A thermodynamic-kinetic analysis of the cytochrome P-450 heme pocket.

Spin state changes in the iron center of cytochrome P-450 during the catalytic cycle suggest alterations in the heme environment that insure proper substrate binding, an increase in redox potential, the formation of an active Fe-O complex, and the attack on the substrate. We used the spin state changes of the iron following physico-chemical perturbations, as an intrinsic probe of discrete changes around the heme, or of larger ones in the protein conformation. These environmental perturbations included temperature, solvent, substrate, and ionic environment. Aqueous and hydro-organic buffers provide complementary data and interpretations; the mixed solvent accommodates temperatures suitable for direct reaction rate measurements and amplified low to high spin transition. The results suggest that the group determining the heme spin state is influenced by the electrostatic potential created by several negative charges near the heme; the modulation of the spin state by various factors reflects the modulation of the electrostatic potential and of the internal paH value. Conformational changes of the whole protein are also indicated by the large entropy terms and their variation with experimental conditions.     

Characterization of Mg2+-induced conformational change in the 50S ribosomal subunit by differential hydrogen exchange.

The technique of differential hydrogen exchange allows detection of a conformational change in the 50S subunit of Escherichia coli ribosome when the magnesium concentration is lowered in a range where ribosomal activity is fully preserved. This change is characterized by a seventy-fold acceleration of about thirty labile hydrogens in the case of a Mg2+ jump from 10 mM to 2 mM. The small number of hydrogens involved can explain the difficulty in detecting this change by other methods.     

TgPL2, a patatin‐like phospholipase domain‐containing protein,is involved in the maintenance of apicoplast lipids homeostasis in Toxoplasma

Patatin‐like phospholipases are involved in numerous cellular functions, including lipid metabolism and membranes remodeling. The patatin‐like catalytic domain, whose phospholipase activity relies on a serine‐aspartate dyad and an anion binding box, is widely spread among prokaryotes and eukaryotes. We describe TgPL2, a novel patatin‐like phospholipase domain‐containing protein from the parasitic protist Toxoplasma gondii. TgPL2 is a large protein, in which the key motifs for enzymatic activity are conserved in the patatin‐like domain. Using immunofluorescence assays and immunoelectron microscopy analysis, we have shown that TgPL2 localizes to the apicoplast, a non‐photosynthetic plastid found in most apicomplexan parasites. This plastid hosts several important biosynthetic pathways, which makes it an attractive organelle for identifying new potential drug targets. We thus addressed TgPL2 function by generating a conditional knockdown mutant and demonstrated it has an essential contribution for maintaining the integrity of the plastid. In absence of TgPL2, the organelle is rapidly lost and remaining apicoplasts appear enlarged, with an abnormal accumulation of membranous structures, suggesting a defect in lipids homeostasis. More precisely, analyses of lipid content upon TgPL2 depletion suggest this protein is important for maintaining levels of apicoplast‐generated fatty acids, and also regulating phosphatidylcholine and lysophosphatidylcholine levels in the parasite.     

Microeukaryotic diversity in marine environments,an analysis of surface layer sediments from the East Sea

Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.     

High-pressure SANS and fluorescence unfolding study of calmodulin

Apo-calmodulin, a small soluble mainly α protein, is a calcium-dependent protein activator. Calcium binding affects the calmodulin conformation but also its stability. Calcium free form unfolds between 40 and 80 °C, whereas the calcium-saturated form is stable up to temperatures as high as 100 °C, forbidding comparison of the thermal unfolding pathways of the two forms. Thus, this paper focuses especially on the conformation of pressure-induced unfolding states of both forms of calmodulin, by combining small-angle neutron scattering (SANS) with biophysical techniques such as tyrosines and ANS fluorescence. In contrast to heat denaturation (Gibrat et al., BBA, 2012), the pressure denaturation of calmodulin is reversible up to pressures of 3000 bar (300 MPa). A pressure-induced compact intermediate state has been found for the two calmodulin forms, but their unfolding pathways are different. A domain compaction and an increase of the ANS fluorescence of holo form have been evidenced. On the contrary, a domain dilatation and an ANS fluorescence decrease have been found for the apo form. The pressure induced an increase of the interdomain distance for both calmodulin forms, suggesting that the central linker of calmodulin is flexible in solution.     

Stabilization of P450 2B4 by its association with P450 1A2 revealed by high-pressure spectroscopy

We studied the effect of intermolecular interactions between cytochromes P450 1A2 (CYP1A2) and 2B4 (CYP2B4) on the barotropic inactivation of the ferrous carbonyl complexes of the hemoproteins. When taken separately, these hemoproteins reveal quite distinct barotropic behavior. While the 2B4(Fe(2+))-CO complex is very sensitive to hydrostatic pressures and undergoes P450 --> P420 transition at rather low pressures (P(1/2) = 297 MPa, DeltaV(0) = -61 ml/mol), the 1A2(Fe(2+))-CO is extremely resistant to barotropic inactivation. Only about 8% of the 1A2 was exposed to pressure-induced P450 --> P420 transition (P(1/2) = 420 MPa, DeltaV(0) = -28 ml/mol). The formation of the mixed oligomers of 2B4 and 1A2 was found to have a dramatic effect on the barotropic behavior of 2B4. In the heterooligomers of 1A2 and 2B4, the 2B4 hemoprotein appears to be largely protected from barotropic inactivation. In 1:1 mixed oligomers no more than 25% of the total P450 content undergoes P450 --> P420 inactivation with the molar reaction volume value (DeltaV(0) = -26 ml/mol) similar to those found for pure 1A2. Moreover, interactions between 1A2 and 2B4 results in a displacement of the Soret band of the ferrous carbonyl complex of CYP2B4 to shorter wavelength (from 451.3 to 448.4 nm) and largely strengthens the dependence of the Soret band wavenumber on hydrostatic pressure below 200 MPa. This effect suggests an important hydration of the CYP2B4 heme moiety in response to the interactions with CYP1A2. We discuss these results in terms of the hypothesis that the heterooligomerization of cytochromes P450 in microsomes plays an important role in the control of the activity and coupling of the microsomal monooxygenase.     

Tritium exchange of spectrin versus temperature

Tritium-exchange experiments were performed to assess the dynamics of the spectrin molecule. From the kinetics presented, spectrin appears as a fast-exchanging protein compared to globular proteins. This is easily explained by its known elongated structure. Spectrin tritium exchange is also shown to be highly temperature sensitive, even in buffer conditions that greatly reduce the temperature dependence of hydroxyl catalyst concentration. At high ionic strength, the exchange rates of specific hydrogens deduced from a power-law simulation are shown to exhibit an Arrhenius behavior, with enthalpies ranging from 70 to 140 kjmol^?1. These results are discussed in relation to the known high α-helix content of spectrin. Finally, a molecular model of α-helix opening is proposed that provides satisfactory agreement with the totality of the spectrin behavior in tritium-exchange experiments.     

New trends in cryoenzymology: probing the functional role of protein dynamics by single-step kinetics

Cryoenzymology was initially used to slow down enzyme-catalyzed reactions so as to stabilize intermediates for further study. During the course of this early work, it became clear that cryoenzymology could be extended to other ends and some of these are described. First, the use of a cryosolvent on its own (or together with temperature) as a perturbant has allowed a resolution of the substrate binding steps of certain enzymes (myosin, D-amino acid oxidase, peroxidase and cytochrome P450). Second, by the use of cryosolvent and temperature, coupled with the classical physico-chemical perturbants, one can selectively modulate the various steps of an enzyme pathway. This approach can lead to an understanding of the mechanism of enzyme regulation. Finally, by carrying out experiments over a wide range of temperatures (-30 degrees C- +30 degrees C) and pressure (up to several kbars) in specially constructed fast reaction equipment, one can study the thermodynamic properties of the individual rate constants describing the interconversions of reaction intermediates. Experiments with creatine kinase, cytochrome P450 and peroxidase are described. The thermodynamic parameters delta H, delta G, delta S and delta V are thus measured and when this is done under different solvent conditions one can, at least within the theories available, attempt an approach to the problem of protein dynamics.     

Effect of Facilitation of Local Stakeholder Groups on Equity in Neonatal Survival; Results from the NeoKIP Trial in Northern Vietnam

Background

To operationalize the post-MDG agenda, there is a need to evaluate the effects of health interventions on equity. The aim of this study is to evaluate the effect on equity in neonatal survival of the NeoKIP trial (ISRCTN44599712), a population-based, cluster-randomized intervention trial with facilitated local stakeholder groups for improved neonatal survival in Quang Ninh province in northern Vietnam.

Methods

Semi-structured interviews were conducted with all mothers experiencing neonatal mortality and a random sample of 6% of all mothers with a live birth in the study area during the study period (July 2008-June 2011). Multilevel regression analyses were performed, stratifying mothers according to household wealth, maternal education and mother’s ethnicity in order to assess impact on equity in neonatal survival.

Findings

In the last year of study the risk of neonatal death was reduced by 69% among poor mothers in the intervention area as compared to poor mothers in the control area (OR 0.31, 95% CI 0.15–0.66). This pattern was not evident among mothers from non-poor households. Mothers with higher education had a 50% lower risk of neonatal mortality if living in the intervention area during the same time period (OR 0.50, 95% CI 0.28–0.90), whereas no significant effect was detected among mothers with low education.

Interpretation

The NeoKIP intervention promoted equity in neonatal survival based on wealth but increased inequity based on maternal education.