Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes

Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy

A novel spectroscopic approach for studying the flexibility and mobility in the hydrophobic interior of lipid bilayers at specific depths is proposed. A set of test compounds featuring an azido moiety and a cyano or carboxylic acid moiety, connected by an alkyl chain of different lengths, was synthesized. FTIR data and molecular dynamics calculations indicated that the test compounds in a bilayer are oriented so that the cyano or carboxylic acid moiety is located in the lipid head-group region, while the azido group stays inside the bilayer at the depth determined by its alkyl chain length. We found that the asymmetric stretching mode of the azido group (νN3) can serve as a reporter of the membrane interior dynamics. FTIR and two-dimensional infrared (2DIR) studies were performed at different temperatures, ranging from 22 to 45 °C, covering the Lβ-Lα phase transition temperature of dipalmitoylphosphatidylcholine (∼41 °C). The width of the νN3 peak was found to be very sensitive to the phase transition and to the temperature in general. We introduced an order parameter, SN3, which characterizes restrictions to motion inside the bilayer. 2DIR spectra of νN3 showed different extents of inhomogeneity at different depths in the bilayer, with the smallest inhomogeneity in the middle of the leaflet. The spectral diffusion dynamics of the N3 peak was found to be dependent on the depth of the N3 group location in the bilayer. The obtained results enhance our understanding of the bilayer dynamics and can be extended to investigate membranes with more complex compositions.

Long Vibrational Lifetime R-Selenocyanate Probes for Ultrafast Infrared Spectroscopy: Properties and Synthesis

Ultrafast infrared vibrational spectroscopy is widely used for the investigation of dynamics in systems from water to model membranes. Because the experimental observation window is limited to a few times the probe's vibrational lifetime, a frequent obstacle for the measurement of a broad time range is short molecular vibrational lifetimes (typically a few to tens of picoseconds). Five new long-lifetime aromatic selenocyanate vibrational probes have been synthesized and their vibrational properties characterized. These probes are compared to commercial phenyl selenocyanate. The vibrational lifetimes range between ∼400 and 500 ps in complex solvents, which are some of the longest room-temperature vibrational lifetimes reported to date. In contrast to vibrations that are long-lived in simple solvents such as CCl₄, but become much shorter in complex solvents, the probes discussed here have ∼400 ps lifetimes in complex solvents and even longer in simple solvents. One of them has a remarkable lifetime of 1235 ps in CCl₄. These probes have a range of molecular sizes and geometries that can make them useful for placement into different complex materials due to steric reasons, and some of them have functionalities that enable their synthetic incorporation into larger molecules, such as industrial polymers. We investigated the effect of a range of electron-donating and electron-withdrawing para-substituents on the vibrational properties of the CN stretch. The probes have a solvent-independent linear relationship to the Hammett substituent parameter when evaluated with respect to the CN vibrational frequency and the ipso ¹³C NMR chemical shift.

Modulation of Membrane Fluidity to Control Interfacial Water Structure and Dynamics in Saturated and Unsaturated Phospholipid Vesicles

The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.

Phonon-mediated lipid raft formation in biological membranes

Short-wavelength collective molecular motions, also known as phonons, have recently attracted much interest in revealing dynamic properties of biological membranes through the use of neutron and X-ray scattering, infrared and Raman spectroscopies, and molecular dynamics simulations. Experimentally detecting unique vibrational patterns such as, shear phonon excitations, viscoelastic crossovers, transverse acoustic phonon gaps, and continuous and truncated optical phonon modes in cellular membranes, to name a few, has proven non-trivial. Here, we review recent advances in liquid thermodynamics that have resulted in the development of the phonon theory of liquids. The theory has important predictions regarding the shear vibrational spectra of fluids, namely the emergence of viscoelastic crossovers and transverse acoustic phonon gaps. Furthermore, we show that these vibrational patterns are common in soft (non-crystalline) materials, including, but not limited to liquids, colloids, liquid crystals (mesogens), block copolymers, and biological membranes. The existence of viscoelastic crossovers and acoustic phonon gaps define the self-diffusion properties of cellular membranes and provide a molecular picture of the transient nature of lipid rafts (Bolmatov et al., 2020). Importantly, the timescales (picoseconds) for the formation and dissolution of transient lipid rafts match the lifetime of the formation and breakdown of interfacial water hydrogen bonds. Apart from acoustic propagating phonon modes, biological membranes can also support more energetic non-propagating optical phonon excitations, also known as standing waves or breathing modes. Importantly, optical phonons can be truncated due to the existence of finite size nanodomains made up of strongly correlated lipid-cholesterol molecular pairs. These strongly coupled molecular pairs can serve as nucleation centers for the formation of stable rafts at larger length scales, due to correlations of spontaneous fluctuations (Onsager's regression hypothesis). Finally and importantly, molecular level viscoelastic crossovers, acoustic phonon gaps, and continuous and truncated optical phonon modes may offer insights as to how lipid-lipid and lipid-protein interactions enable biological function.

Effect of DMSO on the Mechanical and Structural Properties of Model and Biological Membranes

Dimethyl sulfoxide (DMSO) is widely used in a number of biological and biotechnological applications, mainly because of its effects on the cell plasma membrane, but the molecular origins of this action are yet to be fully clarified. In this work, we used two- and three-component synthetic membranes (liposomes) and the plasma membrane of human erythrocytes to investigate the effect of DMSO when added to the membrane-solvating environment. Fourier transform infrared spectroscopy and thermal fluctuation spectroscopy revealed significant differences in the response of the two types of liposome systems to DMSO in terms of the bilayer thermotropic behavior, available free volume of the bilayer, its excess surface area, and bending elasticity. DMSO also alters the mechanical properties of the erythrocyte membrane in a concentration-dependent manner and is capable of increasing membrane permeability to ATP at even relatively low concentrations (3% v/v and above). Taken in its entirety, these results show that DMSO is likely to have a differential effect on heterogeneous biological membranes, depending on their local composition and structure, and could affect membrane-hosted biological functions.

Assessing the Location of Ionic and Molecular Solutes in a Molecularly Heterogeneous and Nonionic Deep Eutectic Solvent

Deep eutectic solvents (DES) are emerging sustainable designer solvents viewed as greener and better alternatives to ionic liquids. Nonionic DESs possess unique properties such as viscosity and hydrophobicity that make them desirable in microextraction applications such as oil-spill remediation. This work builds upon a nonionic DES, NMA–LA DES, previously designed by our group. The NMA–LA DES presents a rich nanoscopic morphology that could be used to allocate solutes of different polarities. In this work, the possibility of solvating different solutes within the nanoscopically heterogeneous molecular structure of the NMA–LA DES is investigated using ionic and molecular solutes. In particular, the localized vibrational transitions in these solutes are used as reporters of the DES molecular structure via vibrational spectroscopy. The FTIR and 2DIR data suggest that the ionic solute is confined in a polar and continuous domain formed by NMA, clearly sensing the direct effect of the change in NMA concentration. In the case of the molecular nonionic and polar solute, the data indicates that the solute resides in the interface between the polar and nonpolar domains. Finally, the results for the nonpolar and nonionic solute (W(CO)₆) are unexpected and less conclusive. Contrary to its polarity, the data suggest that the W(CO)₆ resides within the NMA polar domain of the DES, probably by inducing a domain restructuring in the solvent. However, the data are not conclusive enough to discard the possibility that the restructuring comprises not only the polar domain but also the interface. Overall, our results demonstrate that the NMA–LA DES has nanoscopic domains with affinity to particular molecular properties, such as polarity. Thus, the presented results have a direct implication to separation science.

Free volume and dynamics in a lipid bilayer

The lateral diffusion of lipids and of small molecules inside a membrane is strictly related to the arrangement of acyl chains and to their mobility. In this study, we use FTIR and time resolved 2D-IR spectroscopic techniques to characterize the structure and dynamics of the hydrophobic region of palmitoyl-oleylphosphatidylcholine/cholesterol vesicles dispersed in water/dimethylsulfoxide solutions. By means of a non-polar probe, hexacarbonyl tungsten, we monitor the distribution of free volumes inside the bilayer and the conformational dynamics of hydrophobic tails in relation to the different compositions of the membrane or the different compositions of the solvent. Despite the important structural changes induced by the presence of DMSO in the solvating medium, the picosecond dynamics of the membrane is preserved under the different conditions.

Water Structure and Dynamics in the Stern Layer of Micelles: Femtosecond Mid-Infrared Pump-Probe Spectroscopy Study

Molecular-level understanding of the water structure and dynamics in the Stern layer of micelles is important to elucidate the active role of water in biological processes on membrane surfaces. Micelles and reverse micelles are considered to be excellent membrane model systems. Here, to address the question of whether or not the spatial confinement effect on water in reverse micelles and nanometric water pool systems plays a role in modulating water dynamics, we consider four different aqueous micelle solutions and study the water dynamics in the Stern layer of micelles using a femtosecond mid-infrared pump-probe spectroscopy technique. Vibrational energy relaxation and rotational dynamics of the O?D stretch mode of HDO and the azido stretch mode of hydrazoic acid are critically dependent on the charge, polarity, and chemical structure of the surfactant head group. In particular, water molecules in the Stern layer of micelles, which are not in spatially confined environments, are notably different from those in bulk water. This finding clearly indicates that changes in the vibrational and rotational dynamics of water molecules, even in spatially confined systems, are mainly induced by surface effects instead of spatial confinement effects. We believe that the present experimental results are of importance for understanding water-involved biochemical processes on biological membranes.

Self-Assembly of Amphiphiles into Vesicles and Fibrils: Investigation of Structure and Dynamics Using Spectroscopy and Microscopy Techniques

Amphiphiles are a class of molecules which are known to assemble into a variety of nanostructures. The understanding and applications of self-assembled systems are based on what has been learned from biology. Among the vast number of self-assemblies, in this article, we have described the formation, characterization, and dynamics of two important biologically inspired assemblies: vesicles and fibrils. Vesicles, which can be classified into several categories depending on the sizes and components, are of great interest due to their potential applications in drug delivery and as nanoscale reactors. The structure and dynamics of vesicles can also mimic the complex geometry of the cell membrane. On the other hand, the self-assembly of proteins, peptides, and even single amino acids leads to a number of degenerative disorders. Thus, a complete understanding of these self-assembled systems is necessary. In this article, we discuss recent work on vesicular aggregates composed of phospholipids, fatty acids, and ionic as well as nonionic surfactants and single amino acid-based fibrils such as phenylalanine and tyrosine. Beside the characterization, we also emphasize the excited-state dynamics inside the aggregates for a proper understanding of the organization, reactivity, and heterogeneity of the aggregates.

Water at surfaces with tunable surface chemistries

Aqueous interfaces are ubiquitous in natural environments, spanning atmospheric, geological, oceanographic, and biological systems, as well as in technical applications, such as fuel cells and membrane filtration. Where liquid water terminates at a surface, an interfacial region is formed, which exhibits distinct properties from the bulk aqueous phase. The unique properties of water are governed by the hydrogen-bonded network. The chemical and physical properties of the surface dictate the boundary conditions of the bulk hydrogen-bonded network and thus the interfacial properties of the water and any molecules in that region. Understanding the properties of interfacial water requires systematically characterizing the structure and dynamics of interfacial water as a function of the surface chemistry. In this review, we focus on the use of experimental surface-specific spectroscopic methods to understand the properties of interfacial water as a function of surface chemistry. Investigations of the air-water interface, as well as efforts in tuning the properties of the air-water interface by adding solutes or surfactants, are briefly discussed. Buried aqueous interfaces can be accessed with careful selection of spectroscopic technique and sample configuration, further expanding the range of chemical environments that can be probed, including solid inorganic materials, polymers, and water immiscible liquids. Solid substrates can be finely tuned by functionalization with self-assembled monolayers, polymers, or biomolecules. These variables provide a platform for systematically tuning the chemical nature of the interface and examining the resulting water structure. Finally, time-resolved methods to probe the dynamics of interfacial water are briefly summarized before discussing the current status and future directions in studying the structure and dynamics of interfacial water.

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.

3D Probed Lipid Dynamics in Small Unilamellar Vesicles

Single-molecule fluorescence correlation spectroscopy overcomes the resolution barrier of optical microscopy (10≈-20 nm) and is utilized to look into lipid dynamics in small unilamellar vesicles (SUVs; diameter < 100 nm). The fluorescence trajectories of lipid-like tracer 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine (DiD) in the membrane bilayers are acquired at a single-molecule level. The autocorrelation analysis yields the kinetic information on lipid organization, oxygen transport, and lateral diffusion in SUVs' membrane. First, the isomerization feasibility may be restricted by the addition of cholesterols, which form structure conjugation with DiD chromophore. Second, the oxygen transport is prevented from the ultrasmall cluster and cholesterol-rich regions, whereas it can pass through the membrane region with liquid-disordered phase (L_d ) and defects. Third, by analyzing 2D spectra correlating the lipid diffusion coefficient and triplet-state lifetime, the heterogeneity in lipid bilayer can be precisely visualized such as lipid domain with different phases, the defects of lipid packing, and DiD-induced "bouquet" ultrasmall clusters.

Applications of two-dimensional infrared spectroscopy

Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.

Thin and ordered hydrogel films deposited through electrospinning technique; a simple and efficient support for organic bilayers

Thermal behavior of Dipalmitoylphosphatidylcholine (DPPC) bilayers deposited over hydrogel fibers was examined. Thus, membrane stability, water absorption-release, phase transitions and phase transition temperatures were studied through different methods during heating cycles. Hydrogel films were realized using an oligomer mixture (HEMA-PEGDA575/photo-initiator) with adequate viscosity. Then, the fibers were deposited over silicon wafers (hydrophilic substrate) through electrospinning technique using four different voltages: 15, 20, 25 and 30 kV. The films were then exposed to UV light, favoring polymer chain crosslinking and interactions between hydrogel and substrate. For samples deposited at 20 and 25 kV, hierarchical wrinkle folds were observed at surface level, their arrangement distribution depends directly on thickness and associated point defects. DPPC bilayers were then placed over hydrogel scaffold using Langmuir-Blodgett technique. Field emission scanning electron microscopy (FE-SEM) analysis were used to investigate sample surface, micrographies show homogeneous layer formation with chain polymer order/disorder related to applied voltage during hydrogel deposition process, among other parameters. According to the results obtained, it is possible to conclude that the oligomer deposited at 20 kV produce thin homogenous films (~40 nm) with enhanced ability to absorb water and release it in a controlled way during heating cycles. These scaffold properties confer to DPPC membrane thermal stability, which allow an easy detection of phase(s) and phase transitions. Thermal behavior was also studied via Atomic Force Microscopy (roughness analysis). Contact angle measurements corroborate system wettability, supporting the theory that hydrogel thin films act as DPPC membrane enhancers for thermal stability against external stimuli.

Phosphatidylinositol-(4,5)-Bisphosphate Acyl Chains Differentiate Membrane Binding of HIV-1 Gag from That of the Phospholipase Cδ1 Pleckstrin Homology Domain

HIV-1 Gag, which drives virion assembly, interacts with a plasma membrane (PM)-specific phosphoinositide, phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2]. While cellular acidic phospholipid-binding proteins/domains, such as the PI(4,5)P2-specific pleckstrin homology domain of phospholipase Cδ1 (PHPLCδ1), mediate headgroup-specific interactions with corresponding phospholipids, the exact nature of the Gag-PI(4,5)P2 interaction remains undetermined. In this study, we used giant unilamellar vesicles (GUVs) to examine how PI(4,5)P2 with unsaturated or saturated acyl chains affect membrane binding of PHPLCδ1 and Gag. Both unsaturated dioleoyl-PI(4,5)P2 [DO-PI(4,5)P2] and saturated dipalmitoyl-PI(4,5)P2 [DP-PI(4,5)P2] successfully recruited PHPLCδ1 to membranes of single-phase GUVs. In contrast, DO-PI(4,5)P2 but not DP-PI(4,5)P2 recruited Gag to GUVs, indicating that PI(4,5)P2 acyl chains contribute to stable membrane binding of Gag. GUVs containing PI(4,5)P2, cholesterol, and dipalmitoyl phosphatidylserine separated into two coexisting phases: one was a liquid phase, and the other appeared to be a phosphatidylserine-enriched gel phase. In these vesicles, the liquid phase recruited PHPLCδ1 regardless of PI(4,5)P2 acyl chains. Likewise, Gag bound to the liquid phase when PI(4,5)P2 had DO-acyl chains. DP-PI(4,5)P2-containing GUVs showed no detectable Gag binding to the liquid phase. Unexpectedly, however, DP-PI(4,5)P2 still promoted recruitment of Gag, but not PHPLCδ1, to the dipalmitoyl-phosphatidylserine-enriched gel phase of these GUVs. Altogether, these results revealed different roles for PI(4,5)P2 acyl chains in membrane binding of two PI(4,5)P2-binding proteins, Gag and PHPLCδ1. Notably, we observed that nonmyristylated Gag retains the preference for PI(4,5)P2 containing an unsaturated acyl chain over DP-PI(4,5)P2, suggesting that Gag sensitivity to PI(4,5)P2 acyl chain saturation is determined directly by the matrix-PI(4,5)P2 interaction, rather than indirectly by a myristate-dependent mechanism.

IMPORTANCE

Binding of HIV-1 Gag to the plasma membrane is promoted by its interaction with a plasma membrane-localized phospholipid, PI(4,5)P2. Many cellular proteins are also recruited to the plasma membrane via PI(4,5)P2-interacting domains represented by PHPLCδ1. However, differences and/or similarities between these host proteins and viral Gag protein in the nature of their PI(4,5)P2 interactions, especially in the context of membrane binding, remain to be determined. Using a novel giant unilamellar vesicle-based system, we found that PI(4,5)P2 with an unsaturated acyl chain recruited PHPLCδ1 and Gag similarly, whereas PI(4,5)P2 with saturated acyl chains either recruited PHPLCδ1 but not Gag or sorted these proteins to different phases of vesicles. To our knowledge, this is the first study to show that PI(4,5)P2 acyl chains differentially modulate membrane binding of PI(4,5)P2-binding proteins. Since Gag membrane binding is essential for progeny virion production, the PI(4,5)P2 acyl chain property may serve as a potential target for anti-HIV therapeutic strategies.

β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes

An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump–probe spectroscopy.

Computer investigations of influences of molar fraction and acyl chain length of lipids on the nanoparticle–biomembrane interactions

Structural variations of the heterogeneous membrane: (a) a water defect, (b) the membrane buckling.