such as heparin and RNA, were able to modulate PS and PT in vitro. Heparin apparently stabilized the condensates in a gel-like state, and RNA apparently induced a solid-like state of the protein even in the absence of PEG. Conditions that destabilize p53C into a molten globule conformation also produced liquid droplets in the absence of crowding. The disordered transactivation domain (TAD) modulated both phase separation and amyloid aggregation. In summary, our data provide mechanistic insight into the formation of p53 condensates and conditions that may result in the formation of aggregated structures, such as mutant amyloid oligomers, in cancer. The pathway of mutant p53 from liquid droplets to gel-like and solid-like (amyloid) species may be a suitable target for anticancer therapy.

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF).     

Electrospray ionization quadrupole time-of-flight and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometric analyses to solve micro-heterogeneity in post-translationally modified peptides from Phoneutria nigriventer (Aranea, Ctenidae) venom

Previous studies of the fractionated venom of the Brazilian armed spider Phoneutria nigriventer, obtained by gel filtration, have demonstrated the presence of a fraction PhM, a pool of small peptides (up to 2000 Da) that provoke contractions in smooth muscle of guinea pig ileum. Initial attempts to sequence these peptides were largely unsuccessful because of the low purification yield and the fact that the majority seemed to be blocked at their N-termini. In the present work, analysis of this venom fraction by mass spectrometry has revealed the existence of a highly complex mixture of peptides with molecular weights corresponding to those observed for the muscle-active peptides previously described (800-1800 Da). These peptides appear to be a family of isoforms with some particular features. The amino acid sequences of 15 isoforms have been determined by tandem mass spectrometry (MS/MS) using both electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q/ToFMS) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-ToF/ToFMS). These molecules contain post-translational modifications such as proteolysis and C-terminal amidation, which combine to generate additional isoforms. All the isoforms sequenced in this study possess an N-terminal pyroglutamic acid residue. A search for sequence similarities with other peptides in databanks revealed that these peptides are structurally related to the tachykinins, a family of neuro-hormone peptides. The data obtained in this study will be essential for the subsequent steps of this research, the synthesis of these peptides and pharmacological characterization of their biological activity.     

Behavior of evaporating droplets at nonsoluble and soluble surfaces: Modeling with molecular resolution

Liquid droplets in equilibrium with vapor are simulated at solidlike surfaces using the cooperative motion algorithm (CMA). These droplets behave like real droplets, i.e., the densities of the coexistent liquid and vapor phases obey empirical relations such as rho l - rho v proportional, variant (1 - T/Tc)(1/3). Droplet evaporation was studied under various interaction conditions, i.e., nonsoluble and soluble substrates. In the last case, substrate particles migrate toward the liquid-vapor interface to minimize the droplet surface energy. This leads to the formation of a microwell surrounded by a ringlike deposit on the substrate surface. It is shown that the ring formation in the first stages of evaporation results in pinning of the droplet contact area.     

Parallel implementation of a Monte Carlo molecular stimulation program

Molecular simulation methods such as molecular dynamics and Monte Carlo are fundamental for the theoretical calculation of macroscopic and microscopic properties of chemical and biochemical systems. These methods often rely on heavy computations, and one sometimes feels the need to run them in powerful massively parallel machines. For moderate problem sizes, however, a not so powerful and less expensive solution based on a network of workstations may be quite satisfactory. In the present work, the strategy adopted in the development of a parallel version is outlined, using the message passing model, of a molecular simulation code to be used in a network of workstations. This parallel code is the adaptation of an older sequential code using the Metropolis Monte Carlo method. In this case, the message passing interface was used as the interprocess communications library, although the code could be easily adapted for other message passing systems such as the parallel virtual machine. For simple systems it is shown that speedups of 2 can be achieved for four processes with this cheap solution. For bigger and more complex simulated systems, even better speedups might be obtained, which indicates that the presented approach is appropriate for the efficient use of a network of workstations in parallel processing.     

Reconstruction of the free energy in the metastable region using the path ensemble

By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent distributions from which we reconstruct the free energy as a function of the magnetic field, temperature, and system size. From the reconstructed free energy, we obtain the free-energy barrier that is associated with the transition from a metastable state to the stable equilibrium state. Although mean-field theory predicts a sharp transition between the metastable and the unstable region where the free-energy barrier is zero, the results for the nearest-neighbor Ising model show that the free-energy barrier does not go to zero.     

Biosynthesis and antioxidant activity of 4NRC β-glycoside

This Letter describes glycosylation of 4-Nerolidylcatechol (4-NRC) the major secondary metabolite from Pothomorphe peltata and Pothomorphe umbellata showing remarkable antioxidant, antimalarial, anti-inflammatory, and anti-HIV activities. One step biosynthesis was catalyzed by Cunninghamella echinulata ATCC 9245 and the reaction was undertaken in PDSM medium at 27 °C, 200 rpm for 96 h. After purification by silica gel flash column chromatography the 4-NRC β-glycoside was identified by ultrahigh resolution mass spectrometry and ¹H NMR. The antioxidant activity was evaluated by differential pulse voltammetry.     

Mechanism of aziridination of styrene catalyzed by copper(I) bis(oxazoline)

Experimental studies show that copper complexes can be effectively anchored onto the pores of mesoporous solids, having a good catalytic performance in several reactions, among them the aziridination of olefins and in particular, styrene. In this work, the mechanism of the aziridination of styrene catalyzed by a bis(oxazoline) copper(I) complex was studied in detail by means of density functional theory (DFT) calculations. For such reactions in the homogeneous phase, our calculations revealed a wide diversity of reaction‐pathways, which have not been considered in previous studies, and should be taken into account due to the small energy differences between them. What is more, our results show that there is a strong dependence on the chosen DFT functional. This has profound implications on the way the heterogeneous reaction is studied. © 2013 Wiley Periodicals, Inc.