X-ray diffraction analysis of cytochrome b5 reconstituted in egg phosphatidylcholine vesicles.

Cytochrome b5 was reconstituted asymmetrically into large unilamellar egg phosphatidylcholine vesicles. Asymmetry was preserved after sedimentation and partial dehydration to form oriented stacks of membranes. The periodicity of the centrosymmetric unit cell ranged between 145 and 175 A, depending upon the water content of the oriented multilayer. X-ray diffraction data were collected to a resolution of 12 A and phase factors were unambiguously assigned by a swelling analysis to a resolution of 15 A. The lower-resolution profile structures clearly showed a highly asymmetric single membrane containing the heme peptide segment of the cytochrome on one side of the membrane bilayer. The higher-resolution data were also analyzed and profile structures were compared with various models for the distribution of cytochrome b5 nonpolar peptide within the membrane bilayer region. The data favor an asymmetric distribution of protein mass within the membrane bilayer.     

Bilayer structure and physical dynamics of the cytochrome b5 dimyristoylphosphatidylcholine interaction.

Cytochrome b5 is a microsomal membrane protein which provides reducing potential to delta 5-, delta 6-, and delta 9-fatty acid desaturases through its interaction with cytochrome b5 reductase. Low angle x-ray diffraction has been used to determine the structure of an asymmetrically reconstituted cytochrome b5:DMPC model membrane system. Differential scanning calorimetry and fluorescence anisotropy studies were performed to examine the bilayer physical dynamics of this reconstituted system. These latter studies allow us to constrain structural models to those which are consistent with physical dynamics data. Additionally, because the nonpolar peptide secondary structure remains unclear, we tested the sensitivity of our model to different nonpolar peptide domain configurations. In this modeling approach, the nonpolar peptide moiety was arranged in the membrane to meet such chemically determined criteria as protease susceptibility of carboxyl- and amino-termini, tyrosine availability for pH titration and tryptophan 109 location, et cetera. In these studies, we have obtained a reconstituted cytochrome b5:DMPC bilayer structure at approximately 6.3 A resolution and conclude that the nonpolar peptide does not penetrate beyond the bilayer midplane. Structural correlations with calorimetry, fluorescence anisotropy and acyl chain packing data suggest that asymmetric cytochrome b5 incorporation into the bilayer increases acyl chain order. Additionally, we suggest that the heme peptide:bilayer interaction facilitates a discreet heme peptide orientation which would be dependent upon phospholipid headgroup composition.     

Neutron scattering shows that cytochrome b5 penetrates deeply into the lipid bilayer

Cytochrome b5 was asymmetrically reconstituted into small lipid vesicles made of a highly deuterated phospholipid. Small-angle neutron diffraction patterns were collected in a series of H2O-D2O mixtures from vesicles consisting of lipid and native or trypsinized cytochrome b5. The second moment of the radial distribution of scattering density in the vesicles was derived from these data and was compared to values calculated from three proposed models, which differ by the degree that cytochrome b5 penetrates the lipid bilayer. The model in which the hydrophobic domain of the protein is distributed across the bilayer agreed most closely with the data.     

Preparation and Characterization of Electrospun PLCL/Poloxamer Nanofibers and Dextran/Gelatin Hydrogels for Skin Tissue Engineering

In this study, two different biomaterials were fabricated and their potential use as a bilayer scaffold for skin tissue engineering applications was assessed. The upper layer biomaterial was a Poly(ε-caprolactone-co-lactide)/Poloxamer (PLCL/Poloxamer) nanofiber membrane fabricated using electrospinning technology. The PLCL/Poloxamer nanofibers (PLCL/Poloxamer, 9/1) exhibited strong mechanical properties (stress/strain values of 9.37±0.38 MPa/187.43±10.66%) and good biocompatibility to support adipose-derived stem cells proliferation. The lower layer biomaterial was a hydrogel composed of 10% dextran and 20% gelatin without the addition of a chemical crosslinking agent. The 5/5 dextran/gelatin hydrogel displayed high swelling property, good compressive strength, capacity to present more than 3 weeks and was able to support cells proliferation. A bilayer scaffold was fabricated using these two materials by underlaying the nanofibers and casting hydrogel to mimic the structure and biological function of native skin tissue. The upper layer membrane provided mechanical support in the scaffold and the lower layer hydrogel provided adequate space to allow cells to proliferate and generate extracellular matrix. The biocompatibility of bilayer scaffold was preliminarily investigated to assess the potential cytotoxicity. The results show that cell viability had not been affected when cocultured with bilayer scaffold. As a consequence, the bilayer scaffold composed of PLCL/Poloxamer nanofibers and dextran/gelatin hydrogels is biocompatible and possesses its potentially high application prospect in the field of skin tissue engineering.     

Use of carboxypeptidase Y in studies of the mode of insertion of cytochrome b5 into lipid vesicles

Carboxypeptidase Y preparations from baker's yeast have been found to exhibit endopeptidase activity when cytochrome b5 was used as substrate. As the susceptibility of cytochrome b5 to attack by carboxypeptidase Y has been used to distinguish between two modes of insertion of cytochrome b5 into lipid bilayer, one which has the C terminal buried in the lipid bilayer and one which has a free C terminal, caution should be taken when employing carboxypeptidase Y preparations for this type of studies.     

A mean-field model of the alkane-saturated lipid bilayer above its phase transition. I. Development of the model

A statistical mechanical model of a bilayer of dipalmitoyl-3-sn-phosphatidylcholine molecules in equilibrium with an aqueous phase saturated with an n-alkane is presented. A mean-field approach developed in previous work on a solventless bilayer (Gruen, Biochim. Biophys. Acta. 595:161--183, 1980) is extended to allow alkane chains to exist in the hydrophobic core of the membrane. As the alkane chains are chemically similar to the lipid chains, much of the analysis follows directly from the solventless model. Novel features of the present model are the inclusion of (a) a term which models the free energy cost of creating space for alkane conformations, (b) a term which constrains the chains to pack evenly in the hydrophobic region of the membrane, and (c) a term which estimates the free energy of mixing of the lipid and alkane molecules in the plane of the bilayer. On uptake of alkane, the dimensions of the bilayer increase. Allowance is made for an increase in thickness and/or an increase in area per lipid. A thermodynamic framework is established which allows evaluation of the free energy of a bilayer of arbitrary dimensions with a view to predicting the equilibrium structure.     

Intramembrane position of the fluorescent tryptophanyl residue in membrane-bound cytochrome b5

We have developed a method to measure the intramembrane position of the fluorescent tryptophanyl residue in whole cytochrome b5 and the nonpolar membrane binding segment when these molecules are bound to phospholipid vesicles [Koppel, D.E., Fleming, P., & Strittmatter, P. (1979) Biochemistry (preceding paper in this issue)]. The method utilizes excitation energy transfer from the donor tryptophanyl residue in the protein to trinitrophenyl or danysl acceptor groups on the surface of the phospholipid bilayer. It was determined that that single fluorescent tryptophanyl residue in vesicle-bound cytochrome b5 and the nonpolar segment is located approximately 20-22 A below the surface of the bilayer. This position represents a minimum depth of penetration of this portion of the cytochrome in the membrane.     

Cytochrome b5 induced flip-flop of phospholipids in sonicated vesicles

Cytochrome b5 induced flip-flop of phosphatidylethanolamine (PE) in sonicated vesicles prepared from a 9:1 mixture of phosphatidylcholine (PC) to phosphatidylethanolamine was determined as follows. First, vesicles having a nonequilibrium distribution of PE across the bilayer were prepared by amidinating the external amino groups with isethionyl acetimidate. Amidinated cytochrome b5 was then added, and after the protein was completely bound, the rate of appearance of fresh PE on the outer surface was determined by removing aliquots at timed intervals and titrating the external amino groups with trinitrobenzenesulfonic acid. The results show an initial rapid phase of flip-flop (especially in the presence of salt) followed by a very slow phase, at 25 degrees C. Similar results were obtained when cytochrome b5 was introduced into the amidinated vesicles by spontaneous transfer from PC donor vesicles. These results indicate that the accumulation of the transferable ("loose") form of cytochrome b5 on the outer surface of a vesicle causes a transient, global destabilization of the bilayer that is relieved by lipid flip-flop. We speculate that this mechanism may be a significant driving force for the transfer of amphipathic molecules across membranes.     

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP₂), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP₂, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.     

Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation

In this study, homology modeling, molecular docking and molecular dynamics simulation were performed to explore structural features and binding mechanism of some inhibitors of chemokine receptor type 5 (CCR5), and to construct a model for designing new CCR5 inhibitors for preventing HIV attachment to the host cell. A homology modeling procedure was employed to construct a 3D model of CCR5. For this procedure, the X-ray crystal structure of bovine rhodopsin (1F88A) at 2.80? resolution was used as template. After inserting the constructed model into a hydrated lipid bilayer, a 20ns molecular dynamics (MD) simulation was performed on the whole system. After reaching the equilibrium, twenty-four CCR5 inhibitors were docked in the active site of the obtained model. The binding models of the investigated antagonists indicate the mechanism of binding of the studied compounds to the CCR5 obviously. Moreover, 3D pictures of inhibitor-protein complex provided precious data regarding the binding orientation of each antagonist into the active site of this protein. One additional 20 ns MD simulation was performed on the initial structure of the CCR5-ligand 21 complex, resulted from the previous docking calculations, embedded in a hydrated POPE bilayer to explore the effects of the presence of lipid bilayer in the vicinity of CCR5-ligand complex. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.     

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution.

This is the first in a series of papers concerned with methods for the determination of the structures of fluid phospholipid bilayers in the liquid-crystalline (L alpha) phase. The basic approach is the joint refinement of quasimolecular models (King and White, 1986. Biophys. J. 49:1047-1054) using x-ray and neutron diffraction data. We present here (a) the rationale for quasimolecular models, (b) the nature of the resolution problem for thermally disordered bilayers, and (c) an analysis of the resolution of experiments in which Gaussian functions are used to describe the distribution of submolecular components. We show that multilamellar liquid-crystalline bilayers are best described by the convolution of a perfect lattice function with a thermally disordered bilayer unit cell. Lamellar diffraction measurements on such a system generally yield only 5-10 orders of diffraction data from which transbilayer profiles of the unit cell can be constructed. The canonical resolution of these transbilayer profiles, defined as the Bragg spacing divided by the index of the highest recorded diffraction order, is typically 5-10 A. Using simple model calculations, we show that the canonical resolution is a measure of the widths of the distributions of constituents of the unit cell rather than a measure of the spatial separation of the distributions. The widths provide a measure of the thermal motion of the bilayer constituents which can be described by Gaussian functions. The equilibrium positions of the centers of the distributions can be determined with a precision of 0.1-0.5 A based upon typical experimental errors.     

Membrane-protein structural mapping of chloroplast coupling factor in asolectin vesicles

The spatial relationship of specific sites on chloroplast coupling factor, reconstituted in asolectin vesicles, to the bilayer surface has been studied with fluorescence methods. Fluorescence resonance energy transfer measurements have been used to map the distances of closest approach of the N,N'-dicyclohexylcarbodiimide-binding site and the disulfide on the gamma-polypeptide to the bilayer center. The dicyclohexylcarbodiimide site was labeled with N-cyclohexyl-N'-pyrenylcarbodiimide and the gamma-disulfide site with a coumarinyl derivative. The bilayer center was labeled with 25-[N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-N-methylamino]-27-norc holesterol. The distances obtained, 15 and 43 A, respectively, were combined with previous measurements of the distance of closest approach between these sites and the membrane surface to estimate the perpendicular distances of the sites from the membrane surface. The depth of the dicyclohexylcarbodiimide site was also determined by studying the quenching of fluorescence by 5-, 7-, 12-, and 16-doxylstearic acids. The model developed suggests that the dicyclohexylcarbodiimide site is 6-10 A below the membrane surface and the gamma-disulfide is 16 A above the membrane surface. The distances measured are subject to a considerable uncertainty, but the proposed model provides a useful starting point for further structural studies.     

Mechanism of residence of cytochrome b(5), a tail-anchored protein, in the endoplasmic reticulum

Endoplasmic reticulum (ER) proteins maintain their residency by static retention, dynamic retrieval, or a combination of the two. Tail-anchored proteins that contain a cytosolic domain associated with the lipid bilayer via a hydrophobic stretch close to the COOH terminus are sorted within the secretory pathway by largely unknown mechanisms. Here, we have investigated the mode of insertion in the bilayer and the intracellular trafficking of cytochrome b(5) (b[5]), taken as a model for ER-resident tail-anchored proteins. We first demonstrated that b(5) can acquire a transmembrane topology posttranslationally, and then used two tagged versions of b(5), N-glyc and O-glyc b(5), containing potential N- and O-glycosylation sites, respectively, at the COOH-terminal lumenal extremity, to discriminate between retention and retrieval mechanisms. Whereas the N-linked oligosaccharide provided no evidence for retrieval from a downstream compartment, a more stringent assay based on carbohydrate acquisition by O-glyc b(5) showed that b(5) gains access to enzymes catalyzing the first steps of O-glycosylation. These results suggest that b(5) slowly recycles between the ER and the cis-Golgi complex and that dynamic retrieval as well as retention are involved in sorting of tail-anchored proteins.     

Electric field-driven transformations of a supported model biological membrane--an electrochemical and neutron reflectivity study

A mixed bilayer of cholesterol and dimyristoylphosphatidylcholine has been formed on a gold-coated block of quartz by fusion of small unilamellar vesicles. The formation of this bilayer lipid membrane on a conductive surface allowed us to study the influence of the support's surface charge on the structure and hydration of the bilayer lipid membrane. We have employed electrochemical measurements and the specular reflection of neutrons to measure the thickness and water content in the bilayer lipid membrane as a function of the charge on the support's surface. When the surface charge density is close to zero, the lipid vesicles fuse directly on the surface to form a bilayer with a small number of defects and hence small water content. When the support's surface is negatively charged the film swells and incorporates water. When the charge density is more negative than −8 μC cm⁻², the bilayer starts to detach from the metal surface. However, it remains in a close proximity to the metal electrode, being suspended on a thin cushion of the electrolyte. The field-driven transformations of the bilayer lead to significant changes in the film thicknesses. At charge densities more negative than −20 μC cm⁻², the bilayer is ~37 Å thick and this number is comparable to the thickness determined for hydrated multilayers of dimyristoylphosphatidylcholine from x-ray diffraction experiments. The thickness of the bilayer decreases at smaller charge densities to become equal to ~26 Å at zero charge. This result indicates that the tilt of the acyl chains with respect to the bilayer normal changes from ~35° to 59° by moving from high negative charges (and potentials) to zero charge on the metal.     

Interaction of pulmonary surfactant protein SP-A with DPPC/egg-PG bilayers

In the mixture of lipids and proteins which comprise pulmonary surfactant, the dominant protein by mass is surfactant protein A (SP-A), a hydrophilic glycoprotein. SP-A forms octadecamers that interact with phospholipid bilayer surfaces in the presence of calcium. Deuterium NMR was used to characterize the perturbation by SP-A, in the presence of 5 mM Ca²⁺, of dipalmitoyl phosphatidylcholine (DPPC) properties in DPPC/egg-PG (7:3) bilayers. Effects of SP-A were uniformly distributed over the observed DPPC population. SP-A reduced DPPC chain orientational order significantly in the gel phase but only slightly in the liquid-crystalline phase. Quadrupole echo decay times for DPPC chain deuterons were sensitive to SP-A in the liquid-crystalline mixture but not in the gel phase. SP-A reduced quadrupole splittings of DPPC choline β-deuterons but had little effect on choline α-deuteron splittings. The observed effects of SP-A on DPPC/egg-PG bilayer properties differ from those of the hydrophobic surfactant proteins SP-B and SP-C. This is consistent with the expectation that SP-A interacts primarily at bilayer surfaces.     

Distribution of cytochrome b5 between small and large unilamellar phospholipid vesicles

Cytochrome b5 is an amphipathic integral membrane protein that spontaneously inserts, post-translationally, into intracellular membranes. When added to preformed phospholipid vesicles, it binds in a so-called "loose" or transferable configuration, characterized by the ability of the protein to rapidly equilibrate between vesicles. In a preliminary report we showed that the distribution of cytochrome b5 among a heterogeneous population of small sonicated phosphatidylcholine vesicles (212 to about 350 A in diameter) lies in favor of the smallest vesicles by a factor of at least 20 (Greenhut, S.F. and Roseman, M.A. (1985) J. Biol. Chem. 260, 5883-5886). In the present studies we have attempted to determine the maximal extent to which bilayer curvature can influence the intervesicle distribution of cytochrome b5, by measuring the distribution of the protein between a population of limit-size vesicles 212 A in diameter and a population of large unilamellar vesicles approximately 1000 A in diameter. (The effect of bilayer curvature on the physical properties of the lipids in the large vesicles is considered to be negligible.) The results show that cytochrome b5 favors the small vesicle population by a factor of about 200. This observation suggests that the formation of highly curved regions in biological membranes (or the formation of regions in which the physical state of the lipids is similar to that in small vesicles) may cause the accumulation of certain membrane proteins at those sites. We also observed that a significant fraction (11-20%) of the cytochrome b5, when added directly to the large vesicles, spontaneously inserts into the "tight," physiologically proper configuration. A possible mechanism is discussed.     

Effect of the phase state of lipids on their interaction with cobra cytotoxin

Interaction between cytotoxin of the Central Asia cobra venom and dimiristoylphosphatidylcholine bilayer depending on its phase state was studied by ESR with spin label. A conclusion can be drawn that the efficiency of cytotoxin effect on the membranes depends on their phase state. Cytotoxin molecules are incorporated into myophile region of the bilayer, only if the latter is in the liquid crystal state. The interaction between cytotoxins and lipids of the bilayer in a gel state is in the main conditioned by electrostatic forces.     

Effect of cytochrome b5 on the size, density, and permeability of phosphatidylcholine vesicles.

Cytochrome b5, isolated from rabbit liver by a procedure using detergent, was incubated with phosphatidylcholine bilayer vesicles at 37 degrees for 30 min. A comparison of a number of physical properties was made between the cytochrome b5-phosphatidylcholine complex (at a molar ratio of 1:1000) and the phosphatidylcholine vesicles. The binding of the protein to the vesicle caused no aggregation and no detectable change in Stokes radius of the vesicle as monitored by gel filtration. Only small increases in s20 (from 2.67 up to 3.82 X 10(-13) s) and density (from 1.025 up to 1.042 g ml(-1)) were observed upon binding of the cytochrome b5 to phosphatidylcholine vesicles. At molar ratios of 5:1000, and above, two types of complexes could be detected by sucrose density gradient centrifugation: one had a molar ratio of approximately 1.066 g ml(-1)) the other, a more constant ratio of 20:1000 (density greater than 1.107 g ml(-1)). Cytochrome b5 was also incubated with phosphatidylcholine vesicles prepared with ferricyanide trapped inside. The leakage of the ferricyanide from inside the vesicles was increased when cytochrome b5 was present, but the vesicles, although leaking, were not completely depleted of their ferricyande, and so must still be intact. It is suggested that at molar ratios of cytochrome b5 to phosphatidylcholine below 5:1000, the binding of the protein causes minimal change in vesicle structure.     

Membrane Partitioning of Anionic,Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling,Local Disordering,and Cholesterol Depletion

Intracellular uptake of nanoparticles (NPs) may induce phase transitions, restructuring, stretching, or even complete disruption of the cell membrane. Therefore, NP cytotoxicity assessment requires a thorough understanding of the mechanisms by which these engineered nanostructures interact with the cell membrane. In this study, extensive Coarse-Grained Molecular Dynamics (MD) simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC) phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the bilayer core reveal that the hydrophobic and hydrophilic ligands of the NP surface rearrange to form optimal contacts with the lipid bilayer, leading to the so-called snorkeling effect. Inside cholesterol-containing bilayers, the NP induces rearrangement of the structure of the lipid bilayer in its vicinity from the liquid-ordered to the liquid phase spanning a distance almost twice its core radius (8–10 nm). Based on the physical insights obtained in this study, we propose a mechanism of cellular anionic NPpartitioning, which requires structural rearrangements of both the NP and the bilayer, and conclude that the translocation of anionic NPs through cholesterol-rich membranes must be accompanied by formation of cholesterol-lean regions in the proximity of NPs.     

Mitsunobu Reactions of 5‐Fluorouridine with the Terpenols Phytol and Nerol: DNA Building Blocks for a Biomimetic Lipophilization of Nucleic Acids

The cancerostatic 5‐fluorouridine (5‐FUrd; 1 ) was sequentially sugar‐protected by introduction of a 2′,3′‐O‐heptylidene ketal group (→ 2 ), followed by 5′‐O‐monomethoxytritylation (→ 3 ). This fully protected derivative was submitted to Mitsunobu reactions with either phytol ((Z and E)‐isomer) or nerol ((Z)‐isomer) to yield the nucleoterpenes 4a and 4b . Both were 5′‐O‐deprotected with 2% Cl₂CHCOOH in CH₂Cl₂ to yield compounds 5a and 5b , respectively. These were converted to the 5′‐O‐cyanoethyl phosphoramidites 6a and 6b , respectively. Moreover, the 2′,3′‐O‐(1‐nonyldecylidene) derivative, 7a , of 5‐fluorouridine was resynthesized and labelled at C(5′) with an Eterneon‐480 fluorophor^® (→ 7b ). The resulting nucleolipid was studied with respect to its incorporation in an artificial bilayer, as well as to its aggregate formation. Additionally, two oligonucleotides carrying terminal phytol‐alkylated 5‐fluorouridine tags were prepared, one of which was studied concerning its incorporation in an artificial lipid bilayer.