Iterative approach to computational enzyme design

A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes

Effect of tensile stress on the in-plane resistivity anisotropy in BaFe2As2

The effect of uniaxial tensile stress and the resultant strain on the structural/magnetic transition in the parent compound of the iron arsenide superconductor, BaFe$_2$As$_2$, is characterized by temperature-dependent electrical resistivity, x-ray diffraction and quantitative polarized light imaging. We show that strain induces a measurable uniaxial structural distortion above the first-order magnetic transition and significantly smears the structural transition. This response is different from that found in another parent compound, SrFe$_2$As$_2$, where the coupled structural and magnetic transitions are strongly first order. This difference in the structural responses explains the in-plain resistivity anisotropy above the transition in BaFe$_2$As$_2$. This conclusion is supported by the Ginzburg-Landau - type phenomenological model for the effect of the uniaxial strain on the resistivity anisotropy

Dispersal capacity predicts both population genetic structure and species richness in reef fishes

Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersalrelated traits in influencing the mode and tempo of evolution

Uniaxial strain detwinning of CaFe2As2 and BaFe2As2: optical and transport study

TThe parent compounds of iron-arsenide superconductors, $A$Fe$_{2}$As$_{2}$ ($A$=Ca, Sr, Ba), undergo a tetragonal to orthorhombic structural transition at a temperature $T_{\mathrm{TO}}$ in the range 135 to 205K depending on the alkaline earth element. Below $T_{\mathrm{TO}}$ the free standing crystals split into equally populated structural domains, which mask intrinsic, in-plane, anisotropic properties of the materials. Here we demonstrate a way of mechanically detwinning CaFe$_{2}$As$_{2}$ and BaFe$_{2}$As$_{2}$. The detwinning is nearly complete, as demonstrated by polarized light imaging and synchrotron $X$-ray measurements, and reversible, with twin pattern restored after strain release. Electrical resistivity measurements in the twinned and detwinned states show that resistivity, $\rho$, decreases along the orthorhombic $a_{o}$-axis but increases along the orthorhombic $b_{o}$-axis in both compounds. Immediately below $T_{\mathrm{TO}}$ the ratio $\rho_{bo}/ \rho_{ao}$ = 1.2 and 1.5 for Ca and Ba compounds, respectively. Contrary to CaFe$_{2}$As$_{2}$, BaFe$_{2}$As$_{2}$ reveals an anisotropy in the nominally tetragonal phase, suggesting that either fluctuations play a larger role above $T_{\mathrm{TO}}$ in BaFe$_{2}$As$_{2}$ than in CaFe$_{2}$As$_{2}$, or that there is a higher temperature crossover or phase transition.Comment: extended versio

Relationship between antipyretic effects and cytokine levels in uncomplicated falciparum malaria during different treatment regimes

We have previously shown that both chloroquine and paracetamol (acetaminophen) have antipyretic activity during treatment of acute uncomplicated Plasmodium falciparum malaria in children 1-4 years old. Here, we studied if this effect was accompanied by changes in plasma cytokine levels. The 104 children were treated with either chloroquine or sulfadoxine/pyrimethamine (SP) alone, SP + chloroquine or SP + paracetamol for 4 days. Cytokine levels were determined days 0, 2 and 3, body temperature every sixth hour until 72 h and parasitemia once daily for 4 days. At admission, body temperature correlated with levels of IL-10, IFN-γ and IL-6, and parasitemia correlated with IL-10 and IL-6. Except for TNF-α and IL-1β, where no significant effect was found, all cytokine levels (IL-10, IFN-γ, IL-6, IL-12, IL-13, IL-18 and IL-4) decreased up to day 2 (p \u3c 0.05). IL-6 levels continued to fall from days 2 to 3 (p \u3c 0.05), whereas increased levels were found for several cytokines (IL-12, IL-13, IL-18 and IL-1β) (p \u3c 0.05). The antipyretic effects of chloroquine and paracetamol could not be related to any specific changes in the evaluated cytokine production or in Th1/Th2 or inflammatory/anti-inflammatory cytokine ratios. Alternative mechanisms for antipyretic effects and associations between fever and cytokine levels during uncomplicated P. falciparum malaria are therefore discussed. © 2006 Elsevier B.V. All rights reserved

Antipyretic, parasitologic, and immunologic effects of combining sulfadoxine/pyrimethamine with chloroquine or paracetamol for treating uncomplicated Plasmodium falciparum malaria

Sulfadoxine/pyrimethamine (SP) is increasingly used against malaria in sub-Saharan Africa because of chloroquine resistance. However, chloroquine may have a beneficial antipyretic effect. We therefore compared the combination of SP plus chloroquine, chloroquine alone, SP alone, and SP plus paracetamol in the treatment of uncomplicated Plasmodium falciparum malaria in 175 Tanzanian children (1-4 years old) in a randomized trial. Outcome variables were axillary temperatures every six hours, daily parasitemias, and serum levels of IgG antibodies to P. falciparum. Lower mean temperatures (6-48 hours) were achieved with SP plus chloroquine or paracetamol than with SP alone (P \u3c 0.001) or chloroquine alone (P \u3c 0.05). All three SP-treated groups showed high and similar parasite reduction (0-48 hours), whereas treatment with chloroquine alone was much less effective. Levels of IgG antibodies to P. falciparum increased significantly (P \u3c 0.001) and similarly in the four treatment groups between days 0, 2. and 3. Thus, the addition of chloroquine or paracetamol to SP improved the clinical outcome, but did not affect the parasitologic response or antibody production