Spinodal wrinkling in thin-film poly(ethylene oxide)/polystyrene bilayers

Optical microscopy and atomic force microscopy were used to study a novel roughness-induced wrinkling instability in thin-film bilayers of poly(ethylene oxide) (PEO) and polystyrene (PS). The observed wrinkling morphology is manifested as a periodic undulation at the surface of the samples and occurs when the bilayers are heated above the melting temperature of the semi crystalline PEO (T(m) = 63 Celsius) layer. During the wrinkling of the glassy PS capping layers the system selects a characteristic wavelength that has the largest amplitude growth rate. This initial wavelength is shown to increase monotonically with increasing thickness of the PEO layer. We also show that for a given PEO film thickness, the wavelength can be varied independently by changing the thickness of the PS capping layers. A model based upon a simple linear stability analysis was developed to analyse the data collected for the PS and PEO film thickness dependences of the fastest growing wavelength in the system. The predictions of this theory are that the strain induced in the PS layer caused by changes in the area of the PEO/PS interface during the melting of the PEO are sufficient to drive the wrinkling instability. A consideration of the mechanical response of the PEO and PS layers to the deformations caused by wrinkling then allows us to use this simple theory to predict the fastest growing wavelength in the system.

Structural characterization of the E2 glycoprotein from Sindbis by lysine biotinylation and LC-MS/MS

Sindbis is an Alphavirus capable of infecting and replicating in both vertebrate and invertebrate hosts. Mature Sindbis virus particles consist of an inner capsid surrounded by a host-derived lipid bilayer, which in turn is surrounded by a protein shell consisting of the E1 and E2 glycoproteins. While a homolog of the E1 glycoprotein has been structurally characterized, the amount of structural data on the E2 glycoprotein is considerably less. In this study, the organization of the E2 glycoprotein was probed by surface biotinylation of intact virions. The virus remained fully infectious, demonstrating that the biotinylation did not alter the topology of the proteins involved in infection. Seven sites of modification were identified in the E2 glycoprotein (K70, K76, K97, K131, K149, K202, and K235), while one site of modification in the E1 glycoprotein (K16) was identified, confirming that the E1 protein is almost completely buried in the virus structure.

Photochemical surface mapping of C14S-Sml1p for constrained computational modeling of protein structure

Photochemically generated hydroxyl radicals were used to map solvent-exposed regions in the C14S mutant of the protein Sml1p, a regulator of the ribonuclease reductase enzyme Rnr1p in Saccharomyces cerevisiae. By using high-performance mass spectrometry to characterize the oxidized peptides created by the hydroxyl radical reactions, amino acid solvent-accessibility data for native and denatured C14S Sml1p that revealed a solvent-excluding tertiary structure in the native state were obtained. The data on solvent accessibilities of various amino acids within the protein were then utilized to evaluate the de novo computational models generated by the HMMSTR/Rosetta server. The top five models initially generated by the server all disagreed with both published nuclear magnetic resonance (NMR) data and the solvent-accessibility data obtained in this study. A structural model adjusted to fit the previously reported NMR data satisfied most of the solvent-accessibility constraints. Through minor adjustment of the rotamers of two amino acid side chains for this latter structure, a model that not only provided a lower energy conformation but also completely satisfied previously reported data from NMR and tryptophan fluorescence measurements, in addition to the solvent-accessibility data presented here, was generated.

Formation of [b(n-1) + OH + H]+ ion structural analogs by solution-phase chemistry

Derivatization of a variety of peptides by a method known to enhance anhydride formation is demonstrated by mass spectrometry to yield ions that have elemental composition and fragmentation properties identical to [b(n-1) + OH + H]+ ions formed by gas-phase rearrangement and fragmentation. The [b(n-1) + OH + H]+ ions formed by gas-phase rearrangement and fragmentation and the solution-phase [b(n-1) + OH + H]+ ion structural analogs formed by derivatization chemistry show two different forms of dissociation using multiple-collision CAD in a quadrupole ion trap and unimolecular decomposition in a TOF-TOF; one group yields identical product ions as a truncated form of the peptide with a free C-terminal carboxylic acid and fragments at the same activation energy; the other group fragments differently from the truncated peptide, being more resistant to fragmentation than the truncated peptide and yielding primarily the [b(n-2) + OH + H]+ product ion. Nonergodic electron capture dissociation MS/MS suggests that any structural differences between the specific-fragmenting [b(n-1) + OH + H]+ ions and the truncated peptide is at the C-terminus of the peptide. The specific-fragmentation can be readily observed by MS(n) experiments to occur in an iterative fashion, suggesting that the C-terminal structure of the original [b(n-1) + OH + H]+ ion is maintained after subsequent rearrangement and fragmentation events in peptides which fragment specifically. A mechanism for the formation of specific-fragmenting and nonspecific-fragmenting [b(n-1) + OH + H]+ ions is proposed.

The properties of free polymer surfaces and their influence on the glass transition temperature of thin polystyrene films

We present a detailed study of free polymer surfaces and their effects on the measured glass transition temperature (T(g)) of thin polystyrene (PS) films. Direct measurements of the near-surface properties of PS films are made by monitoring the embedding of 10 and 20 nm diameter gold spheres into the surface of spin-cast PS films. At a temperature T = 378 K( > T(g)), the embedding of the spheres is driven by geometrical considerations arising from the wetting of the gold spheres by the PS. At temperatures below T(g) (363 K < T < 370 K), both sets of spheres embed 3-4 nm into the PS films and stop. These studies suggest that a liquid-like surface layer exists in glassy PS films and also provide an estimate for the lower bound of the thickness of this layer of 3-4 nm. This qualitative idea is supported by a series of calculations based upon a previously developed theoretical model for the indentation of nanoscale spheres into linear viscoelastic materials. Comparing data with simulations shows that this surface layer has properties similar to those of a bulk sample of PS having a temperature of 374 K. Ellipsometric measurements of the T(g) are also performed on thin spin-cast PS films with thicknesses in the range 8 nm < h < 290 nm. Measurements are performed on thin PS films that have been capped by thermally evaporating 5 nm thick metal (Au and Al) capping layers on top of the polymer. The measured T(g) values (as well as polymer metal interface structure) in such samples depend on the metal used as the capping layer, and cast doubt on the general validity of using evaporative deposition to cover the free surface. We also prepared films that were capped by a new non-evaporative procedure. These films were shown to have a T(g) that is the same as that of bulk PS (370+/-1 K) for all film thicknesses measured (> 7 nm). The subsequent removal of the metal layer from these films was shown to restore a thickness-dependent T(g) in these samples that was essentially the same as that observed for uncapped PS films. An estimate of the thickness of the liquid-like surface layer was also extracted from the ellipsometry measurements and was found to be 5+/-1 nm. The combined ellipsometry and embedding studies provide strong evidence for the existence of a liquid-like surface layer in thin glassy PS films. They show that the presence of the free surface is an important parameter in determining the existence of T(g) reductions in thin PS films.

Analysis of Protein Solvent Accessible Surfaces by Photochemical Oxidation and Mass Spectrometry

Protein surfaces are important in most biological processes, including protein-protein interactions, enzymatic catalysis, and protein-ligand binding. We report a method in which hydroxyl radicals generated by a rapid-UV irradiation of a 15% hydrogen peroxide solution were utilized to oxidize specific amino acid side chains of two model proteins (lysozyme, beta-lactoglobulin A), according to the residues' chemical reactivities and the solvent accessibility of the reactive carbons and sulfurs in the residue. Oxidized peptides generated by tryptic digestion were identified by electrospray-Fourier transform mass spectrometry. The specific sites of the stable modification were then identified by reverse-phase liquid chromatography coupled to quadropole ion trap tandem mass spectrometry. The solvent accessibility of the residue was shown to directly affect the rate of oxidation by this method (with the exception of methionine), supporting its use as a rapid measure of the solvent accessibility of specific residues, and in some cases, individual atoms.

Free surfaces cause reductions in the glass transition temperature of thin polystyrene films

The effect of free surfaces on the glass transition temperature (T(g)) of thin polystyrene films was studied. Measurements were performed on films (8 nm<h<290 nm) with one free surface and on films capped with a 5 nm thick metal layer (no free surfaces). Potential problems with evaporative deposition were eliminated by studying samples made of two supported films placed with their free surfaces in contact and annealed. Uncapped films displayed reduced T(g) values for h less, similar 40 nm while all "properly" capped films exhibited a T(g) value the same as that of the bulk polymer (370+/-1 K). When the free surface was restored, the measured T(g) values the same as those of uncapped films of the same thickness. These results show that free surfaces are crucial for observing T(g) reductions in thin polymer films and address the role of the sample preparation history.

Thickness dependence of the dynamics in thin films of isotactic poly (methylmethacrylate)

The film thickness dependence of both the glass transition temperature (T(g)) and the 1 kHz alpha relaxation were studied for thin films of isotactic Poly (methylmethacrylate) (i-PMMA) supported on aluminium substrates. Films in the thickness range 7-200 nm were studied. The ellipsometrically determined T(g) was found to show reductions for films thinner than 60 nm, with the largest observed reduction being 12 K for a 7 nm thick film. Measurements of the T(g) were also performed on i-PMMA films supported on silicon substrates. Dielectric studies of the temperature dependent 1 kHz alpha relaxation peak, showed that the position (T(alpha)) and shape of the peak have no film thickness dependence. This was shown to hold for films with one free surface and films with a 30 nm thermally evaporated capping layer. Capping the films was shown to have no effect on the thickness dependence of either T(g) or T(alpha). The implications of these results are discussed further and the different film thickness dependencies of T(g) and T(alpha) are discussed. This is done within the framework of the Vogel-Fulcher-Tamann (VFT) theory of glass forming materials and also in the context of the existence of a dynamic correlation length xi.

Dielectric and ellipsometric studies of the dynamics in thin films of isotactic poly(methylmethacrylate) with one free surface

We have performed dielectric loss measurements at 1 kHz on thin films of isotactic poly(methyl methacrylate). A key distinction of our studies is that the samples measured were supported films with one free surface rather than films that have metallic electrodes covering both surfaces. This unique sample geometry allows us to eliminate any effects due to evaporation of metal onto the top film surface and provides a unique opportunity to make direct comparisons between dielectric loss and glass transition measurements. Film thicknesses in the range from 6 microm to 7 nm were prepared on Al coated substrates. The dielectric loss peak and ellipsometric glass transition temperature of all films were measured. The dielectric loss was found to exhibit no discernible film thickness dependence in either the temperature of the maximum loss value or the shape of the loss curve. In contrast, the measured T(g) values were found to decrease with decreasing film thickness with a maximum shift of 10 K for a 7-nm film. Dielectric measurements were also made on Al coated films and these samples also showed no shift in the temperature of the loss peak. Finally, the T(g) measurements were also made on Si substrates. These values exhibited an increasing T(g) value with film thickness with a maximum increase of approximately 15 K being measured for a 7-nm film.

Protein surface mapping by chemical oxidation: structural analysis by mass spectrometry

The solvent-accessible surface area of proteins is important in biological function for many reasons, including protein-protein interactions, protein folding, and catalytic sites. Here we present a chemical technique to oxidize amino acid side chains in a model protein, apomyoglobin, and subsequent elucidation of the effect of solvent accessibility on the sites of oxidation. Under conditions of low protein oxidation (zero to three oxygen atoms added per apomyoglobin molecule), we have positively identified five oxidation sites by liquid chromatography-tandem mass spectrometry and high-resolution Fourier transform mass spectrometry. Our results indicate that all oxidized amino acids, with the exception of methionine, have highly solvent-accessible side chains, but the rate of oxidation may not be dictated solely by solvent accessibility and amino acid identity.

Surface denaturation and amyloid fibril formation of insulin at model lipid-water interfaces

We consider the effects that different lipid surfaces have upon the denaturation and subsequent formation of amyloid fibrils of bovine insulin. The adsorption and unfolding kinetics of insulin being adsorbed onto the different lipid surfaces under denaturing conditions are studied using FTIR ATR spectroscopy and are compared to the bulk solution behavior of the protein. Atomic force microscopy studies are also performed to compare the fibrils growing on the different surfaces. This study shows that both the adsorption and unfolding kinetics of insulin can be described by a sum of exponential processes and that different surfaces behave differently, with respect both to one another and to the bulk protein solution. The proteins adsorbed onto the surfaces are observed to have faster unfolding kinetics than those in the bulk, and the fibril-like structures formed at the surfaces are shown to be different in a number of ways from those found in bulk solution. The beta-sheet content and growth kinetics of the adsorbed proteins also differ from those of the bulk system. An attempt is made to describe the observed behavior in terms of simple physical arguments involving adsorption, unfolding, and aggregation of the proteins.

Swelling-induced morphology in ultrathin supported films of poly(d,l-lactide)

In this study we describe a surface morphology that arises when ultrathin supported films of poly(d,l-lactide) are immersed in water. The films are initially flat with a rms roughness of approximately 2 nm. After immersion the surfaces of the films are covered with craters. The craters have a narrow distribution of sizes and are typically micrometers in diameter. They have depths in the 10-100 nm range. In situ atomic force microscopy shows that the craters occur as a result of a blistering process, which occurs when the films delaminate from the silicon substrate. The films buckle away from the substrate to give a nonzero initial diameter and then the blisters proceed to grow until they reach a maximum size. At any point during the growth process, the blisters can be made to collapse by removing the films from water. This phenomenon is explained in terms of a laterally confined swelling film, which has a buckling instability and releases excess strain energy by wrinkling. An expression for the initial buckling wavelength is extracted using the expressions for a buckling plate. Information about the mechanical properties of the films and the surface interaction between the film and substrate can also be obtained by considering the kinetics of blister growth.

The timescale of spinodal dewetting at a polymer/polymer interface

We investigate the dynamics of spinodal dewetting in liquid-liquid polymer systems. Dewetting of poly(methyl-methacrylate) (PMMA) thin films on polystyrene (PS) "substrates" is followed in situ using neutron reflectivity. By following the development of roughness at the PS/PMMA interface and the PMMA surface we extract characteristic growth times for the dewetting process. These characteristic growth times are measured as a function of the molecular weight of the two polymers. By also carrying out experiments in the regime where the dynamics are independent of the PS molecular weight, we are able to use dewetting to probe the scaling of the PMMA thin film viscosity with temperature and molecular weight. We find that this scaling reflects bulk behaviour. However, absolute values are low compared to bulk viscosities, which we suggest may be due in part to slippage at the polymer/polymer interface.

An oligopeptide transporter gene family in Arabidopsis

We have identified nine oligopeptide transporter (OPT) orthologs (AtOPT1 to AtOPT9) in Arabidopsis. These proteins show significant sequence similarity to OPTs of Candida albicans (CaOpt1p), Schizosaccharomyces pombe (Isp4p), and Saccharomyces cerevisiae (Opt1p and Opt2p). Hydrophilicity plots of the OPTs suggest that they are integral membrane proteins with 12 to 14 transmembrane domains. Sequence comparisons showed that the AtOPTs form a distinct subfamily when compared with the fungal OPTs. Two highly conserved motifs (NPG and KIPPR) were found among all OPT members. The identification of multiple OPTs in Arabidopsis suggests that they may play different functional roles. This idea is supported by the fact that AtOPTs have a distinct, tissue-specific expression pattern. The cDNAs encoding seven of the AtOPTs were cloned into a yeast vector under the control of a constitutive promoter. AtOPT4 expressed in S. cerevisiae mediated the uptake of KLG-[3H]L. Similarly, expression of five of the seven AtOPT proteins expressed in yeast conferred the ability to uptake tetra- and pentapeptides as measured by growth. This study provides new evidence for multiple peptide transporter systems in Arabidopsis, suggesting an important physiological role for small peptides in plants.

An oligopeptide transporter gene family in Arabidopsis

We have identified nine oligopeptide transporter (OPT) orthologs (AtOPT1 to AtOPT9) in Arabidopsis. These proteins show significant sequence similarity to OPTs of Candida albicans (CaOpt1p), Schizosaccharomyces pombe (Isp4p), and Saccharomyces cerevisiae (Opt1p and Opt2p). Hydrophilicity plots of the OPTs suggest that they are integral membrane proteins with 12 to 14 transmembrane domains. Sequence comparisons showed that the AtOPTs form a distinct subfamily when compared with the fungal OPTs. Two highly conserved motifs (NPG and KIPPR) were found among all OPT members. The identification of multiple OPTs in Arabidopsis suggests that they may play different functional roles. This idea is supported by the fact that AtOPTs have a distinct, tissue-specific expression pattern. The cDNAs encoding seven of the AtOPTs were cloned into a yeast vector under the control of a constitutive promoter. AtOPT4 expressed in S. cerevisiae mediated the uptake of KLG-[3H]L. Similarly, expression of five of the seven AtOPT proteins expressed in yeast conferred the ability to uptake tetra- and pentapeptides as measured by growth. This study provides new evidence for multiple peptide transporter systems in Arabidopsis, suggesting an important physiological role for small peptides in plants.