Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase

Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in > 2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for the development of new therapeutic strategies. Here, we address this important problem by targeting the malarial neutral aminopeptidases that are involved in the terminal stages of hemoglobin digestion and essential for the provision of amino acids used for parasite growth and development within the erythrocyte. We characterize the structure and substrate specificity of one such aminopeptidase, PfA-M1, a validated drug target. The X-ray crystal structure of PfA-M1 alone and in complex with the generic inhibitor, bestatin, and a phosphinate dipeptide analogue with potent in vitro and in vivo antimalarial activity, hPheP[CH2] Phe, reveals features within the protease active site that are critical to its function as an aminopeptidase and can be exploited for drug development. These results set the groundwork for the development of antimalarial therapeutics that target the neutral aminopeptidases of the parasite.

Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases

Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the x-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the x-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA- M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.

A STUDY OF CARBON-MONOXIDE AND NEUTRAL CARBON IN THE S106 MOLECULAR CORE

Maps are presented of J=2-1 and J=3-2 (CO)-O-18 emission from the molecular environment of the bipolar nebula S106, together with complementary observations of the P-3(1)-P-3(0), C I emission. Line splitting observed extensively over the E molecular cloud suggests that it is best explained as the expanding remnant of a thick toroid surrounding the optical lobes. The poor correlation between the observed molecular line emission and dust continuum emission in the E cloud is probably due to a large temperature gradient. Strong C I emission from the protostellar candidate S106 FIR suggests the nearby presence of a powerful source of far-UV radiation, whose energy supply is unlikely to arise from gravitational contraction of a protostar. It is probable that this source is the star S106 LR, which also heats S106 FIR. There is evidence, in both C I and (CO)-O-18, for a predominantly blueshifted outflow from S106 IR, best interpreted as a stellar wind-driven shock into the toroidal remnant. (CO)-O-18 and (CO)-C-13 appear to be depleted, relative to canonical values for their abundances, in S106 FIR, despite its high optical extinction, which should discourage selective photodissociation. Elsewhere in the cloud the C I line profiles show a resemblance to those of (CO)-O-18, with intensity equivalent to a few photodissociation regions (PDRs) along the line of sight.

THE EFFECT OF RAPID NEUTRAL-NEUTRAL REACTIONS ON CHEMICAL-MODELS OF DENSE INTERSTELLAR CLOUDS

Recent experiments on rapid neutral-neutral reactions involving the radical CN at low temperature and the neutral C atom at room temperature suggest that atom-neutral and radical-neutral reactions may be generally more rapid at low temperature than hitherto thought. We have included a variety of rapid neutral-neutral reactions in our gas-phase chemical models of quiescent, dense interstellar clouds. We find the calculated abundances of many molecules to be greatly changed from previous values. In particular, the peak 'early-time' abundances of organic molecules are reduced.

Energy levels, wavefunction compositions and electric dipole transitions in neutral Ca

A configuration-interaction approach, based on the use of B-spline basis sets combined with a model potential including monoelectronic and dielectronic core polarization effects, is employed to calculate term energies and wavefunctions for neutral Ca. Results are reported for singlet and triplet bound states, and some quasi-bound states above the lowest ionization limit, with angular momentum up to L = 4. Comparison with experiment and with other theoretical results shows that this method yields the most accurate energy values for neutral Ca obtained to date. Wavefunction compositions, necessary for labelling the levels, and the effects of semi-empirical polarization potentials on the wavefunctions are discussed, as are some recent identifications of doubly-excited states. It is shown that taking into account dielectronic core polarization changes the energies of the lowest terms in Ca significantly, in general by a few hundred cm(-1), the effect decreasing rapidly for the higher bound states. For Rydberg states with n approximate to 7 the accuracy of the results is often better than a few cm(-1). For series members (or perturbers) with a pronounced 3d character the error can reach 150 cm(-1). The wavefunctions are used to calculate oscillator strengths and lifetimes for a number of terms and these are compared with existing measurements. The agreement is good but points to a need for improved measurements.

Note on the single-shock solutions of the Korteweg-de Vries-Burgers equation

The well-known shock solutions of the Korteweg-de Vries-Burgers equation are revisited, together with their limitations in the context of plasma (astro)physical applications. Although available in the literature for a long time, it seems to have been forgotten in recent papers that such shocks are monotonic and unique, for a given plasma configuration, and cannot show oscillatory or bell-shaped features. This uniqueness is contrasted to solitary wave solutions of the two parent equations (Korteweg-de Vries and Burgers), which form a family of curves parameterized by the excess velocity over the linear phase speed.

A complete analytic theory for structure and dynamics of populations and communities spanning wide ranges in body size

The prediction and management of ecosystem responses to global environmental change would profit from a clearer understanding of the mechanisms determining the structure and dynamics of ecological communities. The analytic theory presented here develops a causally closed picture for the mechanisms controlling community and population size structure, in particular community size spectra, and their dynamic responses to perturbations, with emphasis on marine ecosystems. Important implications are summarised in non-technical form. These include the identification of three different responses of community size spectra to size-specific pressures (of which one is the classical trophic cascade), an explanation for the observed slow recovery of fish communities from exploitation, and clarification of the mechanism controlling predation mortality rates. The theory builds on a community model that describes trophic interactions among size-structured populations and explicitly represents the full life cycles of species. An approximate time-dependent analytic solution of the model is obtained by coarse graining over maturation body sizes to obtain a simple description of the model steady state, linearising near the steady state, and then eliminating intraspecific size structure by means of the quasi-neutral approximation. The result is a convolution equation for trophic interactions among species of different maturation body sizes, which is solved analytically using a novel technique based on a multiscale expansion.

Current-induced atomic dynamics, instabilities, and Raman signals: Quasiclassical Langevin equation approach

We derive and employ a semiclassical Langevin equation obtained from path integrals to describe the ionic dynamics of a molecular junction in the presence of electrical current. The electronic environment serves as an effective nonequilibrium bath. The bath results in random forces describing Joule heating, current-induced forces including the nonconservative wind force, dissipative frictional forces, and an effective Lorentz-type force due to the Berry phase of the nonequilibrium electrons. Using a generic two-level molecular model, we highlight the importance of both current-induced forces and Joule heating for the stability of the system. We compare the impact of the different forces, and the wide-band approximation for the electronic structure on our result. We examine the current-induced instabilities (excitation of runaway "waterwheel" modes) and investigate the signature of these in the Raman signals.

Real-time approach to the optical properties of solids and nanostructures: Time-dependent Bethe-Salpeter equation

Many-body effects are known to play a crucial role in the electronic and optical properties of solids and nanostructures. Nevertheless, the majority of theoretical and numerical approaches able to capture the influence of Coulomb correlations are restricted to the linear response regime. In this work, we introduce an approach based on a real-time solution of the electronic dynamics. The proposed approach reduces to the well-known Bethe-Salpeter equation in the linear limit regime and it makes it possible, at the same time, to investigate correlation effects in nonlinear phenomena. We show the flexibility and numerical stability of the proposed approach by calculating the dielectric constants and the effect of a strong pulse excitation in bulk h-BN.

Electron paramagnetic resonance studies of the neutral nitrogen vacancy in diamond

Despite the numerous experimental and theoretical studies on the negatively charged nitrogen vacancy center (NV-) in diamond and the predictions that the neutral nitrogen vacancy center (NV0) should have an S=1/2 ground state, NV0 has not previously been detected by electron paramagnetic resonance (EPR). We report new EPR data on a trigonal nitrogen-containing defect in diamond with an S=3/2 excited state populated via optical excitation. Analysis of the spin Hamiltonian parameters and the wavelength dependence of the optical excitation leads to assignment of this S=3/2 state to the (4)A(2) excited state of NV0. This identification, together with an examination of the electronic structure of the NV centers in diamond, provides a plausible explanation for the lack of observation (to date) of an EPR signal from the NV0 ground state.