Physico-chemical properties of prostaglandins and related pharmacological compounds. A theoretical study on conformational related activity

Computational study of nisin interaction with model membrane

Nisin is a 34-residue lantibiotic widely used as food preservative. Its mode of action on the bacterial cytoplasmic membrane is unclear. It should form ion channels but a molecular description of the interaction between nisin and phospholipids is lacking. The interactions between nisin and a membrane and the influence of phospholipids are here analysed by molecular modelling. The NMR structures of nisin in a micellar environment were previously determined (Van den Hooven et al., Eur. J. Biochem. 235 (1996) 382-393) Those structures were used to start with. They were refined by running a Monte Carlo procedure at a model lipid/water interface. It was shown that nisin is adsorbing onto the interface, with its N-terminal moiety more deeply inserted in lipids than the C-end, indicating distinct hydrophobic properties of the N- and C-domains. Therefore, we suggest that the N-terminal part is implied in the insertion of nisin in lipids, while the C-terminal moiety could be involved in the initial interaction with the membrane surface. Modelling the interaction of nisin with different neutral or anionic phospholipids shows that it disturbs the lipid organisation. The disturbance is maximal with phosphatidylglycerol. In this system, nisin curves the surface of phosphatidylglycerol layer round suggesting it could induce micelle formation. This could be a preliminary step to pore formation. It suggests that phosphatidylglycerol could have a direct action on nisin insertion and on ion channel formation. Appearance of a curvature also agrees with the 'wedge model' proposed in the literature for the nisin pore formation.

Insulinotropic action of (2S)-2-benzyl-3-(cis-hexahydro-2-isoindolinylcarbonyl) propionate. II. Ionophoretic and conformational aspects

1. The non-sulphonylurea insulinotropic agent sodium (2S)-2-benzyl-3-(cis-hexahydro-2-isoindolinylcarbonyl) propionate (KAD-1229) was found to display calcium ionophoretic activity in an artificial membrane model. 2. Conformation analysis indicated that a complex between calcium and KAD-1229, with a 1:2 stoichiometry, indeed displays favourable attributes for ionophoretic activity across a hydrophobic environment. 3. It is speculated that the ionophoretic property of KAD-1229 might participate to the remodelling of cationic fluxes evoked by this insulinotropic agent in pancreatic islet cells.

Helix-helix interactions in reconstituted high-density lipoproteins

In this work we calculated the ionic interactions between adjacent amphipathic helices of apo A-I and apo A-IV. The calculation of the electrostatic potential around the helices helps identify the charged residues susceptible to form salt bridges between adjacent helices. An estimation of the stability of the different pairs of helices is derived from the calculation of the energy of interaction between contiguous helices at a water/lipid interface after energy minimization. The most stable energetic conformation corresponds to the 17-residue helices oriented anti-parallel and separated by a stretch of 5 residues in an extended beta-strand conformation, as calculated through the 'stereo alphabet' calculation procedure. In a pair of helices, the hydrophobic faces are directed towards the lipid core of the discoidal phospholipid-apolipoprotein complex and the hydrophobic lipid-protein interactions are major determinants for the stability of the complex. Interactions between polar residues located on the opposite face of the helix and water molecules can also contribute to the overall energy of the system. Finally, salt bridge formation between residues of opposite charge along the edge of the helical segments contribute to the cooperativity of the phospholipid-apolipoprotein complex formation. The mode of assembly of the amphipathic helical repeats of the apolipoproteins around the edge of a discoidal complex is therefore determined both by the hydrophobic character of the residues and by the charge complementarity along the edge of the helices which increases the structural stability and determines the relative orientation of the helices.(ABSTRACT TRUNCATED AT 250 WORDS)

Proposition of a three-dimensional representation of the constitutive protein of the hepatitis B surface antigen particles

Hepatitis B surface antigen particles are composed of the major viral envelope protein, the S protein, embedded into a lipid shell. The description of the folding of this protein within the particle membrane could provide helpful information for replacing surface-exposed protein domains by foreign sequences without destabilizing the particle structure. Since the crystallization of the protein in its lipid environment remains inaccessible in the near future, alternative approaches had to be envisaged. We combine here the available experimental structural and topological data with a conformational procedure to identify membrane-associated domains of the HBsAg protein and to propose a three-dimensional description of their assembly within the particle membrane. The proposed protein structure is composed of four membrane-spanning helices and an amphipatic helix located on the inner surface membrane. The transmembrane helices are assembled into a highly hydrophobic complex in which no access to the water environment is allowed. The approach could be extended to other membrane-associated proteins.

Common prevalence of alanine and glycine in mobile reactive centre loops of serpins and viral fusion peptides: do prions possess a fusion peptide?

Serpin reactive centre loops and fusion peptides released by proteolytic cleavage are particularly mobile. Their amino acid compositions reveal a common and unusual abundance of alanine, accompanied by high levels of glycine. These two small residues, which are not simultaneously abundant in stable helices (standard or transmembrane), probably play an important role in mobility. Threonine and valine (also relatively small amino acids) are also abundant in these two kinds of peptides. Moreover, the known 3D structures of an uncleaved serpin reactive centre and a fusion peptide are strikingly similar. Such sequences possess many small residues and are found in several signal peptides and in PrP, a protein associated with spongiform encephalopathies and resembling virus envelope proteins. These properties may be related to the infection mechanisms of these diseases.

Accessibility of aminoglycosides, isolated and in interaction with phosphatidylinositol, to water. A conformational analysis using the concept of molecular hydrophobicity potential

The mode of interaction between aminoglycosides and negatively charged phospholipids plays a critical role in the inhibition of lysosomal phospholipases induced by these antibiotics and therefore in their nephrotoxicity. Previous works suggested that accessibility of the drug interacting with phospholipids to water could be crucial in this respect. We have used the concept of molecular hydrophobicity potential described by Brasseur [J Med Chem 266: 16120-16127, 1991] to visualize the hydrophobic and hydrophilic envelopes around aminoglycosides assembled with phosphatidylinositol molecules, and to obtain a three-dimensional representation of the complex formed. Using a series of different aminoglycosides, we showed that molecules with a lower inhibitory potential (gentamicin B, amikacin and isepamicin) are surrounded by both hydrophobic and hydrophilic envelopes whereas aminoglycosides which are more inhibitory are enveloped primarily by either hydrophilic (kanamycin A or B) or hydrophobic (gentamicin C1a) envelopes. This approach, which is here for the first time applied to the study of drug-lipid complexes, could help in the better understanding of the molecular mechanism of lysosomal phospholipase inhibition induced by aminoglycosides.

Molecular modeling of the amphipathic helices of the plasma apolipoproteins

In this paper we propose a classification of the amphipathic helical repeats occurring in the plasma apolipoprotein sequences. It is based upon the calculation of the molecular hydrophobicity potential around the helical segments. The repeats were identified using a new autocorrelation matrix, based upon similarities of hydrophobic and hydrophilic properties of the amino acid residues within the apolipoprotein sequences. The helices were constructed by molecular modeling, the molecular hydrophobicity potential was calculated, and isopotential contour lines drawn around the helices yielded a three-dimensional visualization of the hydrophobicity potential. Two classes of apolipoproteins could be differentiated by comparing the hydrophobic angles obtained by projection of the isopotential contour lines on a plane perpendicular to the long axis of the helix. The isopotential contour lines around apo AI, AIV, and E are more hydrophilic than hydrophobic, whereas they are of similar intensity for apo AII, CI, and CIII. In both cases discoidal lipid-protein complexes are generated, with the amphipathic helices around the edge of the lipid core. The long axis of the helices is oriented parallel to the phospholipid acyl chains and the hydrophilic side of the helix toward the aqueous phase. As a result of the differences in hydrophobicity potential, the contact between the hydrophobic side of the helices and the phospholipid acyl chains is larger for apo AII, CI, and CIII than for the other apolipoproteins. This might account for the greater stability of the discoidal complexes generated between phospholipids and these apoproteins.

A conformational analysis study of the interaction of amiodarone and cholesterol with lysophosphatidylcholine

The spatial configuration of amiodarone (in both its protonated and neutral forms) and a hydroxylated analog was studied using conformational analysis in a simulated membrane-water environment. The three compounds and cholesterol were studied as isolated molecules and in interaction with lysophosphatidylcholine. The association of the molecules with lysophosphatidylcholine was further characterized by incorporation in a phosphatidylcholine matrix. Calculation of the mean interaction energy, the surface charge density and the hydrophilic and hydrophobic mean molecular areas showed that the protonated form of amiodarone, and to a lesser extent cholesterol form a stable association with lysophosphatidylcholine. This association was further stabilized when incorporated into a phosphatidylcholine matrix so that the mean interaction energy increased to -96.1 kJ/mol (i.e. 60% higher than the mean lipid-lipid energy of interaction). Lysophosphatidylcholine was shown to possess a cone-shaped structure whilst amiodarone was shown to be in the form of an inverted cone. This association of the two cones forms a stable cylindrical structure.