Determination of molecular order in supported lipid membranes by internal reflection Fourier transform infrared spectroscopy

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

The analysis of biological samples with polarized infrared spectroscopy (p-IR) has long been a widely practiced method for the determination of sample orientation and structural properties. In contrast to earlier works, which employed this method to investigate the fundamental chemistry of biological systems, recent interests are moving toward "real-world" applications for the evaluation and diagnosis of pathological states. This focal point review provides an up-to-date synopsis of the knowledge of biological materials garnered through linearly p-IR on biomolecules, cells, and tissues. An overview of the theory with special consideration to biological samples is provided. Different modalities which can be employed along with their capabilities and limitations are outlined. Furthermore, an in-depth discussion of factors regarding sample preparation, sample properties, and instrumentation, which can affect p-IR analysis is provided. Additionally, attention is drawn to the potential impacts of analysis of biological samples with inherently polarized light sources, such as synchrotron light and quantum cascade lasers. The vast applications of p-IR for the determination of the structure and orientation of biological samples are given. In conclusion, with considerations to emerging instrumentation, findings by other techniques, and the shift of focus toward clinical applications, we speculate on the future directions of this methodology.

Selective Gas-Phase Functionalization of SiO2 and SiNx Surfaces with Hydrocarbons

Selective functionalization of dielectric surfaces is required for area-selective atomic layer deposition and etching. We have identified precursors for the selective gas-phase functionalization of plasma-deposited SiO₂ and SiN_x surfaces with hydrocarbons. The corresponding reaction mechanism of the precursor molecules with the two surfaces was studied using in situ surface infrared spectroscopy. We show that at a substrate temperature of 70 °C, cyclic azasilanes preferentially react with an -OH-terminated SiO₂ surface over a -NH_x-terminated SiN_x surface with an attachment selectivity of ∼5.4, which is limited by the partial oxidation of the SiN_x surface. The cyclic azasilane undergoes a ring-opening reaction where the Si-N bond cleaves upon the reaction with surface -OH groups forming a Si-O-Si linkage. After ring opening, the backbone of the grafted hydrocarbon is terminated with a secondary amine, -NHCH₃, which can react with water to form an -OH-terminated surface and release CH₃NH₂ as the product. The surface coverage of the grafted cyclic azasilane is calculated as ∼3.3 × 10¹⁴ cm^-2, assuming that each reacted -OH group contributes to one hydrocarbon linkage. For selective attachment to SiN_x over SiO₂ surfaces, we determined the reaction selectivity of aldehydes. We demonstrate that aldehydes selectively attach to SiN_x over SiO₂ surfaces, and for the specific branched aliphatic aldehyde used in this work, almost no reaction was detected with the SiO₂ surface. A fraction of the aldehyde molecules reacts with surface -NH₂ groups to form an imine (Si-N═C) surface linker with H₂O released as the byproduct. The other fraction of the aldehydes also reacts with surface -NH₂ groups but do not undergo the water-elimination step and remains attached to the surface as an aminoalcohol (Si-NH-COH-). The surface coverage of the grafted aldehyde is calculated as ∼9.8 × 10¹⁴ cm^-2 using a known infrared absorbance cross-section for the -C(CH₃)₃ groups.

Orientation measurements of clay minerals by polarized attenuated total reflection infrared spectroscopy

The orientation and organization of molecular guests within the interlayer of clay minerals control the reactivity and performance of tailored organo-clay materials. Such a detailed investigation of hybrid structure on the molecular scale is usually provided by computational methods with limited experimental validation. In this study, polarized attenuated total reflection infrared spectroscopy was used to extract quantitative orientation measurements of montmorillonite particles. The validity of the evanescent electric field amplitude calculations necessary to derive the order parameter was critically evaluated to propose a methodology for determining the orientation of the normal to the clay layer relative to a reference axis, enabling comparison with the results obtained from X-ray scattering experiments and molecular dynamic simulations. Subsequently, the orientation of the interlayer water dipole and surface hydroxyls with respect to the normal of the clay layer was experimentally determined, showing good agreement with molecular simulations. This methodology may provide quantitative insights into the molecular-level description of interfacial processes between organic molecules and clay minerals.

FTIR Analysis of Proteins and Protein-Membrane Interactions

Fourier transform infrared (FTIR) spectroscopy has become one of the major techniques of structural characterization of proteins, peptides, and protein-membrane interactions. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or intermolecular interactions. The sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as ¹³C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, the structural features of membrane pore forming proteins and peptides, and much more. The purpose of this chapter was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, is also presented.

Structure Formation in Langmuir Peptide Films As Revealed from Coarse-Grained Molecular Dynamics Simulations

Molecular dynamics simulations in conjunction with the Martini coarse-grained model have been used to investigate the (nonequilibrium) behavior of helical 22-residue poly(γ-benzyl-l-glutamate) (PBLG) peptides at the water/vapor interface. Preformed PBLG mono- or bilayers homogeneously covering the water surface laterally collapse in tens of nanoseconds, exposing significant proportions of empty water surface. This behavior was also observed in recent AFM experiments at similar areas per monomer, where a complete coverage had been assumed in earlier work. In the simulations, depending on the area per monomer, either elongated clusters or fibrils form, whose heights (together with the portion of empty water surface) increase over time. Peptides tend to align with respect to the fiber axis or with the major principal axis of the cluster, respectively. The aspect ratio of the cluster observed is 1.7 and, hence, comparable to though somewhat smaller than the aspect ratio of the peptides in α-helical conformation, which is 2.2. The heights of the fibrils is 3 nm after 20 ns and increases to 4.5 nm if the relaxation time is increased by 2 orders of magnitude, in agreement with the experiment. Aggregates with heights of about 3 or 4.5 nm are found to correspond to local bi- or trilayer structures, respectively.

Simple, Direct Routes to Polymer Brush Traps and Nanostructures for Studies of Diffusional Transport in Supported Lipid Bilayers

Patterned poly(oligo ethylene glycol) methyl ether methacrylate (POEGMEMA) brush structures may be formed by using a combination of atom-transfer radical polymerization (ATRP) and UV photopatterning. UV photolysis is used to selectively dechlorinate films of 4-(chloromethyl)phenyltrichlorosilane (CMPTS) adsorbed on silica surfaces, by exposure either through a mask or using a two-beam interferometer. Exposure through a mask yields patterns of carboxylic acid-terminated adsorbates. POEGMEMA may be grown from intact Cl initiators that were masked during exposure. Corrals, traps, and other structures formed in this way enable the patterning of proteins, vesicles, and, following vesicle rupture, supported lipid bilayers (SLBs). Bilayers adsorbed on the carboxylic acid-terminated surfaces formed by C-Cl bond photolysis in CMPTS exhibit high mobility. SLBs do not form on POEGMEMA. Using traps consisting of carboxylic acid-functionalized regions enclosed by POEGMEMA structures, electrophoresis may be observed in lipid bilayers containing a small amount of a fluorescent dye. Segregation of dye at one end of the traps was measured by fluorescence microscopy. The increase in the fluorescence intensity was found to be proportional to the trap length, while the time taken to reach the maximum value was inversely proportional to the trap length, indicating uniform, rapid diffusion in all of the traps. Nanostructured materials were formed using interferometric lithography. Channels were defined by exposure of CMPTS films to maxima in the interferogram, and POEGMEMA walls were formed by ATRP. As for the micrometer-scale patterns, bilayers did not form on the POEGMEMA structures, and high lipid mobilities were measured in the polymer-free regions of the channels.

Nanoscale investigation of the interaction of colistin with model phospholipid membranes by Langmuir technique, and combined infrared and force spectroscopies

Colistin (Polymyxin E), an antimicrobial peptide, is increasingly put forward as salvage for severe multidrug-resistant infections. Unfortunately, colistin is potentially toxic to mammalian cells. A better understanding of the interaction with specific components of the cell membranes may be helpful in controlling the factors that may enhance toxicity. Here, we report a physico-chemical study of model phospholipid (PL) mono- and bilayers exposed to colistin at different concentrations by Langmuir technique, atomic force microscopy (AFM) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). The effect of colistin on chosen PL monolayers was examined. Insights into the topographical and elastic changes in the PL bilayers within time after peptide injection are presented via AFM imaging and force spectra. Finally, changes in the PL bilayers' ATR-FTIR spectra as a function of time within three bilayer compositions, and the influence of colistin on their spectral fingerprint are examined together with the time-evolution of the Amide II and νCO band integrated intensity ratios. Our study reveals a great importance in the role of the PL composition as well as the peptide concentration on the action of colistin on PL model membranes.

Surface grafted chitosan gels. Part I. Molecular insight into the formation of chitosan and poly(acrylic acid) multilayers

Composite polyelectrolyte multilayers of chitosan and low molecular weight poly(acrylic acid) (PAA) have been assembled by sequential adsorption as a first step toward building a surface anchored chitosan gel. Silane chemistry was used to graft the first chitosan layer to prevent film detachment and decomposition. The assembly process is characterized by nonlinear growth behavior, with different adsorption kinetics for chitosan and PAA. In situ analysis of the multilayer by means of surface sensitive total internal reflection Raman (TIRR) spectroscopy, combined with target factor analysis of the spectra, provided information regarding composition, including water content, and ionization state of weak acidic and basic groups present in the thin composite film. Low molecular weight PAA, mainly in its protonated form, diffuses into and out of the composite film during adsorption and rinsing steps. The higher molecular weight chitosan shows a similar behavior, although to a much lower extent. Our data demonstrate that the charged monomeric units of chitosan are mainly compensated by carboxylate ions from PAA. Furthermore, the morphology and mechanical properties of the multilayers were investigated in situ using atomic force microscopy operating in PeakForce tapping mode. The multilayer consists of islands that grow in lateral dimension and height during the build-up process, leading to close to exponentially increasing roughness with deposition number. Both diffusion in and out of at least one of the two components (PAA) and the island-like morphology contribute to the nonlinear growth of chitosan/PAA multilayers.

Structural characterization of membrane proteins and peptides by FTIR and ATR-FTIR spectroscopy

Fourier transform infrared (FTIR) spectroscopy is widely used in structural characterization of proteins or peptides. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or upon intermolecular interactions. Sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as (13)C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, and molecular architecture of membrane pore or channel forming proteins and peptides. The purpose of this article was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, are also presented.

Enantioselective adsorption of surfactants monitored by ATR-FTIR

The selectivity of adsorption of chiral surfactants to a chiral monolayer at the solid-liquid interface was studied using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). One enantiomer of the chiral surfactant was deuterated, which causes a change in the IR absorption frequency, and allows independent measurement of the adsorption of each molecule. Both the surfactant, N-lauroyl phenylalanine (NLP), and the chiral monolayer, N-L-phenylalaninoyl, 11-undecyl-silicon, were amino acid derivatives. An enantiomeric excess of 56 +/- 22% of the L over D was observed for adsorption to the interface between a carbon tetrachloride solution containing a quasi-racemate of N-lauroyl phenylalanine and the N-L-phenylalaninoyl, 11-undecyl monolayer film on silicon. In contrast, equimolar adsorption occurred from an equimolar mixture of hydrogenated and deuterated forms of the L surfactant. The measured enantiomeric excess strongly depended on the density of chiral surface groups: the higher the density of chiral groups on the surface, the better the enantiodiscrimination, even though the total adsorption was roughly constant. This nonlinear behavior indicates that more than one chiral surface group is required for significant selectivity.

Peptide-induced domain formation in supported lipid bilayers: direct evidence by combined atomic force and polarized total internal reflection fluorescence microscopy

Direct visualization of the mechanism(s) by which peptides induce localized changes to the structure of membranes has high potential for enabling understanding of the structure-function relationship in antimicrobial and cell-penetrating peptides. We have applied a combined imaging strategy to track the interaction of a model antimicrobial peptide, PFWRIRIRR-amide, with bacterial membrane-mimetic supported phospholipid bilayers comprised of POPE/TOCL. Our in situ studies revealed rapid reorganization of the POPE/TOCL membrane into localized TOCL-rich domains with a concomitant change in the organization of the membranes themselves, as reflected by changes in fluorescent-membrane-probe order parameter, upon introduction of the peptide.

Protein secondary structure content in solution, films and tissues: redundancy and complementarity of the information content in circular dichroism, transmission and ATR FTIR spectra

The paper presents a simple and robust method to determine protein secondary structure from circular dichroism, transmission and attenuated total reflection (ATR) Fourier transform infrared spectra. It is found that the different spectroscopic methods bring valuable but roughly identical information on the secondary structure of proteins. ATR and transmission FTIR spectra display distinct differences, yet the secondary structure can be predicted from their spectra with roughly the same success. It is also found that one wavenumber or wavelength includes the large majority of the information correlated with secondary structure content and no more than 3 significant independent wavenumbers/wavelengths could be found for any of the spectroscopic data. This finding indicates that more complex linear combinations of the absorbance or ellipticities will not further improve secondary structure predictions. Furthermore, the information content in CD, transmission and ATR FTIR spectra is largely redundant. If combining CD and FTIR results in some improvement of structure prediction quality, the improvement is too modest to prompt spectroscopists to collect different spectroscopic data for structure prediction purposes. On the other hand, the data collected show that the quality of the FTIR spectrometers is such that biosensors or imaging methods sampling from 10(-9) to 10(-15) g yield spectra of sufficient quality to analyze protein secondary structure. These new techniques open the way to a new area of research, both in protein conformational response to ligand and imaging at sub-cellular scales.

Probing membrane order and topography in supported lipid bilayers by combined polarized total internal reflection fluorescence-atomic force microscopy

Determining the local structure, dynamics, and conformational requirements for protein-protein and protein-lipid interactions in membranes is critical to understanding biological processes ranging from signaling to the translocating and membranolytic action of antimicrobial peptides. We report here the application of a combined polarized total internal reflection fluorescence microscopy-in situ atomic force microscopy platform. This platform's ability to image membrane orientational order was demonstrated on DOPC/DSPC/cholesterol model membranes containing the fluorescent membrane probe, DiI-C(20) or BODIPY-PC. Spatially resolved order parameters and fluorophore tilt angles extracted from the polarized total internal reflection fluorescence microscopy images were in good agreement with the topographical details resolved by in situ atomic force microscopy, portending use of this technique for high-resolution characterization of membrane domain structures and peptide-membrane interactions.

Bioactive and structural metabolites of pseudomonas and burkholderia species causal agents of cultivated mushrooms diseases

Pseudomonas tolaasii, P. reactans and Burkholderia gladioli pv. agaricicola, are responsible of diseases on some species of cultivated mushrooms. The main bioactive metabolites produced by both Pseudomonas strains are the lipodepsipeptides (LDPs) tolaasin I and II and the so called White Line Inducing Principle (WLIP), respectively, LDPs which have been extensively studied for their role in the disease process and for their biological properties. In particular, their antimicrobial activity and the alteration of biological and model membranes (red blood cell and liposomes) was established. In the case of tolaasin I interaction with membranes was also related to the tridimensional structure in solution as determined by NMR combined with molecular dynamic calculation techniques. Recently, five news minor tolaasins, tolaasins A-E, were isolated from the culture filtrates of P. tolaasii and their chemical structure was determined by extensive use of NMR and MS spectroscopy. Furthermore, their antimicrobial activity was evaluated on target micro-organisms (fungi-including the cultivated mushrooms Agaricus bisporus, Lentinus edodes, and Pleurotus spp.-chromista, yeast and bacteria). The Gram positive bacteria resulted the most sensible and a significant structure-activity relationships was apparent. The isolation and structure determination of bioactive metabolites produced by B. gladioli pv. agaricicola are still in progress but preliminary results indicate their peptide nature. Furthermore, the exopolysaccharide (EPS) from the culture filtrates of B. gladioli pv. agaricicola, as well as the O-chain and lipid A, from the lipopolysaccharide (LPS) of the three bacteria, were isolated and the structures determined.

Bioactive and Structural Metabolites of Pseudomonas and Burkholderia Species Causal Agents of Cultivated Mushrooms Diseases

Pseudomonas tolaasii, P. reactans and Burkholderia gladioli pv. agaricicola, are responsible of diseases on some species of cultivated mushrooms. The main bioactive metabolites produced by both Pseudomonas strains are the lipodepsipeptides (LDPs) tolaasin I and II and the so called White Line Inducing Principle (WLIP), respectively, LDPs which have been extensively studied for their role in the disease process and for their biological properties. In particular, their antimicrobial activity and the alteration of biological and model membranes (red blood cell and liposomes) was established. In the case of tolaasin I interaction with membranes was also related to the tridimensional structure in solution as determined by NMR combined with molecular dynamic calculation techniques. Recently, five news minor tolaasins, tolaasins A-E, were isolated from the culture filtrates of P. tolaasii and their chemical structure was determined by extensive use of NMR and MS spectroscopy. Furthermore, their antimicrobial activity was evaluated on target micro-organisms (fungi–-including the cultivated mushrooms Agaricus bisporus, Lentinus edodes, and Pleurotus spp.–-chromista, yeast and bacteria). The Gram positive bacteria resulted the most sensible and a significant structure-activity relationships was apparent. The isolation and structure determination of bioactive metabolites produced by B. gladioli pv. agaricicola are still in progress but preliminary results indicate their peptide nature. Furthermore, the exopolysaccharide (EPS) from the culture filtrates of B. gladioli pv. agaricicola, as well as the O-chain and lipid A, from the lipo-polysaccharide (LPS) of the three bacteria, were isolated and the structures determined.

Nanobubbles at the interface between water and a hydrophobic solid

A very thin layer (5-80 nm) of gas phase, consisting of discrete bubbles with only about 40 000 molecules, is quite stable at the interface between a hydrophobic solid and water. We prepare this gas phase from either ambient air or from CO(2)(g) through a solvent exchange method reported previously. In this work, we examine the interface using attenuated total internal reflection infrared spectroscopy. The presence of rotational fine structure in the spectrum of CO(2) and D(2)O proves that molecules are present in the gas phase at the interface. The air bubbles are stable for more than 4 days, whereas the CO(2) bubbles are only stable for 1-2 h. We determine the average gas pressure inside the CO(2) bubbles from the IR spectrum in two ways: from the width of the rotational fine structure (P(gas) < 2 atm) and from the intensity in the IR spectrum (P(gas) = 1.1 +/- 0.4 atm). The small difference in gas pressure between the bubbles and the ambient (1 atm) is consistent with the long lifetime. The dimensions and curvature of a set of individual bubbles was determined by atomic force microscopy. The pressures of individual bubbles calculated from the measured curvature using the Laplace equation fall into the range P(gas) = 1.0-1.7 atm, which is concordant with the average pressure measured from the IR spectrum. We believe that the difference in stability of the CO(2) bubbles and the air bubbles is due to a combination of the much lower pressure of CO(2) in the atmosphere and the greater solubility of CO(2) in water, compared to N(2) and O(2). As expected, smaller bubbles have a shorter average lifetime than larger bubbles, and the average pressure and the curvature of individual bubbles decreases with time. Surface plasmon resonance measurements provide supporting evidence that the film is in the gas state: the thin film has a lower refractive index than water, and there are few common contaminants that satisfy this condition. Interfacial gas bubbles are not ubiquitous on hydrophobic solids: bubble-free and bubble-decorated hydrophobic interfaces can be routinely prepared.

Protein folding in membranes: insights from neutron diffraction studies of a membrane beta-sheet oligomer

Studies of the assembly of the hexapeptide Acetyl-Trp-Leu(5) (AcWL(5)) into beta-sheets in membranes have provided insights into membrane protein folding. Yet, the exact structure of the oligomer in the lipid bilayer is unknown. Here we use neutron diffraction to study the disposition of the peptides in bilayers. We find that pairs of adjacent deuterium-labeled leucines have no well-defined peak or dip in the transmembrane distribution profiles, indicative of heterogeneity in the depth of membrane insertion. At the same time, the monomeric homolog AcWL(4) exhibits a homogeneous, well-defined, interfacial location in neutron diffraction experiments. Thus, although the bilayer location of monomeric AcWL(4) is determined by hydrophobicity matching or complementarity within the bilayer, the AcWL(5) molecules in the oligomer are positioned at different depths within the bilayer because they assemble into a staggered transmembrane beta-sheet. The AcWL(5) assembly is dominated by protein-protein interactions rather than hydrophobic complementarity. These results have implications for the structure and folding of proteins in their native membrane environment and highlight the importance of the interplay between hydrophobic complementarity and protein-protein interactions in determining the structure of membrane proteins.

A mechanistic link between oxidative stress and membrane mediated amyloidogenesis revealed by infrared spectroscopy

The fully developed lesion of Alzheimer's disease is a dense plaque composed of fibrillar amyloid beta-proteins (Abeta) with a characteristic and well-ordered beta-sheet secondary structure. Because the incipient lesion most likely develops when these proteins are first induced to form beta-sheet structure, it is important to understand factors that induced Abeta to adopt this conformation. In this review, we describe the application of polarized attenuated total internal reflection infrared FT-IR spectroscopy for characterizing the conformation, orientation, and rate of accumulation of Abeta on lipid membranes. We also describe the application and yield of linked analysis, whereby multiple spectra are fit simultaneously with component bands that are constrained to share common fitting parameters. Results have shown that membranes promote beta-sheet formation under a variety of circumstances that may be significant to the pathogenesis of Alzheimer's disease.

The lipid dependence of melittin action investigated by dual-color fluorescence burst analysis

Dual-color fluorescence-burst analysis was used to study melittin-induced leakage of macromolecules from liposomes of various lipid compositions. To perform dual-color fluorescence-burst analysis, fluorescently labeled size-marker molecules were encapsulated into liposomes, labeled with a second lipid-attached fluorophore. By correlating the fluorescence bursts, resulting from the liposomes diffusing through the detection volume of a dual-color confocal microscope, the distribution of size-marker molecules over the liposomes was determined. It was found that melittin causes leakage via two different mechanisms: 1), For liposomes composed of neutral bilayer-forming lipids, low melittin concentrations induced pore formation with the pore size depending on the melittin concentration. 2), For liposomes containing anionic and/or nonbilayer forming lipids, melittin induced fusion or aggregation of liposomes accompanied by a-specific leakage. Experiments with liposomes prepared from Escherichia coli lipid extracts and intact cells of Lactococcus lactis indicate that both mechanisms are physiologically relevant.

A nanoscale gas state

We show that a very thin (5-80 nm) gas phase can exist for a long time (>1 h) at the interface between a hydrophobic solid and water. We create the gas phase from CO2, which allows us to determine the chemical identity, phase state, and density via infrared spectroscopy. The average density reveals that the gas is at approximately atmospheric pressure, which explains the unexpectedly long lifetime of the gas phase under ambient conditions. The nanoscale gas phase is reproducibly created under conditions where gas solubility is varied.

WLIP and tolaasin I, lipodepsipeptides from Pseudomonas reactans and Pseudomonas tolaasii, permeabilise model membranes

The activity of the White Line Inducing Principle (WLIP) and tolaasin I, produced by virulent strains of Pseudomonas reactans and Pseudomonas tolaasii, respectively, was comparatively evaluated on lipid membranes. Both lipodepsipeptides were able to induce the release of calcein from large unilamellar vesicles. Their activity was dependent on the toxin concentration and liposome composition and in particular it increased with the sphingomyelin content of the membrane. Studies of dynamic light scattering suggested a detergent-like activity for WLIP at high concentration (> 27 microM). This effect was not detected for tolaasin I at the concentrations tested (< 28 microM). Differences were also observed in lipodepsipeptides secondary structure. In particular, the conformation of the smaller WLIP changed slightly when it passed from the buffer solution to the lipid environment. On the contrary, we observed a valuable increment in the helical content of tolaasin I which was inserted in the membrane core and oriented parallel to the lipid acyl chains.

Three-Stage Multilayer Formation Kinetics during Adsorption of an Anionic Fluorinated Surfactant onto Germanium. 1. Concentration Effect

The adsorption of tetraethylammonium perfluorooctylsulfonate (TEA-FOS) from aqueous solution onto hydroxylated germanium is studied using in situ polarized attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). The adsorption is monitored at a series of bulk solution concentrations spanning from well below to above the critical micelle concentration (CMC; 1.0 mM). The kinetics of adsorption is followed by monitoring the intensity of the fluorocarbon bands. The orientation of the fluorocarbon director with respect to the germanium surface is determined by circular dichroism measurements of CF2 stretching bands. At bulk concentrations ranging from 10% of the CMC to at least 500% of the CMC, the adsorption occurs in an unusual sequence of three stages. Initially, rapid adsorption occurs within 200 min, leading to coverage of a monolayer or less. A long period of slow adsorption follows, during which we hypothesize that surfactant molecules form clusters, some of which serve as nuclei for multilayer growth. This stage concludes suddenly with an acceleration in the rate of adsorption, which eventually leads to multilayer formation. Because this is an anionic surfactant adsorbing onto a negatively charged surface at pH 6, the tetraethylammonium ions must mediate the interactions between the surfactant headgroups and the surface. The dichroism measurements show that TEA-FOS is initially oriented randomly or somewhat parallel to the surface, but over time adopts an orientation somewhat normal to the surface. This behavior is consistent with initial adsorption at isolated sites, followed by aggregation into isotropic admicelles, and finally growth into flattened admicelles. The sudden onset of accelerated adsorption can be explained either by autoaccelerating adsorption or nucleation and growth of a hydrophobic multilayer structure.

Properties of nonfused liposomes immobilized on an L1 Biacore chip and their permeabilization by a eukaryotic pore-forming toxin

The L1 chip is used intensively for protein-membrane interaction studies in Biacore surface plasmon resonance systems. The exact form of captured lipid membranes on the chip is, however, not precisely known. Evidence exists that the vesicles both remain intact after the binding to the chip and fuse to form a large single-bilayer membrane. In this study, we were able to bind up to approximately 11,500 resonance units of zwitterionic liposomes (100 nm in diameter) at a low flow rate. We show by fluorescence microscopy that the entire surface of the flow cell is covered homogeneously by liposomes. Negatively charged vesicles (i.e., those composed of phosphatidylcholine/phosphatidylglycerol [1:1]) always deposited less densely, but we were able to increase the density slightly with the use of calcium chloride that promotes fusion of the vesicles. Finally, we used zwitterionic liposomes loaded with fluorescent probe calcein to show that they remain intact after the capture on the L1 chip. The fluorescence was lost only after we used equinatoxin, a well-studied pore-forming toxin, to perform on-chip permeabilization of vesicles. The characteristics of permeabilization process for chip-immobilized liposomes are similar to those of liposomes free in solution. All results collectively suggest that liposomes do not fuse to form a single bilayer on the surface of the chip.

Morphological behavior of lipid bilayers induced by melittin near the phase transition temperature

Morphological changes of DMPC, DLPC, and DPPC bilayers containing melittin (lecithin/melittin molar ratio of 10:1) around the gel-to-liquid crystalline phase transition temperatures (Tc) were examined by a variety of biophysical methods. First, giant vesicles with the diameters of approximately 20 microm were observed by optical microscopy for melittin-DMPC bilayers at 27.9 degrees C. When the temperature was lowered to 24.9 degrees C (Tc = 23 degrees C for the neat DMPC bilayers), the surface of vesicles became blurred and dynamic pore formation was visible in the microscopic picture taken at different exposure times. Phase separation and association of melittin molecules in the bilayers were further detected by fluorescent microscopy and mass spectrometry, respectively. These vesicles disappeared completely at 22.9 degrees C. It was thus found that the melittin-lecithin bilayers reversibly undergo their fusion and disruption near the respective Tcs. The fluctuation of lipids is, therefore, responsible for the membrane fusion above the Tc, and the association of melittin molecules causes membrane fragmentation below the Tc. Subsequent magnetic alignments were observed by solid-state (31)P NMR spectra for the melittin-lecithin vesicles at a temperature above the respective Tcs. On the other hand, additional large amplitude motion induced by melittin at a temperature near the Tc breaks down the magnetic alignment.

Disorder influence on linear dichroism analyses of smectic phases

Linear dichroism, the unequal absorption of parallel and perpendicular linear polarized light, is often used to determine the anisotropic ordering of rodlike polymers in a smectic phase, such as helices in a lipid bilayer. It is a measure of two properties of the sample: 1), orientation of the chromophore transition dipole moment (TDM) and 2), disorder. Since it is the orientation of the chromophore TDM that is needed for high resolution structural studies, it is imperative to either deconvolve sample disorder, or at a minimum, estimate its effect upon the calculated TDM orientation. Herein, a rigorous analysis of the effects of disorder is undertaken based on the recently developed Gaussian disorder model implemented in linear dichroism data. The calculation of both the rod tilt and rotational pitch angles as a function of the disorder and dichroism, yield the following conclusions: Disorders smaller than 5 degrees have a vanishingly small effect on the calculated polymer orientation, whereas values smaller than 10 degrees have a negligible effect on the calculated parameters. Disorders larger than 10 degrees have an appreciable effect on the calculated orientational parameters and as such must be estimated before any structural characterization. Finally the theory is tested on the HIV vpu transmembrane domain, employing experimental mosaicity measurements from x-ray reflectivity rocking scans and linear dichroism.

Evaluation of the ordering of membranes in multilayer stacks built on an ATR-FTIR germanium crystal with atomic force microscopy: the case of the H(+),K(+)-ATPase-containing gastric tubulovesicle membranes

Polarized attenuated total reflection Fourier transform infrared spectra were recorded on multilayer stacks of native gastric tubulovesicle membranes. The spectral intensity and linear dichroism were measured for average thicknesses ranging between 0 and 100 bilayers. Atomic force microscopy was used to investigate the orientation of the membranes at the top of the stack. Height profiles were obtained along randomly drawn lines and slopes were computed over various distances. Orientation distribution functions were obtained from the slopes and decomposed into Legendre polynomials. It was found that the second Legendre polynomials coefficient characterizing the membrane orientation was always larger than 0.9. It could therefore be concluded that the membrane tilt does not significantly contribute to the infrared dichroism, even for the largest thicknesses tested.

Conformation, orientation, and adsorption kinetics of dermaseptin B2 onto synthetic supports at aqueous/solid interface

The antimicrobial activity of cationic amphipathic peptides is due mainly to the adsorption of peptides onto target membranes, which can be modulated by such physicochemical parameters as charge and hydrophobicity. We investigated the structure of dermaseptin B2 (Drs B2) at the aqueous/synthetic solid support interface and its adsorption kinetics using attenuated total reflection Fourier transform infrared spectroscopy and surface plasmon resonance. We determined the conformation and affinity of Drs B2 adsorbed onto negatively charged (silica or dextran) and hydrophobic supports. Synthetic supports of differing hydrophobicity were obtained by modifying silica or gold with omega-functionalized alkylsilanes (bromo, vinyl, phenyl, methyl) or alkylthiols. The peptide molecules adsorbed onto negatively charged supports mostly had a beta-type conformation. In contrast, a monolayer of Drs B2, mainly in the alpha-helical conformation, was adsorbed irreversibly onto the hydrophobic synthetic supports. The conformational changes during formation of the adsorbed monolayer were monitored by two-dimensional Fourier transform infrared spectroscopy correlation; they showed the influence of peptide-peptide interactions on alpha-helix folding on the most hydrophobic support. The orientation of the alpha-helical Drs B2 with respect to the hydrophobic support was determined by polarized attenuated total reflection; it was around 15 +/- 5 degrees. This orientation was confirmed and illustrated by a molecular dynamics study. These combined data demonstrate that specific chemical environments influence the structure of Drs B2, which could explain the many functions of antimicrobial peptides.

Structural and functional implications of the instability of the ADP/ATP transporter purified from mitochondria as revealed by FTIR spectroscopy

The ADP/ATP transporter shows a high instability when solubilized, making it difficult to obtain functional protein with sufficient purity for long-term spectroscopic studies. When solubilized in the detergent dodecyl maltoside the protein is in equilibrium between the so-called CATR and BA conformations and in a few hours it becomes nonfunctional, unable to bind either its inhibitors or its substrates. By Fourier transform infrared spectroscopy, we studied the structural changes involved in this denaturation process. To do so, the carboxyatractyloside-inhibited protein was used as a structural model for the protein in the CATR conformation and its spectrum was compared with that of the unliganded time-inactivated protein. From the difference spectra of the amide I, amide II, and amide A bands combined with dichroism spectra of the carboxyatractyloside-inhibited protein, we concluded that few structural differences exist between both states, affecting as few as 11 amino acids (3.5% of the protein); the structural changes consisted in the disappearance of large loop structure and the appearance of aggregated strands. We hypothesize that some mitochondrial loop (tentatively loop M1) shows a high tendency to aggregate, being responsible for the observed features. The functional consequences of this hypothesis are discussed.

Reversible immobilization of peptides: surface modification and in situ detection by attenuated total reflection FTIR spectroscopy

A generic method is described for the reversible immobilization of polyhistidine-bearing polypeptides and proteins on attenuated total reflecting (ATR) sensor surfaces for the detection of biomolecular interactions by FTIR spectroscopy. Nitrilotriacetic acid (NTA) groups are covalently attached to self-assembled monolayers of either thioalkanes on gold films or mercaptosilanes on silicon dioxide films deposited on germanium internal reflection elements. Complex formation between Ni2+ ions and NTA groups activates the ATR sensor surface for the selective binding of polyhistidine sequences. This approach not only allows a stable and reversible immobilization of histidine-tagged peptides (His-peptides) but also simultaneously allows the direct in situ quantification of surface-adsorbed molecules from their specific FTIR spectral bands. The surface concentrations of both NTA and His-peptide on silanized surfaces were determined to be 1.1 and 0.4 molecules nm-2, respectively, which means that the surface is densely covered. A comparison of experimental FTIR spectra with simulated spectra reveals a surface-enhancement effect of one order of magnitude for the gold surfaces. With the presented sensor surfaces, new ways are opened up to investigate, in situ and with high sensitivity and reproducibility, protein-ligand, protein-protein, protein-DNA interactions, and DNA hybridization by ATR-FTIR spectroscopy.

Ligand-induced differences in secondary structure of the Vibrio parahaemolyticus Na+/galactose cotransporter

A detailed structural study of the prokaryotic sodium/galactose transporter (vSGLT) from Vibrio parahaemolyticus using attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy reveals stepwise increases in alpha-helicity upon binding of sodium and D-galactose. These increases in helicity correlate with decreases in beta-structural elements. The changes are accompanied by stepwise reductions in the degree of H/D exchange (HDX), suggesting reduced accessibility of water to the protein backbone. The data demonstrate discrete conformational changes from one intermediate to the next during the catalytic cycle of the protein and are interpreted in a model of the symport reaction mechanism.

Implications of threonine hydrogen bonding in the glycophorin A transmembrane helix dimer

The transmembrane helix of glycophorin A contains a seven-residue motif, LIxxGVxxGVxxT, that mediates protein dimerization. Threonine is the only polar amino acid in this motif with the potential to stabilize the dimer through hydrogen-bonding interactions. Polarized Fourier transform infrared spectroscopy is used to establish a robust protocol for incorporating glycophorin A transmembrane peptides into membrane bilayers. Analysis of the dichroic ratio of the 1655-cm(-1) amide I vibration indicates that peptides reconstituted by detergent dialysis have a transmembrane orientation with a helix crossing angle of <35 degrees. Solid-state nuclear magnetic resonance spectroscopy is used to establish high resolution structural restraints on the conformation and packing of Thr-87 in the dimer interface. Rotational resonance measurement of a 2.9-A distance between the gamma-methyl and backbone carbonyl carbons of Thr-87 is consistent with a gauche- conformation for the chi1 torsion angle. Rotational-echo double-resonance measurements demonstrate close packing (4.0 +/- 0.2 A) of the Thr-87 gamma-methyl group with the backbone nitrogen of Ile-88 across the dimer interface. The short interhelical distance places the beta-hydroxyl of Thr-87 within hydrogen-bonding range of the backbone carbonyl of Val-84 on the opposing helix. These results refine the structure of the glycophorin A dimer in membrane bilayers and highlight the complementary role of small and polar residues in the tight association of transmembrane helices in membrane proteins.

Membrane-induced folding of cecropin A

Lipid membranes manifest a diverse array of surface forces that can fold and orient an approaching protein. To better understand these forces and their ability to influence protein function, we have used infrared spectroscopy with isotopic editing to characterize the 37-residue membrane-active antimicrobial polypeptide cecropin A as it approached, adsorbed onto, and finally penetrated various lipid membranes. Intermediate stages in this process were isolated for study by the use of internal reflection and Langmuir trough techniques. Results indicate that this peptide adopts well-ordered secondary structure while superficially adsorbed to a membrane surface. Its conformation is predominantly alpha-helical, although some beta structure is likely to be present. The longitudinal axis of the helical structure, and the transverse axes of any beta structure, are preferentially oriented parallel to the membrane surface. The peptide expands the membrane against pressure when it penetrates the membrane surface, but its structure and orientation do not change. These observations indicate that interactions between the peptide and deeper hydrophobic regions of the membrane provide energy to perform thermodynamic work, but separate and distinct interactions between the peptide and superficial components of the membrane are responsible for peptide folding. These results have broad implications for our understanding of the mechanism of action and the specificity of these antimicrobial peptides.

Accelerated accumulation of amyloid beta proteins on oxidatively damaged lipid membranes

The fully developed lesion of Alzheimer's Disease is a dense plaque composed of fibrillar amyloid beta-proteins with a characteristic and well-ordered beta-sheet secondary structure. Because the incipient lesion most likely develops when these proteins are first induced to form beta-sheet secondary structure, it is important to understand factors that induce amyloid beta-proteins to adopt this conformation. In this investigation we used a novel form of infrared spectroscopy that can characterize the conformation, orientation, and rate of accumulation of the protein on various lipid membranes to determine whether oxidatively damaged phospholipid membranes induce the formation of beta-sheet secondary structure in a 42-residue amyloid beta-protein. We found that membranes containing oxidatively damaged phospholipids accumulated amyloid beta-protein significantly faster than membranes containing only unoxidized or saturated phospholipids. Accelerated accumulation was also seen when 3 mol % G(M1) ganglioside was incorporated into a saturated phosphatidylcholine membrane. The accumulated protein more completely adopted a beta-sheet conformation on oxidized membranes, and the plane of the beta-sheet was oriented parallel to the plane of the membrane. These results indicate that oxidatively damaged phospholipid membranes promote beta-sheet formation by amyloid beta-proteins, and they suggest a possible role for lipid peroxidation in the pathogenesis of Alzheimer's Disease.

Orientation of the infrared transition moments for an alpha-helix

Appropriate values for the orientation of the amide transition dipoles are essential to the growing use of isotopically edited vibrational spectroscopy generally in structural biology and to infrared dichroism measurements on membrane-associated alpha-helices, in particular. The orientations of the transition moments for the amide vibrations of an alpha-helix have been determined from the ratio of intensities of the A- and E(1)-symmetry modes in the infrared spectra of poly(gamma-methyl-L-glutamate)(x)-co-(gamma-n-octadecyl-L-glutamate)( y) oriented on silicon substrates. Samples possessing a high degree of alignment were used to facilitate band fitting. Consistent results were obtained from both attenuated total reflection and transmission experiments with polarized radiation, yielding values of Theta(I) = 38 degrees, Theta(II) = 73 degrees, and Theta(A) = 29 degrees, relative to the helix axis, for the amide I, amide II, and amide A bands, respectively. The measurements are discussed both in the context of the somewhat divergent older determinations, and in relation to the helix geometry and results on model amide compounds, to resolve current uncertainties in the literature.

Conformation and dynamics of melittin bound to magnetically oriented lipid bilayers by solid-state (31)P and (13)C NMR spectroscopy

The conformation and dynamics of melittin bound to the dimyristoylphosphatidylcholine (DMPC) bilayer and the magnetic orientation in the lipid bilayer systems were investigated by solid-state (31)P and (13)C NMR spectroscopy. Using (31)P NMR, it was found that melittin-lipid bilayers form magnetically oriented elongated vesicles with the long axis parallel to the magnetic field above the liquid crystalline-gel phase transition temperature (T(m) = 24 degrees C). The conformation, orientation, and dynamics of melittin bound to the membrane were further determined by using this magnetically oriented lipid bilayer system. For this purpose, the (13)C NMR spectra of site-specifically (13)C-labeled melittin bound to the membrane in the static, fast magic angle spinning (MAS) and slow MAS conditions were measured. Subsequently, we analyzed the (13)C chemical shift tensors of carbonyl carbons in the peptide backbone under the conditions where they form an alpha-helix and reorient rapidly about the average helical axis. Finally, it was found that melittin adopts a transmembrane alpha-helix whose average axis is parallel to the bilayer normal. The kink angle between the N- and C-terminal helical rods of melittin in the lipid bilayer is approximately 140 degrees or approximately 160 degrees, which is larger than the value of 120 degrees determined by x-ray diffraction studies. Pore formation was clearly observed below the T(m) in the initial stage of lysis by microscope. This is considered to be caused by the association of melittin molecules in the lipid bilayer.

Secondary structure, orientation, oligomerization, and lipid interactions of the transmembrane domain of influenza hemagglutinin

Influenza virus hemagglutinin (HA), the viral envelope glycoprotein that mediates fusion between the viral and cellular membranes, is a homotrimer of three subunits, each containing two disulfide-linked polypeptide chains, HA(1) and HA(2). Each HA(2) chain spans the viral membrane with a single putative transmembrane alpha-helix near its C-terminus. Fusion experiments with recombinant HAs suggest that this sequence is required for a late step of membrane fusion, as a glycosylphosphatidylinositol-anchored analogue of HA only mediates "hemifusion" of membranes, i.e., the merging of the proximal, but not distal, leaflets of the two juxtaposed lipid bilayers [Kemble et al. (1994) Cell 76, 383-391]. To find a structural explanation for the function of the transmembrane domain of HA(2) in membrane fusion, we have studied the secondary structure, orientation, oligomerization, and lipid interactions of a synthetic peptide representing the transmembrane segment of X:31 HA (TMX31) by circular dichroism and attenuated total reflection Fourier transform infrared spectroscopy and by gel electrophoresis. The peptide was predominantly alpha-helical in detergent micelles and in phospholipid bilayers. The helicity was increased in lipid bilayers composed of acidic lipids compared to pure phosphatidylcholine bilayers. In planar lipid bilayers, the helices were oriented close to the membrane normal. TMX31 aggregated into small heat-resistant oligomers composed of two to five subunits in SDS micelles. Amide hydrogen exchange experiments indicated that a large fraction of the helical residues were accessible to water, suggesting the possibility that TMX31 forms pores in lipid bilayers. Finally, the peptide increased the acyl chain order in lipid bilayers, which may be related to the preferential association of HA with lipid "rafts" in the cell surface and which may be an important prerequisite for complete membrane fusion.

Lipid-induced conformation and lipid-binding properties of cytolytic and antimicrobial peptides: determination and biological specificity

While antimicrobial and cytolytic peptides exert their effects on cells largely by interacting with the lipid bilayers of their membranes, the influence of the cell membrane lipid composition on the specificity of these peptides towards a given organism is not yet understood. The lack of experimental model systems that mimic the complexity of natural cell membranes has hampered efforts to establish a direct correlation between the induced conformation of these peptides upon binding to cell membranes and their biological specificities. Nevertheless, studies using model membranes reconstituted from lipids and a few membrane-associated proteins, combined with spectroscopic techniques (i.e. circular dichroism, fluorescence spectroscopy, Fourier transform infra red spectroscopy, etc.), have provided information on specific structure-function relationships of peptide-membrane interactions at the molecular level. Reversed phase-high performance chromatography (RP-HPLC) and surface plasmon resonance (SPR) are emerging techniques for the study of the dynamics of the interactions between cytolytic and antimicrobial peptides and lipid surfaces. Thus, the immobilization of lipid moieties onto RP-HPLC sorbent now allows the investigation of peptide conformational transition upon interaction with membrane surfaces, while SPR allows the observation of the time course of peptide binding to membrane surfaces. Such studies have clearly demonstrated the complexity of peptide-membrane interactions in terms of the mutual changes in peptide binding, conformation, orientation, and lipid organization, and have, to a certain extent, allowed correlations to be drawn between peptide conformational properties and lytic activity.

Quantitation of secondary structure in ATR infrared spectroscopy

Polarized attenuated total reflection infrared spectroscopy of aligned membranes provides essential information on the secondary structure content and orientation of the associated membrane proteins. Quantitation of the relative content of different secondary structures, however, requires allowance for geometric relations of the electric field components (E(x), E(y), E(z)) of the evanescent wave, and of the components of the infrared transition moments, in combining absorbances (A and A(perpendicular)) measured with radiation polarized parallel with and perpendicular to, respectively, the plane of incidence. This has hitherto not been done. The appropriate combination for exact evaluation of relative integrated absorbances is A + (2E(z)(2)/E(y)(2) - E(x)(2)/E(y)(2))A(perpendicular), where z is the axis of ordering that is normal to the membrane plane, and the x-axis lies in the membrane plane within the plane of incidence. This combination can take values in the range approximately from A - 0.4A(perpendicular) to A + 2.7A(perpendicular), depending on experimental conditions and the attenuated total reflection crystal used. With unpolarized radiation, this correction is not possible. Similar considerations apply to the dichroic ratios of multicomponent bands, which are also treated.

Lipoprotein A-I structure

High density lipoproteins are produced by the liver as protein-lipid complexes with a characteristic discoidal shape. A crystal structure is available for the chief protein component of these complexes, apolipoprotein A-I, but controversy about how this protein is situated with respect to the lipid components has flourished for lack of experimental techniques that can characterize protein structure in a lipid environment. New spectroscopic techniques developed to address this problem now indicate that apolipoprotein A-I is arranged as a helical belt around a bilayer of phospholipids. This is an important step towards understanding how these lipoproteins regulate cholesterol transport.

The structure of human lipoprotein A-I. Evidence for the "belt" model

The two main competing models for the structure of discoidal lipoprotein A-I complexes both presume that the protein component is helical and situated around the perimeter of a lipid bilayer disc. However, the more popular "picket fence" model orients the protein helices perpendicular to the surface of the lipid bilayer, while the alternative "belt" model orients them parallel to the bilayer surface. To distinguish between these models, we have investigated the structure of human lipoprotein A-I using a novel form of polarized internal reflection infrared spectroscopy that can characterize the relative orientation of protein and lipid components in the lipoprotein complexes under native conditions. Our results verify lipid bilayer structure in the complexes and point unambiguously to the belt model.