Impacts of the carbonyl group location of ester bond on interfacial properties of sugar-based surfactants: experimental and computational evidences.

Interfacial properties of surfactants are dependent on the conformation adopted by the hydrophilic headgroup or/and the hydrophobic tail at the boundary limit of two immiscible phases. Here, we demonstrate the impacts of the carbonyl group (-CO-) location of the ester bond of sugar-based surfactants by comparing some properties of two closely related esters, octyl glucuronate and glucose octanoate, at the air-water interface. The carbonyl group location influences the rate and extent of interfacial adsorption and the rheology properties of sugar esters at the air-water interface, which were evaluated by dynamic surface tension and complex surface viscoelastic measurements.

Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling.

Background: Lipocalins are widely distributed in nature and are found in bacteria, plants, arthropoda and vertebra. In hematophagous arthropods, they are implicated in the successful accomplishment of the blood meal, interfering with platelet aggregation, blood coagulation and inflammation and in the transmission of disease parasites such as Trypanosoma cruzi and Borrelia burgdorferi. The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure.

Tilted peptides: a structural motif involved in protein membrane insertion?

Tilted peptides are short hydrophobic protein fragments characterized by an asymmetric distribution of their hydrophobic residues when helical. They are able to interact with a hydrophobic/hydrophilic interface (such as a lipid membrane) and to destabilize the organized system into which they insert. They were detected in viral fusion proteins and in proteins involved in different biological processes involving membrane insertion or translocation of the protein in which they are found.

Lipid-destabilizing properties of the hydrophobic helices H8 and H9 from colicin E1.

Colicins are toxic proteins produced by Escherichia coli that must cross the membrane to exert their activity. The lipid insertion of their pf domain is linked to a conformational change which enables the penetration of a hydrophobic hairpin. They provide useful models to more generally study insertion of proteins, channel formation and protein translocation in and across membranes.

Tilted properties of the 67-78 fragment of alpha-synuclein are responsible for membrane destabilization and neurotoxicity.

Alpha-synuclein is a 140 residue protein associated with Parkinson's disease. Intraneural inclusions called Lewy bodies and Lewy neurites are mainly composed of alpha-synuclein aggregated into amyloid fibrils. Other amyloidogenic proteins, such as the beta amyloid peptide involved in Alzheimer's disease and the prion protein (PrP) associated with Creuztfeldt-Jakob's disease, are known to possess "tilted peptides".

Mode of membrane interaction and fusogenic properties of a de novo transmembrane model peptide depend on the length of the hydrophobic core.

Model peptides composed of alanine and leucine residues are often used to mimic single helical transmembrane domains. Many studies have been carried out to determine how they interact with membranes. However, few studies have investigated their lipid-destabilizing effect.

Tilted peptides: the history.

Nature has selected peptide motifs for protein functions. It is clear that specific sequence motifs can identify families of enzymes. These sequence motifs are one dimensional signatures and nature has also developed two dimension motifs which cannot be read in the one dimension of sequence language but can be detected in the three dimensional properties of a secondary structure.

The N-terminal 12 residue long peptide of HIV gp41 is the minimal peptide sufficient to induce significant T-cell-like membrane destabilization in vitro.

Here, we predicted the minimal N-terminal fragment of gp41 required to induce significant membrane destabilization using IMPALA. This algorithm is dedicated to predict peptide interaction with a membrane. We based our prediction of the minimal fusion peptide on the tilted peptide theory.

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.

Aromatic side-chain interactions in proteins: near- and far-sequence Tyr-X pairs.

In the present study, an extensive analysis of the aromatic Tyr-X interactions is performed on a data set of 593 PDB structures, X being Phe, His, Tyr, and Trp. The nonredundant Tyr-X pairs (2645) were retained and separated by both the residue distance in the sequence and the secondary structures they bridge. Similar to the Phe-X and His-X pairs, the far-sequence Tyr-X pairs (X partner > five apart in the sequence: 74%) show comparable secondary structures and conformers for either type of X partner, in contrast with the near-sequence Tyr-X pairs (26%).

Distribution of hydrophobic residues is crucial for the fusogenic properties of the Ebola virus GP2 fusion peptide.

The lipid-destabilizing properties of the N-terminal domain of the GP2 of Ebola virus were investigated. Our results suggest that the domain of Ebola virus needed for fusion is shorter than that previously reported. The fusogenic properties of this domain are related to its oblique orientation at the lipid/water interface owing to an asymmetric distribution of the hydrophobic residues when helical.

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.

Insertion of X-ray structures of proteins in membranes.

Few structures of membrane proteins are known and their relationships with the membrane are unclear. In a previous report, 20 X-ray structures of transmembrane proteins were analyzed in silico for their orientation in a 36A-thick membrane [J. Mol.

A fast method to predict protein interaction sites from sequences.

A simple method for predicting residues involved in protein interaction sites is proposed. In the absence of any structural report, the procedure identifies linear stretches of sequences as "receptor-binding domains" (RBDs) by analysing hydrophobicity distribution. The sequences of two databases of non-homologous interaction sites eliciting various biological activities were tested; 59-80 % were detected as RBDs.

Tilted peptides: a motif for membrane destabilization (hypothesis).

Cell life depends on the dynamics of molecular processes: molecule folding, organelle building and transformations involving membrane fusion, protein activation and degradation. To carry out these processes, the hydrophilic/hydrophobic interfaces of amphipathic systems such as membranes and native proteins must be disrupted. In the past decade, protein fragments acting in the disruption of interfaces have been evidenced: they are named the tilted or oblique peptides.

IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies.

The lipid bilayer is crucial for the folding of integral membrane proteins. This article presents an empirical method to account for water-lipid interfaces in the insertion of molecules interacting with bilayers. The interactions between the molecule and the bilayer are described by restraint functions designed to mimic the membrane effect.