Modulation of binding properties of amphiphilic DNA containing multiple dodecyl phosphotriester linkages to lipid bilayer membrane

DNA is a promising functional molecule to modify and design lipid membrane functions. In order to use DNA in a hydrophilic–hydrophobic interface including lipid membrane, we have developed an amphiphilic DNA having dodecyl phosphotriester linkages (dod-DNA). Herein, we report the binding of a series of amphiphilic dod-DNAs to the lipid bilayer membrane. Surface plasmon resonance (SPR) assay and fluorescent microscopy showed that dod-DNA having three dodecyl groups at each end strongly bound to lipid membrane due to the slow dissociation rate and the dod-DNA can be used as a linear template for molecular arrangement on the membrane surface.     

Adsorption of monovalent cations to bilayer membranes containing negative phospholipids.

The electrophoretic mobilities of multilamellar phosphatidylserine vesicles were measured in solutions containing monovalent cations, and the xi potentials, the electrostatic potentials at the hydrodynamic plane of shear, were calculated from the Helmholtz--Smoluchowski equation. In the presence of 0.1 M lithium, sodium, ammonium, potassium, rubidium, cesium, tetraethylammonium, and tetramethylammonium chloride, the xi potentials were -60, -62, -72, -73, -77, -80, -82, and -91 mV, respectively. Similar results were obtained with phosphatidylglycerol vesicles; different results were obtained with cardiolipin, phosphatidylinositol, and phosphatidic acid vesicles. The phosphatidylserine results are interpreted in terms of the Stern equation, a combination of the Gouy equation from the theory of the diffuse double layer, the Boltzmann relation, and the Langmuir adsorption isotherm. Evidence is presented that suggests the hydrodynamic plane of shear is 2 A from the surface of the membrane in solutions containing the alkali metal cations. With this assumption, the intrinsic association constants of the above monovalent cations with phosphatidylserine are 0.8, 0.6, 0.17, 0.15, 0.08, 0.05, 0.03, and 0 M-1, respectively. The validity of this approach was tested in two ways. First, the xi potentials of vesicles formed from mixtures of phosphatidylserine and a zwitterionic lipid, phosphatidylcholine, were measured in solutions containing different concentrations of sodium. All the data could be described by the Stern equation if the "relaxation" of the ionic atmosphere, which is predicted by classic electrostatic and hydrodynamic theory to occur at low salt concentrations and high potentials, was circumvented by using only large (diameter greater than 13 micrometers) vesicles for these measurements. Second, the fluorescent probe 2-(p-toluidinyl)naphthalene-6-sulfonate was used to estimate the potential at the surface of phosphatidylserine and phosphatidylglycerol vesicles sonicated in 0.1 M NaCl. Reasonable agreement with the predicted values of the surface potential was obtained.     

Structure of polymerizable lipid bilayers. V. Synthesis, bilayer structure and properties of diacetylenic ether and ester lipids.

Four diacetylenic phosphatidylcholines (PC's) have been synthesized and the structures of bilayers of these lipids have been determined at low resolution by low-angle X-ray diffraction. The PC's all have 18-carbon chains but differ with respect to the ether/ester linkage at the sn-1 and sn-2 positions and the relative position of the diacetylene moiety: diester-PC (1): 1,2-bis(octadeca-4',6'-diynoyl)-sn-glycero-3-phosphocholine diester-PC (2): 1-(octadeca-4',6'-diynoyl)-2-(octadeca-5',7'-diynoy l)-sn- glycero-3-phosphocholine diester-PC (3): 1,2-bis(octadeca-8',10'-diynoyl)-sn-glycerol-3-phosphocholin e diether-PC (4): 1-O-(octadeca-4',6'-diynyl)-2-O-(octadeca-5",7"-din yl)-sn- glycero-3-phosphocholine Only (1) exhibits the typical bilayer profile, whereas (2), (3) and (4) show evidence of interdigitation and/or significant disorder. Only (1) polymerized effectively upon illumination with 254 nm light, turning deep blue in seconds, indicating the formation of long, well-ordered polydiacetylenic structures. Liposomes of these derivatives were tested for permeability by osmotic swelling. Polymerized liposomes of (1) underwent osmotic swelling with urea, glycerol, and acetamide more rapidly than did liposomes of stearoyl-oleoyl-PC, but the initial rates of osmotic swelling of polymerized liposomes of (1) were 3-10-times lower than those of unpolymerized liposomes of (1). Blue polymerized multilayer samples of (1) exhibited an irreversible thermochromic transition to red at approx. 40 degrees C. Differential scanning calorimetry with liposome suspensions of (1) revealed an endotherm at 28.3 degrees C with a transition enthalpy of 40 J/g. PC (1) is a potentially useful diacetylenic lipid which exhibits facile, complete polymerization and a bilayer thickness comparable to that of biomembrane lipids.     

Permeability of bilayer phospholipid membranes to superoxide oxygen radicals

Lecithin monolayer liposomes (1000 A in diameter) loaded with cytochrome c were placed into the external solution, in which O2 superoxide radicals were regenerated by the xanthine-xanthine oxidase system. The penetration of superoxide radicals across the liposomal membranes was followed by cytochrome c reduction in the interval volume of the liposomes. The effects of lipid membrane modifiers and temperature on this process were investigated. The results obtained were used for calculation of the permeability coefficients of bilayer lipid membranes for O(2) (P'O(2) = (7.6 +/- 0.3) . 10(-8) cm . s-1) or HO . 2(P'HO(2) = 4.9 x 10(-4) cm . s-1). The effect of the transmembrane electric potential (concentration gradient of H+, valinomycin) on the permeability of liposomal membranes for the superoxide radical was studied. The superoxide radical was down to penetrate across the bilayer lipid membranes in an unloaded state. Using an intramolecular cholesterol-amphotericin B-complex, the superoxide radicals were shown to penetrate across the bilayer lipid membranes, predominantly via the anionic channels.     

Adsorption of divalent cations to bilayer membranes containing phosphatidylserine

The Stern equation, a combination of the Langmuir adsorption isotherm, the Boltzmann relation, and the Grahame equation from the theory of the diffuse double layer, provides a simple theoretical framework for describing the adsorption of charged molecules to surfaces. The ability of this equation to describe the adsorption of divalent cations to membranes containing brain phosphatidylserine (PS) was tested in the following manner. Charge reversal measurements were first made to determine the intrinsic 1:1 association constants of the divalent cations with the anionic PS molecules: when the net charge of a PS vesicle is zero one-half of the available sites are occupied by divalent cations. The intrinsic association constant, therefore, is equal to the reciprocal of the divalent cation concentration at which the mobility of a PS vesicle reverses sign. The Stern equation with this association constant is capable of accurately describing both the zeta potential data obtained with PS vesicles at other concentrations of the divalent cations and the data obtained with with vesicles formed from mixtures of PS and zwitterionic phospholipids. Independent measurements of the number of ions adsorbed to sonicated PS vesicles were made with a calcium-sensitive electrode. The results agreed with the zeta potential results obtained with multilamellar vesicles. When membranes are formed at 20 degrees C in 0.1 M NaCl, the intrinsic 1:1 association constants of Ni, Co, Mn, Ba, Sr, Ca, and Mg with PS are 40, 28, 25, 20, 14, 12, and 8 M-1, respectively.     

Properties of lipid bilayer membranes made from lipids containing phytanic acid

Besides the preparation of phytanic acid (3,7,11,15-tetramethylhexadecylic acid) according to the Dumas-Stass reaction, the synthesis of four different lipids containing phytanic acid residues is described. Diphytanoyl phophatidylcholine was systhesized beginning from glycerylphosphorylcholine, whereas the other lipids, diphytanoyl phosphatidylethanolamine, diphytanoyl phosphatidylserine and monophytanoyl glyceride were prepared by total synthesis.Some properties of lipid bilayer membranes made from the lipids containing phytanic acid were investigated. The specific capacity of these membranes was measured. Its value of approximately 400 nF cm^?2 was found to be similar to the value of membranes from lipids with unbranched fatty acid residues. Charge pulse experiments were performed using dipicrylamine as a molecular probe of membrane structure. The results were discussed on the basis of a higher viscosity of the membranes from lipids containing phytanic acid residues compared with unbranched fatty acid residues.     

Computation of mixed phosphatidylcholine-cholesterol bilayer structures by energy minimization.

The energetically preferred structures of dimyristoylphosphatidylcholine (DMPC)-cholesterol bilayers were determined at a 1:1 mole ratio. Crystallographic symmetry operations were used to generate planar bilayers of cholesterol and DMPC. Energy minimization was carried out with respect to bond rotations, rigid body motions, and the two-dimensional lattice constants. The lowest energy structures had a hydrogen bond between the cholesterol hydroxyl and the carbonyl oxygen of the sn-2 acyl chain, but the largest contribution to the intermolecular energy was from the nonbonded interactions between the flat alpha surface of cholesterol and the acyl chains of DMPC. Two modes of packing in the bilayer were found; in structure A (the global minimum), unlike molecules are nearest neighbors, whereas in structure B (second lowest energy) like-like intermolecular interactions predominate. Crystallographic close packing of the molecules in the bilayer was achieved, as judged from the molecular areas and the bilayer thickness. These energy-minimized structures are consistent with the available experimental data on mixed bilayers of lecithin and cholesterol, and may be used as starting points for molecular dynamics or other calculations on bilayers.     

RNA base-amino acid interaction strengths derived from structures and sequences.

We investigate RNA base-amino acid interactions by counting their contacts in structures and their implicit contacts in various functional sequences where the structures can be assumed to be preserved. These frequencies are cast into equations to extract relative interaction energetics. Previously we used this approach in considering the major groove interactions of DNA, and here we apply it to the more diverse interactions observed in RNA. Structures considered are the three different tRNA synthetase complexes, the U1A spliceosomal protein with an RNA hairpin and the BIV TAR-Tat complex. We use binding data for the base frequencies for the seryl, aspartyl and glutaminyl tRNA-synthetase and U1 RNA-protein complexes. We compare with the previously reported DNA major groove peptide contacts the results for atoms of RNA bases, usually in the major groove. There are strong similarities between the rank orders of interacting bases in the DNA and the RNA cases. The apparent strongest RNA interaction observed is between arginine and guanine which was also one of the strongest DNA interactions. The similar data for base atomic interactions, whether base paired or not, support the importance of strong atomic interactions over local structure considerations, such as groove width and alpha-helicity.     

Modulation of the bilayer to hexagonal phase transition of phosphatidylethanolamines by acylglycerols

The effect of mono-, di- and triacylglycerols on the bilayer to hexagonal phase (HII) transition was studied by differential scanning calorimetry and 31P-NMR spectroscopy. The acylglycerols were mixed with either dielaidoylphosphatidylethanoline or with 1-palmitoyl-2-oleoylphosphatidylethanolamine. Acylglycerols of lauric, oleic and stearic acids were utilized. All of the acylglycerols lowered the bilayer to HII phase transition temperature. Diacylglycerols were much better HII phase promoters than monoacylglycerols while triacylglycerols were the most potent bilayer phase destabilizers. Fatty acid composition generally had less of an effect except for the monoacylglycerols where bilayer destabilization increased from monolaurin to monostearin to monoolein. The most marked difference in behaviour resulting from changes in the fatty acid composition of the acylglycerol occurred with tristearin. This was the only acylglycerol which decreased the bilayer to HII phase transition temperature only below a mol fraction of 0.005. Above this mol fraction, further addition of tristearin had no effect on the bilayer to HII phase transition. These results suggest that the tristearin has limited solubility in phosphatidylethanolamine.     

Modulation of a gated ion channel admittance in lipid bilayer membranes.

A future class of amperometric biosensors may utilize gated ion channels such as acetylcholine and glutamate receptors as chemical detection components. In this study, bilayer lipid membranes containing voltage-dependent anion channels (VDAC) were used to model an ion-channel-based biosensor which could continuously monitor AC amperometric changes resulting from induced changes in channel conductance. The in-phase and quadrature components of the induced alternating membrane current were monitored as a function of the applied DC offset voltage which was superimposed on the sinusoidal test voltage. The accuracy and sensitivity of the AC-measured VDAC response was dependent on the magnitude of the AC test voltage relative to the DC offset necessary for channel closure. The VDAC channel appears to be a suitable model protein for AC impedance-based biosensor fabrication.     

Transgenic maize plants of tropical and subtropical genotypes obtained from calluses containing organogenic and embryogenic-like structures derived from shoot tips

A highly efficient system for the production of transgenic maize plants starting from tropical and subtropical genotypes was developed. The method is based on particle bombardment of organogenic calli derived from shoot tips. Six tropical maize genotypes were successfully transformed and regenerated using this protocol. Genetic transformation was confirmed by Southern blot analysis of T0 plants and segregation analysis of the resistance marker in the T1 progeny. Plant transfer into the greenhouse was 100% successful, and no problems of fertility were observed with the transgenic plants produced with this transformation protocol.     

Elastic deformation and failure of lipid bilayer membranes containing cholesterol.

Giant bilayer vesicles were reconstituted from several lipids and lipid/cholesterol (CHOL) mixtures: stearolyloleoylphosphatidylcholine (SOPC), bovine sphingomyelin (BSM), diarachidonylphosphatidylcholine (DAPC), SOPC/CHOL, BSM/CHOL, DAPC/CHOL, and extracted red blood cell (RBC) lipids with native cholesterol. Single-walled vesicles were manipulated by micropipette suction and several membrane material properties were determined. The properties measured were the elastic area compressibility modulus K, the critical areal strain alpha c, and the tensile strength tau lys, from which the failure energy or membrane toughness Tf was calculated. The elastic area expansion moduli for these lipid and lipid/cholesterol bilayers ranged from 57 dyn/cm for DAPC to 1,734 dyn/cm for BSM/CHOL. The SOPC/CHOL series and RBC lipids had intermediate values. The results indicated that the presence of cholesterol is the single most influential factor in increasing bilayer cohesion, but only for lipids where both chains are saturated, or mono- or diunsaturated. Multiple unsaturation in both lipid chains inhibits the condensing effect of cholesterol in bilayers. The SOPC/CHOL system was studied in more detail. The area expansion modulus showed a nonlinear increase with increasing cholesterol concentration up to a constant plateau, indicating a saturation limit for cholesterol in the bilayer phase of approximately 55 mol% CHOL. The membrane compressibility was modeled by a property-averaging composite theory involving two bilayer components, namely, uncomplexed lipid and a lipid/cholesterol complex of stoichiometry 1/1.22. The area expansion modulus of this molecular composite membrane was evaluated by a combination of the expansion moduli of each component scaled by their area fractions in the bilayer. Bilayer toughness, which is the energy stored in the bilayer at failure, showed a maximum value at approximately 40 mol% CHOL. This breakdown energy was found to be only a fraction of the available thermal energy, implying that many molecules (approximately 50-100) may be involved in forming the defect structure that leads to failure. The area expansion modulus of extracted RBC lipids with native cholesterol was compared with recent measurements of intact RBC membrane compressibility. The natural membrane was also modeled as a simple composite made up to a compressible lipid/cholesterol matrix containing relatively incompressible transmembrane proteins. It appears that the interaction of incompressible proteins with surrounding lipid confers enhanced compressibility on the composite structure.     

Averaging data derived from images of helical structures with different symmetries.

There are many examples of macromolecules that form helical tubes or crystals, which are useful for structure determination by electron microscopy and image processing. Helical crystals can be thought of as two-dimensional crystals that have been rolled into a cylinder such that two lattice points are superimposed. In many real cases, helical crystals of a particular macromolecule derive from an identical two-dimensional lattice but have different lattice points superimposed, thus producing different helical symmetries which cannot be simply averaged in Fourier-space. When confronted with this situation, one can select images corresponding to one of the observed symmetries at the expense of reducing the number of images that can be used for data collection and averaging, or one can calculate separate density maps from each symmetry, then align and average them together in real-space. Here, we present a third alternative, which is based on averaging of the Fourier-Bessel coefficients, gn,l(r), and which allows the inclusion of data from all symmetry groups derived from a common two-dimensional lattice. The method is straightforward and simple in practice and is shown, through a specific example with real data, to give results comparable to real-space averaging.     

Preparation and characterization of recombinant proricin containing an alternative protease-sensitive linker sequence.

The aim of this study was to determine the feasibility of utilizing a factor Xa-specific cleavage site within a recombinant protein containing the ricin A chain (RTA) sequence. Release of RTA is believed to be an essential step during the intracellular phase of ricin intoxication. Failure to incorporate such cleavage sites in fusions containing RTA results in a loss of toxin action (O'Hare, M., et al. (1990) FEBS Lett. 273,200. Kim, J., and Weaver, R.F. (1988) Gene 68,315). In this report we describe the introduction of a factor Xa-specific site in the linker of proricin, which we use here as a model substrate. Upon purification of the recombinant mutant proricin after expression in Xenopus oocytes, we demonstrate that the protease does have access to the engineered recognition sequence (albeit at low efficiency) and that the presence of the latter does not interfere with disulfide bond formation or the lectin activity of the ricin B chain moiety. Upon cleavage and reduction, the RTA polypeptide displays ribosome-inactivating ability, indicating that the presence of the modified linker at its C-terminus does not interfere with its catalytic activity. The general applicability of using such a cleavage site in recombinant fusions with RTA is discussed.     

Hydrophobic folding units derived from dissimilar monomer structures and their interactions.

We have designed an automated procedure to cut a protein into compact hydrophobic folding units. The hydrophobic units are large enough to contain tertiary non-local interactions, reflecting potential nucleation sites during protein folding. The quality of a hydrophobic folding unit is evaluated by four criteria. The first two correspond to visual characterization of a structural domain, namely, compactness and extent of isolation. We use the definition of Zehfus and Rose (Zehfus MH, Rose GD, 1986, Biochemistry 25:35-340) to calculate the compactness of a cut protein unit. The isolation of a unit is based on the solvent accessible surface area (ASA) originally buried in the interior and exposed to the solvent after cutting. The third quantity is the hydrophobicity, equivalent to the fraction of the buried non-polar ASA with respect to the total non-polar ASA. The last criterion in the evaluation of a folding unit is the number of segments it includes. To conform with the rationale of obtaining hydrophobic units, which may relate to early folding events, the hydrophobic interactions are implicitly and explicitly applied in their generation and assessment. We follow Holm and Sander (Holm L, Sander C, 1994, Proteins 19:256-268) to reduce the multiple cutting-point problem to a one-dimensional search for all reasonable trial cuts. However, as here we focus on the hydrophobic cores, the contact matrix used to obtain the first non-trivial eigenvector contains only hydrophobic contracts, rather than all, hydrophobic and hydrophilic, interactions. This dataset of hydrophobic folding units, derived from structurally dissimilar single chain monomers, is particularly useful for investigations of the mechanism of protein folding. For cases where there are kinetic data, the one or more hydrophobic folding units generated for a protein correlate with the two or with the three-state folding process observed. We carry out extensive amino acid sequence order independent structural comparisons to generate a structurally non-redundant set of hydrophobic folding units for fold recognition and for statistical purposes.     

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys

Two-body inter-residue contact potentials for proteins have often been extracted and extensively used for threading. Here, we have developed a new scheme to derive four-body contact potentials as a way to consider protein interactions in a more cooperative model. We use several datasets of protein native structures to demonstrate that around 500 chains are sufficient to provide a good estimate of these four-body contact potentials by obtaining convergent threading results. We also have deliberately chosen two sets of protein native structures differing in resolution, one with all chains' resolution better than 1.5 A and the other with 94.2% of the structures having a resolution worse than 1.5 A to investigate whether potentials from well-refined protein datasets perform better in threading. However, potentials from well-refined proteins did not generate statistically significant better threading results. Our four-body contact potentials can discriminate well between native structures and partially unfolded or deliberately misfolded structures. Compared with another set of four-body contact potentials derived by using a Delaunay tessellation algorithm, our four-body contact potentials appear to offer a better characterization of the interactions between backbones and side chains and provide better threading results, somewhat complementary to those found using other potentials.     

Solid-phase synthesis of peptidosulfonamide containing peptides derived from Leu-enkephalin

Using Boc or Fmoc-protected β-substituted aminoethanesulfonyl chlorides (2-substituted taurylchlorides) the solid-phase synthesis of dipeptidosulfonamides as well as peptidosulfonamide containing peptides derived from Leu-enkephalin is described. The binding activity of the peptidosulfonamide YGGFL derivatives is reported.