Model for the interaction of amphiphilic helices with troponin C and calmodulin

Crystals of troponin C are stabilized by an intermolecular interaction that involves the packing of helix A from the N-terminal domain of one molecule onto the exposed hydrophobic cleft of the C-terminal domain of a symmetry related molecule. Analysis of this molecular recognition interaction in troponin C suggests a possible mode for the binding of amphiphilic helical molecules to troponin C and to calmodulin. From the template provided by this troponin C packing, it has been possible to build a model of the contact region of mastoporan as it might be bound to the two Ca2+ binding proteins. A possible binding mode of melittin to calmodulin is also proposed. Although some of the characteristics of binding are similar for the two amphiphilic peptides, the increased length of melittin requires a significant bend in the calmodulin central helix similar to that suggested recently for the myosin light chain kinase calmodulin binding peptide (Persechini and Kretsinger: Journal of Cardiovascular Pharmacology 12:501-512, 1988). Not only are the hydrophobic interactions important in this model, but there are several favorable electrostatic interactions that are predicted as a result of the molecular modeling. The regions of troponin-C and calmodulin to which amphiphilic helices bind are similar to the regions to which the neuroleptic drugs such as trifluoperazine have been predicted to bind (Strynadka and James: Proteins 3:1-17, 1988).     

Theoretical conformational analysis of phospholipids bilayers

We present a computational approach describing the conformation of lipid molecules (1-2-dipalmitoyl-sn-glycero-3 phosphocholine (DPPC)) organized in bilayers. The classical semi-empirical method used in peptide conformational analysis has been extended successfully to lipids. The excellent agreement between our theoretical predictions and recent experimental data on the molecular organization of lipid bilayers suggests that the method could be a valuable tool in the lipid conformational analysis but also in the prediction of orientation and mode of insertion of amphiphilic molecules into the lipid bilayer.     

Physicochemical characterization of α-, β-, and γ-cyclodextrins bioesterified with decanoate chains used as building blocks of colloidal nanoparticles

Nanoparticles of amphiphilic α-, β-, and γ-cyclodextrins were obtained by formulation of cyclodextrins enzymatically transesterified with vinyl decanoate. The product of this synthesis is a mixture of bioesterified cyclodextrins with various degrees of substitution (DS) presenting for a same DS different regio-isomers. In a first step, the efficiency of a MALDI-TOF procedure to characterize the average molecular weight of the derivative bulk mixture was demonstrated by comparing the results with those obtained from complementary NMR and HPLC techniques. In a second step, the ultrastructure of nanoparticles prepared from three different batches of synthesis was investigated and correlated with the average molecular weight and DS of the parent derivative.     

Acetylcholinesterases of the nematode Steinernema carpocapsae. Characterization of two types of amphiphilic forms differing in their mode of membrane association.

We analyzed the molecular forms of acetylcholinesterase (AChE) in the nematode Steinernema carpocapsae. Two major AChEs are involved in acetylcholine hydrolysis. The first class of AChE is highly sensitive to eserine (IC50 = 0.05 microM). The corresponding molecular forms are: an amphiphilic 14S form converted into a hydrophilic 14.5S form by mild proteolysis and two hydrophilic 12S and 7S forms. Reduction of the amphiphilic 14S form with 10 mM dithiothreitol produces hydrophilic 7S and 4S forms, indicating that it is an oligomer of hydrophilic catalytic subunits linked by disulfide bond(s) to a hydrophobic structural element that confers the amphiphilicity to the complex. Sedimentation coefficients suggest that 4S, 7S, 12S forms correspond to hydrophilic monomer, dimer, tetramer and that the 14S form is also a tetramer linked to one structural element. The second class of AChE is less sensitive to eserine (IC50 = 0.1 mM). Corresponding molecular forms are hydrophilic and amphiphilic 4S forms (monomers) and a major amphiphilic 7S form converted into a hydrophilic dimer by Bacillus thuringiensis phosphatidylinositol-specific phospholipase C. This amphiphilic 7S form thus possesses a glycolipid anchor. It appears that Steinernema (a very primitive invertebrate) presents AChEs with two types of membrane association that closely resemble those described for amphiphilic G2 and G4 forms of AChE in more evolved animals.     

Synthesis and characterisation of sulfated amphiphilic alpha-, beta- and gamma-cyclodextrins: application to the complexation of acyclovir

The synthesis of sulfated amphiphilic alpha-, beta- and gamma-cyclodextrins was achieved according to the standard protection-deprotection procedure. The formation of inclusion complexes between the amphiphilic alpha-, beta- and gamma-cyclodextrins and an antiviral molecule, acyclovir (ACV) was investigated by UV-visible spectroscopy (UV-Vis) and electrospray ionisation mass spectrometry (ESIMS). UV-Vis spectroscopy allowed determination of the stoichiometry and stability constants of complexes, whereas ESIMS, a soft ionisation technique, allowed the detection of the inclusion complexes. The results showed that the non-sulfated amphiphilic cyclodextrins exhibit a 1:2 stoichiometry with acyclovir, while sulfated amphiphilic cyclodextrins, except gamma-cyclodextrin, exhibit a 1:1 stoichiometry indicating the loss of one interaction site. Non-covalent interactions between acyclovir and non-sulfated amphiphilic cyclodextrins appear to take place both in the cavity of the cyclodextrin and inside the hydrophobic zone generated by alkanoyl chains. In contrast, in the case of sulfated amphiphilic cyclodextrins, the interactions appear to involve only the hydrophobic region of the alkanoyl chains.     

Molecular dynamics simulations of a lipovitellin-derived amphiphilic beta-sheet homologous to apoB-100 beta-sheets at a hydrophobic decane-water interface

Lipovitellin, an egg-yolk lipoprotein, transports lipids in a pocket surrounded by amphiphilic beta-sheets. Its X-ray structure provides possibilities to study interactions between lipophilic beta-sheets and lipids at the atomic level. Here, we studied a 67-residue-long amphiphilic beta-sheet of lipovitellin previously suggested a suitable working model for studies of the lipid-binding behaviour of amphiphilic beta-sheet regions in apolipoprotein B-100 (apoB-100). We performed four molecular dynamics simulations with different starting configurations to define characteristics of the amphiphilic beta-sheet model at a decane-water interface. In each simulation the model beta-sheet bound keenly to the decane layer via its hydrophobic surface. The structural profiles showed unchanged secondary structure of the beta-sheet during the attachment. Also, aromatic side chains, especially tryptophans and tyrosines, mediated the attachment to the hydrophobic layer and influenced the orientation of the decane molecules that are in contact with the beta-sheet. In conclusion, the present simulations reveal high affinity of a lipovitellin-derived amphiphilic beta-sheet to a hydrophobic decane layer. They lay thereby the basis for further studies of the interaction between amphiphilic beta-sheets and lipids in complex molecular systems, like LDL particles, in which the large apoB-100 is the main protein component.     

Interaction of dopamine and acetylcholine with an amphiphilic resorcinarene receptor in aqueous micelle system

The molecular recognition of neurotransmitters, dopamine and acetylcholine with an amphiphilic resorcinarene receptor was investigated in an aqueous sodium dodecylsulfate (SDS) micelle system by 1H NMR measurements. The interaction distances of these neurotransmitters from the hydrophilic cavity of the amphiphilic receptor were estimated based on the calculation of the ring current shift using the atomic coordinates obtained from molecular dynamics calculation.     

Conversion of the amphiphilic galactosyltransferase from human mammary carcinoma cells to an active hydrophilic enzyme form by limited proteolysis

As analyzed by a phase-separation technique, the Triton X-114 extract of human mammary carcinoma cells (MCF-7 cells) contain an amphiphilic form of galactosyltransferase (UDPgalactose: D-glucose 4-beta-D-galactosyltransferase, EC 2.4.1.22), while the galactosyltransferase activity released by these cells represents a hydrophilic form of the enzyme. When the amphiphilic galactosyltransferase was subjected to limited proteolysis with thermolysin, this treatment generated a hydrophilic form of the enzyme. With respect to Km for UDPgalactose the kinetic data were very similar for the amphiphilic, for the released and the hydrophilic galactosyltransferases produced by proteinase treatment. Differences were detected in electrophoretic and gel chromatographic properties. The hydrophilic enzymes showed a greater electrophoretic mobility on non-denaturing polyacrylamide gels than did the amphiphilic form. On Sepharose 6B column chromatography, the amphiphilic galactosyltransferase appeared to be of higher molecular weight than the hydrophilic enzyme.     

Automated docking of substrates to proteins by simulated annealing

The Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.     

Investigation of antibacterial mode of action for traditional and amphiphilic aminoglycosides

Aminoglycoside represents a class of versatile and broad spectrum antibacterial agents. In an effort to revive the antibacterial activity against aminoglycoside resistant bacteria, our laboratory has developed two new classes of aminoglycoside, pyranmycin and amphiphilic neomycin (NEOF004). The former resembles the traditional aminoglycoside, neomycin. The latter, albeit derived from neomycin, appears to exert antibacterial action via a different mode of action. In order to discern that these aminoglycoside derivatives have distinct antibacterial mode of action, RNA-binding affinity and fluorogenic dye were employed. These studies, together with our previous investigation, confirm that pyranmycin exhibit the traditional antibacterial mode of action of aminoglycosides by binding toward the bacterial rRNA. On the other hand, the amphiphilic neomycin, NEOF004 disrupts the bacterial cell wall. In a broader perspective, it verifies that structurally modified neomycin can exert different antibacterial mode of action leading to the revival of activity against aminoglycoside resistant bacteria.     

Self-assembly of surfactant aqueous solution confined in a Janus amphiphilic nanotube

Abstract

In recent years, Janus amphiphilic nanotubes with complex surfaces have been synthesized. However, the self-assembly behaviour of surfactant solutions confined in a Janus amphiphilic nanotube has not been investigated so far. We performed molecular simulations to investigate the morphologies and phase diagrams of a surfactant confined in Janus amphiphilic nanotube consisting of both hydrophobic and hydrophilic surfaces. We derived a phase diagram of the representative snapshots of equilibrium morphologies. Morphologies that were not observed in the bulk eventuated in confined systems. Moreover, the self-assembled structures were found to be dependent on the spatial confinement. Furthermore, the self-assembled structures confined in hydroneutral and Janus amphiphilic nanotubes were compared. The results suggested that the self-assembled structures confined in the Janus amphiphilic nanotube resembled that confined in the hydroneutral nanotube owing to a strong confinement effect. Further developments in controlling the morphologies and self-assemblies will greatly advance their applications of these materials in nanofluidic devices, or for nanopatterning.     

Functional differentiation of amphiphilic helices of the apolipoproteins by hydrophobic moment analysis

The amphiphilic character of different plasma apolipoproteins was investigated by a combination of established hydrophobicity analysis methods. These methods proved to be powerful in the detection of amphiphilic phospholipid-binding domains. Within this class of lipid-binding domains, lecithin-cholesterol acyltransferase activating and non-activating helices could be differentiated by calculating hydrophobic moments at different angles. We conclude that the hydrophobic characteristics of the different helices determined the mode of lipid binding and the substrate properties of these phospholipid-protein complexes for the lecithin-cholesterol acyltransferase reaction.     

Structural and functional properties of Langmuir films of antibodies based on amphiphilic polyelectrolytes

We optimized the procedure for the formation of Langmuir films of antibodies based on amphiphilic polyelectrolytes and studied the physicochemical and immunochemical properties of the films obtained. Their immunochemical properties were compared with the immunochemical activity of antibodies in Langmuir films without amphiphilic polyelectrolytes and with antibodies adsorbed on the surface of polystyrene and graphite. The efficiency of immune adsorption by the films based on amphiphilic polyelectrolytes was shown to be greater; the affinity of antibodies and surface concentration of their active conformation depended on the type of amphiphilic polyelectrolytes used to obtain the films. We investigated the structure of these films at the surface of highly oriented pyrolytic graphite using the method of atomic force microscopy. Changes in the structure of the films under study caused by the increase of surface pressure were demonstrated.     

Characterisation of a potential biomarker of phospholipidosis from amiodarone-treated rats

A novel and relatively simple analytical method for the separation, characterisation and semi-quantitation of phospholipids (PLs) from extracts of complex biological samples has been developed. This methodology allows PL extracts from cells and tissues to be analysed by liquid chromatography (LC) coupled to electrospray ionisation mass spectrometry (ESI-MS). Complex mixtures of PLs were separated on a high-performance liquid chromatography (HPLC) system using 0.5% ammonium hydroxide in methanol/water/hexane/formate mixture with UV detection at 205 nm. Identification and structural characterisation of molecular species were carried out utilising ESI-MS and MS/MS in the negative ion mode.The abnormal accumulation of PLs (phospholipidosis) was induced in male Sprague-Dawley rats by administration of the cationic amphiphilic drug (CAD), amiodarone. Analysis of the PL profile of liver and lung tissues, lymphocytes and serum from treated rats was carried out using this analytical procedure (LC-ESI/MS/MS). Differences in PL profiles between treated and untreated animals were highlighted by principal component analysis (PCA). This led to the selection of a potential metabolic marker of phospholipidosis (PLD) identified as a lyso-bis-phosphatidic acid (LBPA) derivative, also known as bis(monoglycero)phosphate (BMP). This PL was absent in control animals but was present in quantifiable amounts in all samples from amiodarone-treated rats.     

Monitoring of detergent binding to amphiphilic proteins by means fo micelles containing the hydrophobic dye Sudan Black B

A simple method for detecting micellar binding of Triton X-100 to amphiphilic proteins is described. The hydrophobic dye Sudan Black B is incorporated into Triton micelles. Binding of the coloured micelles to serum apoliproteins, as well as to amphiphilic proteins, of erythrocyte and fat globule membranes renders these visible as dark bands after sucrose density gradient centrifugation. In contrast, the hydrophilic proteins present in lipoprotein-free serum do not show detergent binding. The method does not permit accurate quantification of detergent binding, but may serve as a pilot procedure for initial detection of amphiphilic proteins and for monitoring their isolation from crude solubilized membrane material. The sensitivity of the assay corresponds to that obtained with [³H]Triton X-100.