Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation.

The plant plasma membrane (PM) is an essential barrier between the cell and the external environment, controlling signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols, and phospholipids. The glycosyl inositol phosphoryl ceramides (GIPCs), representing up to 40% of total sphingolipids, are assumed to be almost exclusively in the outer leaflet of the PM.

Structural polymorphism of two CPP: an important parameter of activity.

Despite numerous investigations, the important structural features of Cell Penetrating Peptides (CPPs) remain unclear as demonstrated by the difficulties encountered in designing new molecules. In this study, we focused our interest on Penetratin and Transportan and several of their variants. Penetratin W48F and Penetratin W48F/W56F exhibit a reduced and a complete lack of cellular uptake, respectively; TP07 and TP10 present a similar cellular uptake as Transportan and TP08, TP13 and TP15 display no or weak internalization capacity.

Partial atomic charges of amino acids in proteins.

Using a semiempirical quantum mechanical procedure (FCPAC) we have calculated the partial atomic charges of amino acids from 494 high-resolution protein structures. To analyze the influence of the protein's environment, we considered each residue under two conditions: either as the center of a tripeptide with PDB structure geometry (free) or as the center of 13-16 amino acid clusters extracted from the PDB structure (buried). The partial atomic charges from residues in helices and in sheets were separated.

Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix.

What determines the shape of the allowed regions in the Ramachandran plot? Although Ramachandran explained these regions in terms of 1-4 hard-sphere repulsions, there are discrepancies with the data where, in particular, the alphaR, alphaL, and beta-strand regions are diagonal. The alphaR-region also varies along the alpha-helix where it is constrained at the center and the amino terminus but diffuse at the carboxyl terminus. By analyzing a high-resolution database of protein structures, we find that certain 1-4 hard-sphere repulsions in the standard steric map of Ramachandran do not affect the statistical distributions.

Aromatic side-chain interactions in proteins. Near- and far-sequence His-X pairs.

Several studies have analysed aromatic interactions, involving mostly phenylalanine, tyrosine and tryptophan. Only a few studies have considered histidine as an interacting aromatic residue. An extensive analysis of aromatic His-X interactions is performed here on a data set of 593 PDB structures: 68% of the histidine are involved in aromatic pairs and 1271 non-redundant His-X pairs were analysed.