beta-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties

The location of the membrane lipid bilayer relative to a transmembrane protein structure is important in protein engineering. Since it is not present on the determined structures, it is essential to automatically define the membrane embedded protein region in order to test mutation effects or to design potential drugs. beta-Barrel transmembrane proteins, present in nature as outer membrane proteins (OMPs), comprise one of the two transmembrane protein fold classes. Lately, the number of their determined structures has increased and this enables the implementation and evaluation of structure-based annotation methods and their more comprehensive study. In this paper, we propose two new algorithms for (i) the geometric modelling of beta-barrels and (ii) the detection of the transmembrane region of a beta-barrel transmembrane protein. The geometric modelling algorithm combines a non-linear least square minimization method and a genetic algorithm in order to find the characteristics (axis, radius) of a shape with axial symmetry which best models a beta-barrel. The transmembrane region is detected by profiling the external residues of the beta-barrel along its axis in terms of hydrophobicity and existence of aromatic and charged residues. TbB-Tool implements these algorithms and is available in . A non-redundant set of 22 OMPs is used in order to evaluate the algorithms implemented and the results are very satisfying. In addition, we quantify the abundance of all amino acids and the average hydrophobicity for external and internal beta-stranded residues along the axis of beta-barrel, thus confirming and extending other researchers' results.     

Aromatically functionalized cyclic tricholate macrocycles: aggregation, transmembrane pore formation, flexibility, and cooperativity

The aggregation of macrocyclic oligocholates with introverted hydrophilic groups and aromatic side chains was studied by fluorescence spectroscopy and liposome leakage assays. Comparison between the solution and the membrane phase afforded insight into the solvophobically driven aggregation. The macrocycles stacked over one another in lipid membranes to form transmembrane nanopores, driven by a strong tendency of the water molecules in the interior of the amphiphilic macrocycles to aggregate in a nonpolar environment. The aromatic side chains provided spectroscopic signatures for stacking, as well as additional driving force for the aggregation. Smaller, more rigid macrocycles stacked better than larger, more flexible ones because the cholate building blocks in the latter could rotate outward and diminish the conformation needed for the water-templated hydrophobic stacking. The acceptor-acceptor interactions among naphthalenediimide (NDI) groups were more effective than the pyrene-NDI donor-acceptor interactions in promoting the transmembrane pore formation of the oligocholate macrocycles.     

Macromolecular aggregation: Complexation due to hydrogen bonding and hydrophobic association

This paper reports the main results of the studies carried out in our laboratory on various kinds of polymer aggregation in aqueous and organic solutions. (1) In solutions of a polymer blend with controllable hydrogen bonding, a transition from individual polymer coils to intermolecular complex is observed as the hydrogen bonding interaction increases to a certain level. This is found to be a general phenomenon of polymer blends in which hydrogen bonding is adjustable. (2) A new kind of aggregation behavior of block ionomers based on SEBS is found and studied by fluorospectroscopy. The results explore that the block ionomer can form dispersion of hydrophobic aggregates in water stabilized by rare ionic groups. (3) Fluorocarbon-containing PNIPAM in water establishes hydrophobic association. Fluorocarbon-modified pyrene (PycoRf) is found to be qualified to serve as a fluorescent probe to monitor the association.     

Phospholipase D-mediated aggregation, fusion, and precipitation of phospholipid vesicles

Large unilamellar vesicles with a diameter of 100 nm were prepared from the zwitterionic phospholipid POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at pH 8.0. After addition to these vesicles of the enzyme phospholipase D (PLD) from Streptomyces sp. AA586 at 40 degrees C, the terminal phosphate ester bond of POPC was hydrolyzed, yielding the negatively charged POPA (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acid) and the positively charged choline. While the reaction yield in the presence of 1 mM Ca2+ reached 100%, the yield was only approximately 68% in the absence of Ca2+. Furthermore, in the absence of Ca2+, the size of the vesicles did not change significantly with time upon PLD addition, as judged from turbidity, dynamic light scattering, and electron microscopy measurements. In the presence of 1 mM Ca2+, however, PLD addition resulted in vesicle aggregation, fusion, and precipitation, originating from the interaction of Ca2+ ions with the negatively charged phospholipids formed in the membranes. Vesicle fusion was monitored by using a novel fusion assay system involving vesicles containing entrapped trypsin and vesicles containing entrapped chymotrypsinogen A. After vesicle fusion, chymotrypsinogen A transformed into a-chymotrypsin, catalyzed by trypsin inside the fused vesicles. The alpha-chymotrypsin formed could be detected with benzoyl-L-Tyr-p-nitroanilide as a membrane permeable chymotrypsin substrate. The observed vesicle precipitation occurring after vesicle fusion in the presence of 1 mM Ca2+ was correlated with an increase of the main phase transition temperature, Tm, of POPA to values above 40 degrees C.     

Chitosan and its hydrophobic derivatives: Preparation and aggregation in dilute aqueous solutions

This review surveys the main methods of preparing chitosan and its hydrophobic derivatives and their influence on the microstructure of polymers. The experimental data on the aggregation of these polymers in dilute aqueous solutions are summarized. Basic factors affecting aggregation are analyzed, and its general regularities are revealed. It is shown that, in the case of both chitosan and its hydrophobic derivatives, the formation of aggregates is governed by the competition of attraction of associating groups promoting aggregation and their repulsion arising from the presence of charged units and counterions hindering aggregation. Various aggregate models that were proposed for chitosan derivatives with different main-chain lengths and different contents of associating groups are discussed.     

Self-assembly and aggregation of proteins

Recent work on the assembly of small peptides and of proteins into linear and non-linear aggregates is addressed and discussed in view of the challenges in describing food protein assembly.     

Luciferase-streptavidin fusion proteins: Preparation and properties

We constructed plasmids encoding genes of fusion proteins of a thermostable mutant of Luciola mingrelica firefly luciferase (Luc) and streptavidin (SA) with the polyhistidine sequence (His₆) at the N- or C-terminus of the protein: SA-Luc-His₆, His₆-SA-Luc, Luc-SA-His₆. Fusion proteins were produced and purified; their composition, luciferase activity, thermal stability, bioluminescence spectra, and biotin-binding capacity were investigated. Streptavidin introduction does not affect the bioluminescence spectra, but it decreases the thermal stability twofold at 47°C. It was shown by size-exclusion chromatography that, depending on the plasmid structure, the fusion proteins were expressed as dimers, tetramers, and larger oligomers, which differ in luciferase activity and biotin-binding capacity. The His₆-SA-Luc fusion protein demonstrated the most optimal properties.     

Nanoporous microbead supported bilayers: stability, physical characterization, and incorporation of functional transmembrane proteins

The introduction of functional transmembrane proteins into supported bilayer-based biomimetic systems presents a significant challenge for biophysics. Among the various methods for producing supported bilayers, liposomal fusion offers a versatile method for the introduction of membrane proteins into supported bilayers on a variety of substrates. In this study, the properties of protein containing unilamellar phosphocholine lipid bilayers on nanoporous silica microspheres are investigated. The effects of the silica substrate, pore structure, and the substrate curvature on the stability of the membrane and the functionality of the membrane protein are determined. Supported bilayers on porous silica microspheres show a significant increase in surface area on surfaces with structures in excess of 10 nm as well as an overall decrease in stability resulting from increasing pore size and curvature. Comparison of the liposomal and detergent-mediated introduction of purified bacteriorhodopsin (bR) and the human type 3 serotonin receptor (5HT3R) are investigated focusing on the resulting protein function, diffusion, orientation, and incorporation efficiency. In both cases, functional proteins are observed; however, the reconstitution efficiency and orientation selectivity are significantly enhanced through detergent-mediated protein reconstitution. The results of these experiments provide a basis for bulk ionic and fluorescent dye-based compartmentalization assays as well as single-molecule optical and single-channel electrochemical interrogation of transmembrane proteins in a biomimetic platform.     

Cytomimetic large-scale vesicle aggregation and fusion based on host-guest interaction

Herein, we have shown a large-scale cell-mimetic (cytomimetic) aggregation process by using cell-sized polymer vesicles as the building blocks and intervesicular host-guest molecular recognition interactions as the driving force. We first prepared the hyperbranched polymer vesicles named branched polymersomes (BPs) around 5-10 μm through the aqueous self-assembly of a hyperbranched multiarm copolymer of HBPO-star-PEO [HBPO = hyperbranched poly(3-ethyl-3-oxetanemethanol); PEO = poly(ethylene oxide)]. Subsequently, adamantane-functionalized BPs (Ada-BPs) or β-cyclodextrin-functionalized BPs (CD-BPs) were prepared through the coassembly of HBPO-star-PEO and Ada-modified HBPO-star-PEO (HBPO-star-PEO-Ada), or of HBPO-star-PEO and CD-modified HBPO-star-PEO (HBPO-star-PEO-CD), respectively. Macroscopic vesicle aggregates were obtained by mixing CD-BPs and Ada-BPs. The intervesicular host-guest recognition interactions between β-CD units in CD-BPs and Ada units in Ada-BPs, which were proved by (1)H nuclear Overhauser effect spectroscopy (NOESY) spectrum and the fluorescence probe method, are responsible for the vesicle aggregation. Additionally, the vesicle fusion events happened frequently in the process of vesicle aggregation, which were certified by double-labeling fluorescent assay, real-time observation, content mixing assay, and component mixing assay.     

Surfactant-mediated hydrophobic interaction chromatography of proteins: gradient elution

Addition of 3-[(3-cholamidopropyl)dimethylammonio]-l-propanesulphonate (CHAPS) to mobile phases in gradient elution hydrophobic interaction chromatography (HIC) on SynChropak Propyl causes changes in observed elution times for nine globular proteins. The nine proteins showed different percentage reductions in capacity factor, k', demonstrating the ability of CHAPS to change the selectivity of the separations. Three basic types of gradient experiments have been explored for surfactant-mediated gradient elution HIC. Type I gradients are conducted with constant salt and variable surfactant concentration. Type II gradients with variable salt and constant surfactant concentration, and Type III gradients with variable salt and surfactant concentrations. By the criterion of a linear relationship between gradient time and retention time the linear solvent strength condition applies to Type II and Type III gradients. Type III gradients, with the fastest re-equilibration time, are preferable for repetitive analyses. Type I gradients are relatively ineffective in making use of the solvent strength of CHAPS, and Types I and II gradients require long equilibration times due to large changes in surface concentration of CHAPS which occur during elution. The presence of CHAPS had a negligible effect on peak shapes of the proteins examined, except for bovine serum albumin which yielded a narrower, less distorted peak in the presence of CHAPS.     

In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions

Nascent transmembrane (TM) polypeptide segments are recognized and inserted into the lipid bilayer by the cellular translocon machinery. The recognition rules, described by a biological hydrophobicity scale, correlate strongly with physical hydrophobicity scales that describe the free energy of insertion of TM helices from water. However, the exact relationship between the physical and biological scales is unknown, because solubility problems limit our ability to measure experimentally the direct partitioning of hydrophobic peptides across lipid membranes. Here we use microsecond molecular dynamics (MD) simulations in which monomeric polyleucine segments of different lengths are allowed to partition spontaneously into and out of lipid bilayers. This approach directly reveals all states populated at equilibrium. For the hydrophobic peptides studied here, only surface-bound and transmembrane-inserted helices are found. The free energy of insertion is directly obtained from the relative occupancy of these states. A water-soluble state was not observed, consistent with the general insolubility of hydrophobic peptides. The approach further allows determination of the partitioning pathways and kinetics. Surprisingly, the transfer free energy appears to be independent of temperature, which implies that surface-to-bilayer peptide insertion is a zero-entropy process. We find that the partitioning free energy of the polyleucine segments correlates strongly with values from translocon experiments but reveals a systematic shift favoring shorter peptides, suggesting that translocon-to-bilayer partitioning is not equivalent but related to spontaneous surface-to-bilayer partitioning.     

Cruciform pi-systems: effect of aggregation on emission

The solid state properties of cruciform pentamers are examined in thin film preparation, in the single crystalline state and in nanoparticle formulations; emission behavior was found to vary substantially with the solid state morphology. This type of behaviour is an excellent way to manipulate the emissive properties of conjugated [small pi]-systems.     

Modes of conformational changes of proteins adsorbed on a planar hydrophobic polymer surface reflecting their adsorption behaviors

Infrared spectra of hen egg white lysozyme and bovine serum albumin (BSA) adsorbed on a solid poly tris(trimethylsiloxy)silylstyrene (pTSS) surface in D2O solution were measured using attenuated total reflection (ATR) Fourier transform infrared spectroscopy. From the area and shape of the amide I' band of each spectrum, the adsorption amount and the secondary structure were determined simultaneously, as a function of adsorption time. We could show that the average conformation for all the adsorbed lysozyme molecules was solely determined by the adsorption time, and independent of the bulk concentration, while the adsorption amount increased with the bulk concentration as well as the adsorption time. These results suggest that lysozyme molecules form discrete assemblies on the surface, and that the surface assemblies grow over several hours to have a definite architecture independent of the adsorption amount. As for BSA, the extent of the conformational change was solely determined by the adsorption amount, regardless of the bulk concentration and the adsorption time. These differences in the adsorption properties of lysozyme and BSA may reflect differences in their conformational stabilities.     

Reverse-phase high-performance liquid chromatography of virus proteins and other hydrophobic proteins

Summary So far most solvents generally used in reverse phase chromatography (RPC) for separation of peptides and water soluble polypeptides could not be utilized for hydrophobic proteins such as membrane proteins and structural polypeptides of viruses due to their insufficient solubility. But we have introduced a new RP-HPLC solvent system which was very useful in our studies on poliovirus polypeptides. Formic acid in high concentration is an extremely potent solvent for proteins, particularly those that are hydrophobic. Preliminary estimates are made of the concentration of formic acid which is required to completely dissolve hydrophobic proteins. For example, solubilization of structural polypeptides of poliovirus which are absolutely water insoluble requires 60% formic acid. Therefore, we used a proportion of 60% formic acid in all solvents for reversed phase chromatography and applied propanol-2 or acetonitrile as the organic modifiers for gradient elution. Using this mobile phase all four poliovirus polypeptides of three serological types were obtained in high purity by this rapid procedure. In each case, polypeptides were quantitatively eluted independent of the amount of protein (1–1000 μg) injected onto the columns. The solvents used were volatile and easily removed in a short evaporation step. Therefore this solvent system is suited for analytical and for micropreparative separation of proteins for chemical, biochemical and immunological studies. Rechromatography and electrophoresis in SDS-polyacrylamide gels of the separated polypeptides demonstrated that this solvent system with its high proportion of formic acid did not alter their primary structure. There may have been major changes in secondary and tertiary structure. In contrast, alterations of the elution characteristics were observed after reduction of disulfide bridges and several modifications of proteins. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

Modifications of hydrophobic cavity and their effects on the complex formation with a hydrophobic substrate

The derivatives of CP44 ($\text{1}$a) were designed and synthesized to modify the natures of its hydrophobic cavity, and the effects on the complex formation with a hydrophobic substrate in aqueous solution were examined.     

Predicting the behaviour of proteins in hydrophobic interaction chromatography. 1: Using the hydrophobic imbalance (HI) to describe their surface amino acid distribution

This paper focuses on the prediction of the dimensionless retention time of proteins (DRT) in hydrophobic interaction chromatography (HIC) by means of mathematical models based on characteristics of the surface hydrophobicity distribution. We introduce a new parameter, called hydrophobic imbalance (HI), obtained from the three-dimensional structure of proteins. This parameter quantifies the displacement of the superficial geometric centre of the protein when the effect of the hydrophobicity of each amino acid is considered. This parameter is simpler and less expensive than those reported previously. We use HI as a way to incorporate information about the surface hydrophobicity distribution in order to improve the prediction of DRT. We tested the performance of our DRT predictive models in a set of 15 proteins. This set includes four proteins whose DRTs are known as very difficult to predict. By means of the variable HI, it was possible to improve the predictive characteristics obtained by models based on the average surface hydrophobicity (ASH) by 9.1%. Also, we studied linear multivariable models based on characteristics determined from the HI. By using this multivariable model, a correlation coefficient of 0.899 was obtained. With this model, we managed to improve the predictive characteristics shown by previous models based on ASH by 31.8%.     

Studies on synthesis esterified zirconium glyphosates and their hydrophobic properties

A series of new organic-modified zirconium glyphosate compounds were synthesized based on the reactions between esterified glyphosates and ZrOCl₂. FT-IR spectra, solid-state ³¹P MAS NMR and elementary analysis proved the formation of these new compounds. Powder X-ray diffraction (PXRD) patterns and transmission electron microscope (TEM) images proved these compounds had lamellar structures. Scanning electronic microscope (SEM) images showed that solvents used in synthesis had great influence on the morphologies of products. Water contact angle measurements showed that the hydrophobic property of the products was a function of the number of carbon in esterified glyphosates, increased from 0° of zirconium glyphosate to 133° of dodecyl zirconium glyphosate. The present study offered a new route to synthesize organic-modified α-Zr(HPO₄)₂·H₂O (α-ZrP) materials with various morphology and controllable hydrophobic property.