Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.

We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory

Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2

International audienceArchaeal initiation factor 2 (aIF2) is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, "ON" conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, "OFF" conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and its dependence on the ON or OFF conformational state of aIF2, molecular dynamics free energy simulations (MDFE) are a tool of choice. However, the validity of the computed free energies depends on the simulation model, including the force field and the boundary conditions, and on the extent of conformational sampling in the simulations. aIF2 and other GTPases present specific difficulties; in particular, the nucleotide ligand coordinates a divalent Mg(2+) ion, which can polarize the electronic distribution of its environment. Thus, a force field with an explicit treatment of electronic polarizability could be necessary, rather than a simpler, fixed charge force field. Here, we begin by comparing a fixed charge force field to quantum chemical calculations and experiment for Mg(2+):phosphate binding in solution, with the force field giving large errors. Next, we consider GTP and GDP bound to aIF2 and we compare two fixed charge force fields to the recent, polarizable, AMOEBA force field, extended here in a simple, approximate manner to include GTP. We focus on a quantity that approximates the free energy to change GTP into GDP. Despite the errors seen for Mg(2+):phosphate binding in solution, we observe a substantial cancellation of errors when we compare the free energy change in the protein to that in solution, or when we compare the protein ON and OFF states. Finally, we have used the fixed charge force field to perform MDFE simulations and alchemically transform GTP into GDP in the protein and in solution. With a total of about 200 ns of molecular dynamics, we obtain good convergence and a reasonable statistical uncertainty, comparable to the force field uncertainty, and somewhat lower than the predicted GTP/GDP binding free energy differences. The sign and magnitudes of the differences can thus be interpreted at a semiquantitative level, and are found to be consistent with the experimental binding preferences of ON- and OFF-aIF2

Using Polycyclic Aromatic Hydrocarbons (PAHs) as a chemical proxy to indicate Tsunami 2004 backwash in Khao Lak coastal area, Thailand

In this study, we attempted to use PAHs as a chemical proxy to trace the transport of land-derived materials caused by the tsunami backwash to better understand how it may have affected the distribution of sedimentary deposition throughout the seabed of Khao Lak coastal areas. By analyzing the compositions of sedimentary PAHs in combination with application of the multivariate descriptive statistical techniques, PAHs were proven to be a promising chemical proxy to indicate the tsunami backwash in the study area. Their spatial distribution could indicate that the tsunami backwash plays an important role in transporting anthropogenic PAHs to the nearby coastal area as far as approximately 25 km from the shoreline. In addition, the results from diagnostic PAH isomer ratios suggested that road paving asphalt, originated from heavy erosion by the tsunami wave in front of Pakarang Cape, was among the identified sources of PAHs. Principle Component Analysis (PCA) results provided 2 estimated land-derived sources of PAHs, which were the road dust and oil burning sources. These estimated signature sources clearly support our hypothesis that PAHs were transported from the potential sources on land and deposited into the near-shore seabed during tsunami backwash

USING FOURIER TRANSFORM INFRARED (FTIR) TO CHARACTERIZE TSUNAMI DEPOSITS IN NEAR-SHORE AND COASTAL WATERS OF THAILAND

Understanding the tsunami cycle requires a simple method for identification of tsunami backwash deposits. This study investigates Fourier transform infrared (FTIR) spectroscopy followed by careful analysis of variance (ANOVA), Gaussian distribution, hierarchical cluster analysis (HCA) and principal component analysis (PCA) for the discrimination of typical marine sediments and tsunami backwash deposits. In order to test the suitability of FTIR spectra as innovative methods for classifications of tsunami deposits, typical marine sediments and terrestrial soils were classified into three zones, namely zone-1 (i.e. typical marine sediments), zone-2 (i.e. including tsunami backwash deposits) and zone-3 (i.e. coastal terrestrial soils). HCA was performed to group the spectra according to their spectral similarity in a dendrogram and successfully separate FTIR spectra of all three sampling zones into two main clusters with five sub-clusters. The simplicifolious (i.e. single-leafed) type of dendrogram was observed with the strong dissimilarity of terrestrial components in subcluster- 5. Graphical displays of PC1 vs PC2 highlight the prominent features of zone-1, which is explicitly different from those of zone-2 and zone-3. The acceptable discrimination of typical marine sediments and tsunami backwash deposits, even six years after the tsunami on Boxing Day 2004, dramatically demonstrates the potential of the method for the identification of paleotsunami

A systematic overview of published antimalarial drug trials.

Systematic database searches identified 435 antimalarial drug treatment trials, involving 82,616 patients, conducted and published between 1966 and December 2002. Of these trials 72% were randomised; 64 (15%) trials involved severe malaria, 47 (11%) studied Plasmodium vivax, 3 Plasmodium malariae or Plasmodium ovale, and the remainder (74%) assessed treatment responses in uncomplicated falciparum malaria. Twelve trials (2.7%) specifically evaluated antimalarial treatments in pregnant women. Overall 49% of trials were conducted in Asia (29% from Thailand alone) and 42% in Africa. Half of all the patients studied had been in trials published in the past 7 years. There has been a recent rise in the proportion of trial enrolling children, and a tripling in the average number of patients recruited per trial (from approximately 100 in the 1970s to 300 currently). Chloroquine was given to over half the patients in antimalarial drug trials (n = 53552) compared with artemisinin derivatives (n = 12463), mefloquine-sulphadoxine-pyrimethamine (n = 9153), mefloquine (n = 5546) and sulphadoxine-pyrimethamine (n = 5909). The quality of safety and efficacy data for recently evaluated drugs contrasts with a relative paucity of data for older 'established' compounds

High throughput assay for the determination of lumefantrine in plasma.

A high throughput bioanalytical assay for the determination of lumefantrine in plasma has been developed and validated extensively. The within-day precisions for lumefantrine were 5.2, 3.5 and 2.5% at 200, 2000 and 15000 ng/mL, respectively. The between-day precisions were 4.0, 2.8 and 3.1% at 200, 2000 and 15000 ng/mL, respectively. The lower limits of quantification (LLOQ) and the limits of detection (LOD) were 25 and 10 ng/mL, respectively using 0.250 mL plasma. The average recovery of lumefantrine was 85% and independent upon concentration. The use of 96-well plate format and short chromatographic run has increased the daily sample throughput four times. The assay is particularly suitable for large therapeutic drug monitoring studies using day 7 sampling

High throughput assay for the determination of lumefantrine in plasma.

A high throughput bioanalytical assay for the determination of lumefantrine in plasma has been developed and validated extensively. The within-day precisions for lumefantrine were 5.2, 3.5 and 2.5% at 200, 2000 and 15000 ng/mL, respectively. The between-day precisions were 4.0, 2.8 and 3.1% at 200, 2000 and 15000 ng/mL, respectively. The lower limits of quantification (LLOQ) and the limits of detection (LOD) were 25 and 10 ng/mL, respectively using 0.250 mL plasma. The average recovery of lumefantrine was 85% and independent upon concentration. The use of 96-well plate format and short chromatographic run has increased the daily sample throughput four times. The assay is particularly suitable for large therapeutic drug monitoring studies using day 7 sampling

A systematic overview of published antimalarial drug trials.

Systematic database searches identified 435 antimalarial drug treatment trials, involving 82,616 patients, conducted and published between 1966 and December 2002. Of these trials 72% were randomised; 64 (15%) trials involved severe malaria, 47 (11%) studied Plasmodium vivax, 3 Plasmodium malariae or Plasmodium ovale, and the remainder (74%) assessed treatment responses in uncomplicated falciparum malaria. Twelve trials (2.7%) specifically evaluated antimalarial treatments in pregnant women. Overall 49% of trials were conducted in Asia (29% from Thailand alone) and 42% in Africa. Half of all the patients studied had been in trials published in the past 7 years. There has been a recent rise in the proportion of trial enrolling children, and a tripling in the average number of patients recruited per trial (from approximately 100 in the 1970s to 300 currently). Chloroquine was given to over half the patients in antimalarial drug trials (n = 53552) compared with artemisinin derivatives (n = 12463), mefloquine-sulphadoxine-pyrimethamine (n = 9153), mefloquine (n = 5546) and sulphadoxine-pyrimethamine (n = 5909). The quality of safety and efficacy data for recently evaluated drugs contrasts with a relative paucity of data for older 'established' compounds

The novel antibiotic rhodomyrtone traps membrane proteins in vesicles with increased fluidity

<div><p>The acylphloroglucinol rhodomyrtone is a promising new antibiotic isolated from the rose myrtle <i>Rhodomyrtus tomentosa</i>, a plant used in Asian traditional medicine. While many studies have demonstrated its antibacterial potential in a variety of clinical applications, very little is known about the mechanism of action of rhodomyrtone. Preceding studies have been focused on intracellular targets, but no specific intracellular protein could be confirmed as main target. Using live cell, high-resolution, and electron microscopy we demonstrate that rhodomyrtone causes large membrane invaginations with a dramatic increase in fluidity, which attract a broad range of membrane proteins. Invaginations then form intracellular vesicles, thereby trapping these proteins. Aberrant protein localization impairs several cellular functions, including the respiratory chain and the ATP synthase complex. Being uncharged and devoid of a particular amphipathic structure, rhodomyrtone did not seem to be a typical membrane-inserting molecule. In fact, molecular dynamics simulations showed that instead of inserting into the bilayer, rhodomyrtone transiently binds to phospholipid head groups and causes distortion of lipid packing, providing explanations for membrane fluidization and induction of membrane curvature. Both its transient binding mode and its ability to form protein-trapping membrane vesicles are unique, making it an attractive new antibiotic candidate with a novel mechanism of action.</p></div