Geometrical Membrane Curvature as an Allosteric Regulator of Membrane Protein Structure and Function

Transmembrane proteins are embedded in cellular membranes of varied lipid composition and geometrical curvature. Here, we studied for the first time the allosteric effect of geometrical membrane curvature on transmembrane protein structure and function. We used single-channel optical analysis of the prototypic transmembrane β-barrel α-hemolysin (α-HL) reconstituted on immobilized single small unilamellar liposomes of different diameter and therefore curvature. Our data demonstrate that physiologically abundant geometrical membrane curvatures can enforce a dramatic allosteric regulation (1000-fold inhibition) of α-HL permeability. High membrane curvatures (1/diameter ∼1/40 nm⁻¹) compressed the effective pore diameter of α-HL from 14.2 ± 0.8 Å to 11.4 ± 0.6 Å. This reduction in effective pore area (∼40%) when combined with the area compressibility of α-HL revealed an effective membrane tension of ∼50 mN/m and a curvature-imposed protein deformation energy of ∼7 k_BT. Such substantial energies have been shown to conformationally activate, or unfold, β-barrel and α-helical transmembrane proteins, suggesting that membrane curvature could likely regulate allosterically the structure and function of transmembrane proteins in general.     

Directed evolution of colE1 plasmid replication compatibility: a fast tractable tunable model for investigating biological orthogonality

Plasmids of the ColE1 family are among the most frequently used in molecular biology. They were adopted early for many biotechnology applications, and as models to study plasmid biology. Their mechanism of replication is well understood, involving specific interactions between a plasmid encoded sense-antisense gene pair (RNAI and RNAII). Due to such mechanism, two plasmids with the same origin cannot be stably maintained in cells—a process known as incompatibility. While mutations in RNAI and RNAII can make colE1 more compatible, there has been no systematic effort to engineer new compatible colE1 origins, which could bypass technical design constraints for multi-plasmid applications. Here, we show that by diversifying loop regions in RNAI (and RNAII), it is possible to select new viable colE1 origins compatible with the wild-type one. We demonstrate that sequence divergence is not sufficient to enable compatibility and pairwise interactions are not an accurate guide for higher order interactions. We identify potential principles to engineer plasmid copy number independently from other regulatory strategies and we propose plasmid compatibility as a tractable model to study biological orthogonality.     

The effects of dominance,species ranking and species matching on some similarity indices

Abstract. The performance of certain indices of sample similarity was explored with respect to variation in species matching, species ranking and dominance of simulated samples. An index of similarity is suggested which accounts for variation in species matching and ranking rather than for differences in dominance.     

BAR domains, amphipathic helices and membrane-anchored proteins use the same mechanism to sense membrane curvature

The internal membranes of eukaryotic cells are all twists and bends characterized by high curvature. During recent years it has become clear that specific proteins sustain these curvatures while others simply recognize membrane shape and use it as “molecular information” to organize cellular processes in space and time. Here we discuss this new important recognition process termed membrane curvature sensing (MCS). First, we review a new fluorescence-based experimental method that allows characterization of MCS using measurements on single vesicles and compare it to sensing assays that use bulk/ensemble liposome samples of different mean diameter. Next, we describe two different MCS protein motifs (amphipathic helices and BAR domains) and suggest that in both cases curvature sensitive membrane binding results from asymmetric insertion of hydrophobic amino acids in the lipid membrane. This mechanism can be extended to include the insertion of alkyl chain in the lipid membrane and consequently palmitoylated and myristoylated proteins are predicted to display similar curvature sensitive binding. Surprisingly, in all the aforementioned cases, MCS is predominantly mediated by a higher density of binding sites on curved membranes instead of higher affinity as assumed so far. Finally, we integrate these new insights into the debate about which motifs are involved in sensing versus induction of membrane curvature and what role MCS proteins may play in biology.     

Taxonomic distinctness indices for discriminating patterns in freshwater rotifer assemblages

Taxonomic distinctness indices measure the taxonomic relatedness among species and have been used for environmental assessment to detect disturbed habitats. This is the first application of the Average Taxonomic Distinctness (Δ⁺) and Variance in Taxonomic Distinctness (Λ⁺) indices to the presence/absence data of rotifer communities to examine their sensitiveness in discriminating perturbed environments. The 26 Greek lakes studied spanned a wide range of morphological and physical–chemical characteristics. Δ⁺ was significantly correlated (P < 0.05) with maximum depth, salinity and trophic state, while Λ⁺ was correlated only with salinity. The index Δ⁺ identified lakes characterized by periods of increased salinity. Communities in these lakes were less diverse, consisting of more closely related species as seen by the reduced number of families than other lakes with similar species richness. Lakes identified by Λ⁺ had a higher community distinctness than expected due to the overrepresentation of the family Brachionidae; they were also characterized by periods of water-level fluctuations. Both indices were unaffected by sampling effort in terms of number of species and sampling visits; whereas Shannon diversity index (H′) was correlated to species number. Also, based on the randomization test, the taxonomic distinctness indices differentiated lakes anthropogenically disturbed based on the expected patterns of diversity of the area.

     

Hierarchical analysis of the relationship between spatial distribution and abundance of epiphytic lichens (Mt. Olympos-Greece)

The relationship between distribution and abundance of epiphytic lichens on five different substrates (Fagus sylvatica, Pinus nigra, Quercus coccifera, Pinus heldreichii and Quercus pubescens) has been studied. For the first three substrates the above relationship has been studied hierarchically. It was concluded that this relationship is partly represented by the core-satellite distribution. This abundance-distribution pattern could probably be explained by more than one hypothesis and it is probably related with the life strategies of lichen species.     

Spatial distribution and density dependent growth and flowering of Asphodelus aestivus Brot.

Distribution patterns of A. aestivus at four different sites of a degraded mediterranean-type ecosystem (asphodel desert), Thessally, Greece, have been studied. A first order spatial structure was identified at small block sizes and was related to asexual reproduction, a second order structure, at large block sizes, was related to sexual reproduction. Spatial distribution of A. aestivus was associated with soil depth while ecological neighbourhood was discussed in relation to degradation phenomena, especially erosion. Density dependent growth of aboveground biomass and flowering has also been explored. Self-thinning was not detected, whereas the percentage of plants flowering decreases linearly with density and this was attributed to competition for nutrients. A reciprocal equation describes the growth of the aboveground biomass with time. A two-sided competition was displayed by initial plant weight, while the rate of growth of the aboveground biomass was proved independent of density.