Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with <Superscript>2</Superscript>H NMR experiments

Order parameters from deuterium NMR are often used to validate or calibrate molecular dynamics simulations. This paper gives a short overview of the literature in which experimental order parameters from ²H NMR are compared to those calculated from MD simulations. The different ways in which order parameters from experiment are used to calibrate and validate simulations are reviewed. In the second part of this review, a case study of cholesterol in a DMPC bilayer is presented. It is concluded that the agreement between experimental data and simulation is favorable in the hydrophobic region of the membrane, for both the phospholipids and cholesterol. In the interfacial region the agreement is less satisfactory, probably because of the high polarity of this region which makes the correct computation of the electrostatics more complex. Presented at the joint biannual meeting of the SFB-GEIMM-GRIP, Anglet France, 14–19 October, 2006.     

Elevated CO<Subscript>2</Subscript> mitigates the adverse effects of drought on daytime net ecosystem CO<Subscript>2</Subscript> exchange and photosynthesis in a Florida scrub-oak ecosystem

Drought is a normal, recurrent feature of climate. In order to understand the potential effect of increasing atmospheric CO₂ concentration (C _a) on ecosystems, it is essential to determine the combined effects of drought and elevated C _a (EC) under field conditions. A severe drought occurred in Central Florida in 1998 when precipitation was 88 % less than the average between 1984 and 2002. We determined daytime net ecosystem CO₂ exchange (NEE) before, during, and after the drought in the Florida scrub-oak ecosystem exposed to doubled C _a in open-top chamber since May 1996. We measured diurnal leaf net photosynthetic rate (P _N) of Quercus myrtifolia Willd, the dominant species, during and after the drought. Drought caused a midday depression in NEE and P _N at ambient CO₂ concentration (AC) and EC. EC mitigated the midday depression in NEE by about 60 % compared to AC and the effect of EC on leaf P _N was similar to its effect on NEE. Growth in EC lowered the sensitivity of NEE to air vapor pressure deficit under drought. Thus EC would help the scrub-oak ecosystem to survive the consequences of the effects of rising atmospheric CO₂ on climate change, including increased frequency of drought, while simultaneously sequestering more anthropogenic carbon.     

Cosegregation of a novel homozygous CYP11B1 mutation with the phenotype of non-classical congenital adrenal hyperplasia in a consanguineous family

We report a novel missense mutation of CYP11B1 causing non-classical 11beta-hydroxylase deficiency in 3 members of a consanguineous Turkish family. Two siblings presented with clinical evidence of precocious pseudopubarche. Biochemistry suggested 11beta-hydroxylase deficiency and genetic analysis revealed that they were homozygous for the missense mutation L489S within exon 9 of the CYP11B1 gene. The unaffected parents were heterozygotes for the same mutation. In addition, a paternal aunt of the affected siblings presenting with primary infertility and mild hirsutism was found to have the same homozygous mutation. This is the first report of a homozygous mutation in non-classical congenital adrenal hyperplasia that cosegregates with clinical phenotype. The significance of the missense mutation L489S in CYP11B1 is further supported by the conservation of leucine at position 489 in CYP11 genes in eleven other species. Molecular modelling of the enzyme suggests that the mutation L489S in CYP11B1 may alter the enzyme's substrate-binding affinity. These findings suggest that this homozygous mutation affects 11beta-hydroxylase function, resulting in the clinical features of non-classical adrenal hyperplasia in this family.     

Dual-color fluorescence-burst analysis to probe protein efflux through the mechanosensitive channel MscL

The mechanosensitive channel protein of large conductance, MscL, from Escherichia coli has been implicated in protein efflux, but the passage of proteins through the channel has never been demonstrated. We used dual-color fluorescence-burst analysis to evaluate the efflux of fluorescent labeled compounds through MscL. The method correlates the fluctuations in intensity of fluorescent labeled membranes and encapsulated (macro)molecules (labeled with second fluorophore) for each liposome diffusing through the observation volume. The analysis provides quantitative information on the concentration of macromolecules inside the liposomes and the fraction of functional channel proteins. For MscL, reconstituted in large unilamellar vesicles, we show that insulin, bovine pancreas trypsin inhibitor, and other compounds smaller than 6.5 kDa can pass through MscL, whereas larger macromolecules cannot.     

Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length

We investigated the structural and energetic determinants underlying water permeation through peptidic nanopores, motivated by recent experimental findings that indicate that water mobility in single-file water channels displays nonlinear length dependence. To address the molecular mechanism determining the observed length dependence, we studied water permeability in a series of designed gramicidin-like channels of different length using atomistic molecular dynamics simulations. We found that within the studied range of length the osmotic water permeability is independent of pore length. This result is at variance with textbook models, where the relationship is assumed to be linear. Energetic analysis shows that loss of solvation rather than specific water binding sites in the pore form the main energetic barrier for water permeation, consistent with our dynamics results. For this situation, we propose a modified expression for osmotic permeability that fully takes into account water motion collectivity and does not depend on the pore length. Different schematic barrier profiles are discussed that explain both experimental and computational interpretations, and we propose a set of experiments aimed at validation of the presented results. Implications of the results for the design of peptidic channels with desired permeation characteristics are discussed.     

The lipid dependence of melittin action investigated by dual-color fluorescence burst analysis

Dual-color fluorescence-burst analysis was used to study melittin-induced leakage of macromolecules from liposomes of various lipid compositions. To perform dual-color fluorescence-burst analysis, fluorescently labeled size-marker molecules were encapsulated into liposomes, labeled with a second lipid-attached fluorophore. By correlating the fluorescence bursts, resulting from the liposomes diffusing through the detection volume of a dual-color confocal microscope, the distribution of size-marker molecules over the liposomes was determined. It was found that melittin causes leakage via two different mechanisms: 1), For liposomes composed of neutral bilayer-forming lipids, low melittin concentrations induced pore formation with the pore size depending on the melittin concentration. 2), For liposomes containing anionic and/or nonbilayer forming lipids, melittin induced fusion or aggregation of liposomes accompanied by a-specific leakage. Experiments with liposomes prepared from Escherichia coli lipid extracts and intact cells of Lactococcus lactis indicate that both mechanisms are physiologically relevant.     

Dual roles of intermediate filaments in apoptosis

New roles have emerged recently for intermediate filaments (IFs), namely in modulating cell adhesion and growth, and providing resistance to various forms of stress and to apoptosis. In this context, we first summarize findings on the IF association with the cell response to mechanical stress and growth stimulation, in light of growth-related signaling events that are relevant to death-receptor engagement. We then address the molecular mechanisms by which IFs can provide cell resistance to apoptosis initiated by death-receptor stimulation and to necrosis triggered by excessive oxidative stress. In the same way, we examine IF involvement, along with cytolinker participation, in sequential caspase-mediated protein cleavages that are part of the overall cell death execution, particularly those that generate new functional IF protein fragments and uncover neoantigen markers. Finally, we report on the usefulness of these markers as diagnostic tools for disease-related aspects of apoptosis in humans. Clearly, the data accumulated in recent years provide new and significant insights into the multiple functions of IFs, particularly their dual roles in cell response to apoptotic insults.     

An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa

Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.