Multistep Aggregation Pathway of Human Interleukin-1 Receptor Antagonist: Kinetic, Structural, and Morphological Characterization

The complex, multistep aggregation kinetic and structural behavior of human recombinant interleukin-1 receptor antagonist (IL-1ra) was revealed and characterized by spectral probes and techniques. At a certain range of protein concentration (12-27 mg/mL) and temperature (44-48°C), two sequential aggregation kinetic transitions emerge, where the second transition is preceded by a lag phase and is associated with the main portion of the aggregated protein. Each kinetic transition is linked to a different type of aggregate population, referred to as type I and type II. The aggregate populations, isolated at a series of time points and analyzed by Fourier-transform infrared spectroscopy, show consecutive protein structural changes, from intramolecular (type I) to intermolecular (type II) β-sheet formation. The early type I protein spectral change resembles that seen for IL-1ra in the crystalline state. Moreover, Fourier-transform infrared data demonstrate that type I protein assembly alone can undergo a structural rearrangement and, consequently, convert to the type II aggregate. The aggregated protein structural changes are accompanied by the aggregate morphological changes, leading to a well-defined population of interacting spheres, as detected by scanning electron microscopy. A nucleation-driven IL-1ra aggregation pathway is proposed, and assumes two major activation energy barriers, where the second barrier is associated with the type I → type II aggregate structural rearrangement that, in turn, serves as a pseudonucleus triggering the second kinetic event.     

Diversity of free-living ‘naked’ amoeboid organisms

Amoeboid organisms are phylogenetically diverse, some being more closely related to plants or metazoans than to each other. Amoeboid organisms are ecologically successful, having been isolated on all continents, including Antarctica, as well as being the main predators controlling bacterial populations in soil. The classification of these organisms has historically relied upon morphological characteristics. The application of electron microscopy, comparison of enzymic profiles after electrophoretic separation, and analysis of nucleic acid fractions have provided reliable bases for classifying amoeboid organisms. The extent of diversity of these organisms has been recognized, as methods to detect, culture, characterize and identify them has increased. It is reasonable to anticipate that the current 40 000 species of protists will increase substantially as amoeboid organisms are cultivated from poorly accessible niches and from extreme environs.     

Performance of density functionals for the structure and energetics of (M–O)0,± (M=Al,Si, Sc–Zn)

We report the results of the performance of 20 exchange–correlation functionals of density functional theory (DFT) in the structure (Metal–Oxygen bond length) and energetical properties (bond dissociation energy, adiabatic ionisation energy, and adiabatic electron affinity) of twelve metal monoxides (M–O, M=Al, Si, Sc–Zn). The calculated results show that the selected DFT functionals have the ability to reproduce the M–O bond length with a mean deviation of 0.01–0.05 Å, the energy values are reproduced with a mean deviation of 0.20–1.00?eV. In general, the functionals with significant HF exchange show decent performance in the calculation of bond length and harmonic vibrational frequency. These functionals show poor performance in energetics. Our calculated results show that the M06-L, B3LYP, and TPSSh functionals give good performance in both structure and energetical properties of metal monoxides. These functionals are recommended for the studies of structure and energetics in metal oxide systems. Further, our studies indicate that M06-L can be used for the studies in larger molecular systems. Among the 20 DFT functionals, the recently developed N12 functional gives poor performance in the studies of metal monoxides. Hence this functional is not recommended for the studies of structure and energetics in metal oxide systems.