Conformational Changes as Driving Force for Phase Recognition: The Case of Laurdan

Photophysics in Biomembranes: Computational Insight into the Interaction between Lipid Bilayers and Chromophores

Light is ubiquitously available to probe the structure and dynamics of biomolecules and biological tissues. Generally, this cannot be done directly with visible light, because of the absence of absorption by those biomolecules. This problem can be overcome by incorporating organic molecules (chromophores) that show an optical response in the vicinity of those biomolecules. Since those optical properties are strongly dependent on the chromophore's environment, time-resolved spectroscopic studies can provide a wealth of information on biosystems at the molecular scale in a nondestructive way. In this work, we give an overview on the multiscale computational strategy developed by us in the last eight years and prove that theoretical studies and simulations are needed to explain, guide, and predict observations in fluorescence experiments. As we challenge the accepted views on existing probes, we discover unexplored abilities that can discriminate surrounding lipid bilayers and their temperature-dependent as well as solvent-dependent properties. We focus on three archetypal chromophores: diphenylhexatriene (DPH), Laurdan, and azobenzene. Our method shows that conformational changes should not be neglected for the prototype rod-shaped molecule DPH. They determine its position and orientation in a liquid-ordered (Lo) sphingomyelin/cholesterol (SM/Chol) bilayer and are responsible for a strong differentiation of its absorption spectra and fluorescence decay times in dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) membranes, which are at room temperature in liquid-disordered (Ld) and solid-gel (So) phases, respectively. Thanks to its pronounced first excited state dipole moment, Laurdan has long been known as a solvatochromic probe. Since this molecule has however two conformers, we prove that they exhibit different properties in different lipid membrane phases. We see that the two conformers are only blocked in one phase but not in another. Supported by fluorescence anisotropy decay simulations, Laurdan can therefore be regarded as a molecular rotor. Finally, the conformational versatility of azobenzene in saturated Ld lipid bilayers is simulated, along with its photoisomerization pathways. By means of nonadiabatic QM/MM surface hopping analyses (QM/MM-SH), a dual mechanism is found with a torsional mechanism and a slow conversion for trans-to-cis. For cis-to-trans, simulations show a much higher quantum yield and a so-called "pedal-like" mechanism. The differences are related to the different potential energy surfaces as well as the interactions with the surrounding alkyl chains. When tails of increased length are attached to this probe, cis is pushed toward the polar surface, while trans is pulled toward the center of the membrane.

Hydration- and Temperature-Dependent Fluorescence Spectra of Laurdan Conformers in a DPPC Membrane

The widely used Laurdan probe has two conformers, resulting in different optical properties when embedded in a lipid bilayer membrane, as demonstrated by our previous simulations. Up to now, the two conformers' optical responses have, however, not been investigated when the temperature and the phase of the membrane change. Since Laurdan is known to be both a molecular rotor and a solvatochromic probe, it is subject to a profound interaction with both neighboring lipids and water molecules. In the current study, molecular dynamics simulations and hybrid Quantum Mechanics/Molecular Mechanics calculations are performed for a DPPC membrane at eight temperatures between 270K and 320K, while the position, orientation, fluorescence lifetime and fluorescence anisotropy of the embedded probes are monitored. The importance of both conformers is proven through a stringent comparison with experiments, which corroborates the theoretical findings. It is seen that for Conf-I, the excited state lifetime is longer than the relaxation of the environment, while for Conf-II, the surroundings are not yet adapted when the probe returns to the ground state. Throughout the temperature range, the lifetime and anisotropy decay curves can be used to identify the different membrane phases. The current work might, therefore, be of importance for biomedical studies on diseases, which are associated with cell membrane transformations.

Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions

Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.

Generalized polarization and time-resolved fluorescence provide evidence for different populations of Laurdan in lipid vesicles

The solvatochromic dye Laurdan is widely used in sensing the lipid packing of both model and biological membranes. The fluorescence emission maximum shifts from about 440 nm (blue channel) in condensed membranes (So) to about 490 nm (green channel) in the liquid-crystalline phase (Lα). Although the fluorescence intensity based generalized polarization (GP) is widely used to characterize lipid membranes, the fluorescence lifetime of Laurdan, in the blue and the green channel, is less used for that purpose. Here we explore the correlation between GP and fluorescence lifetimes by spectroscopic measurements on the So and Lα phases of large unilamellar vesicles of DMPC and DPPC. A positive correlation between GP and the lifetimes is observed in each of the optical channels for the two lipid phases. Microfluorimetric determinations on giant unilamellar vesicles of DPPC and DOPC at room temperature are performed under linearly polarized two-photon excitation to disentangle possible subpopulations of Laurdan at a scale below the optical resolution. Fluorescence intensities, GP and fluorescence lifetimes depend on the angle between the orientation of the linear polarization of the excitation light and the local normal to the membrane of the optical cross-section. This angular variation depends on the lipid phase and the emission channel. GP and fluorescence intensities in the blue and green channel in So and in the blue channel in Lα exhibit a minimum near 90o. Surprisingly, the intensity in the green channel in Lα reaches a maximum near 90o. The fluorescence lifetimes in the two optical channels also reach a pronounced minimum near 90o in So and Lα, apart from the lifetime in the blue channel in Lα where the lifetime is short with minimal angular variation. To our knowledge, these experimental observations are the first to demonstrate the existence of a bent conformation of Laurdan in lipid membranes, as previously suggested by molecular dynamics calculations.

Membrane interaction and selectivity of novel alternating cationic lipid-nanodisc assembling polymers

Synthetic polymer nanodiscs are self-assembled structures formed from amphipathic copolymers encapsulating membrane proteins and surrounding phospholipids into water soluble discs. These nanostructures have served as an analytical tool for the detergent free solubilisation and structural study of membrane proteins (MPs) in their native lipid environment. We established the polymer-lipid nanodisc forming ability of a novel class of amphipathic copolymer comprised of an alternating sequence of N-alkyl functionalised maleimide (AlkylM) of systematically varied hydrocarbon chain length, and cationic N-methyl-4-vinyl pyridinium iodide (MVP). Using a combination of physicochemical techniques, the solubilisation efficiency, size, structure and shape of DMPC lipid containing poly(MVP-co-AlkylM) nanodiscs were determined. Lipid solubilisation increased with AlkylM hydrocarbon chain length from methyl (MM), ethyl (EtM), n-propyl (PM), iso-butyl (IBM) through to n-butyl (BM) maleimide bearing polymers. More hydrophobic derivatives formed smaller sized nanodiscs and lipid ordering within poly(MVP-co-AlkylM) nanodiscs was affected by nanodisc size. In dye-release assays, shorter N-alkyl substituted polymers, particularly poly(MVP-co-EtM), exhibited low activities against eukaryotic mimetic POPC membrane and increased their liposome disruption as POPC : POPG membrane mixtures increased in their anionic POPG component, resembling the charge profile of bacterial membranes. These trends in membrane selectivity were transferred towards native cell systems in which gram-positive Staphylococcus aureus and gram-negative Acenobacter baumannii bacterial strains were relatively susceptible to disruption by hydrophobic n-butyl- and n-propyl-poly(MVP-co-AlkylM) derivatives compared to human red blood cells (HRBCs), with a more pronounced selectivity resulting from poly(MVP-co-PM). Such selective membrane interaction by less hydrophobic polymers provides a framework for polymer design towards applications including selective membrane component solubilisation, biosensing and antimicrobial development.

Cholesterol as a Subsidiary Component of Sorbitan Surfactant-Based Aggregates: A Study of Formation, Hydrophobicity, and Estimation of Localization of Embedded Molecules

Aggregates of amphiphilic molecules can be used as drug carriers, for which the properties can be modified by mixing with other molecules such as cholesterol. It is important to understand the effects of such additives on the properties because they directly define the material functions. In this work, we investigated the effect of cholesterol on the formation and hydrophobicity of aggregates of sorbitan surfactants. As cholesterol changed its formation from micelles to vesicles, an increase in hydrophobicity was seen, particularly in the middle regions compared with the shallow and deep regions. We show that this gradual hydrophobicity is related to the localization of the embedded molecules. 4-Hydroxy-TEMPO and 4-carboxy-TEMPO were preferentially localized in the shallow region of the aggregates, whereas 4-PhCO₂-TEMPO was preferentially localized in the deep region of the vesicle. The localization of molecules depends on their chemical structure. However, the localization of 4-PhCO₂-TEMPO in micelles was not observed, despite the similar hydrophobicity in the hydrophobic region within the aggregates. The localization of embedded molecules was related to other properties, such as molecular mobility.

Possible Role of Bent Structure of Methylated Lithocholic Acid on Artificial and Plasma Membranes

Bile acids form micelles that are essential for the absorption of dietary lipids. However, excessive bile acid micelles can disrupt the plasma membrane by removing phospholipids, resulting in cell death. We hypothesized that the bent geometrical structure of the steroid scaffold of bile acids decreases the lipid order (similar to unsaturated phospholipids with cis double bonds), disrupting the plasma membrane. Here, lithocholic acid (LCA), a bile acid, was methylated to prevent micellization. Methylated lithocholic acid (Me-LCA) was mixed with a thin phase-separated lipid bilayer comprising 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and cholesterol (Chol). Me-LCA was not localized in the DPPC-rich rigid phase but localized in the DOPC-rich fluid phase, and excess Me-LCA did not affect the phase separation. Me-LCA is distributed in the plasma and organelle membranes. However, Me-LCA with bent structure did not affect the membrane properties, membrane fluidity, and hydrophobicity of liposomes composed of DOPC, DPPC, and Chol and also did not affect the proliferation of cells.

Quantitative Determination of Relative Permittivity Based on the Fluorescence Property of Pyrene Derivatives: An Interpretation of Hydrophobicity in Self-Assembled Aggregates of Nonionic Amphiphiles

Aggregates in aqueous solutions can embed hydrophobic molecules, and their interactions depend on the properties of the aggregates. The electric surface potential, molecular mobility, and gradual hydrophobicity are the properties that regulate the interactions, and it is essential to understand these to quantify the properties. Electric surface potential and molecular mobility are quantified using the zeta potential and NMR measurements. In this study, the quantification of gradual hydrophobicity within the aggregate based on the relative permittivity, also called the dielectric constant, has been estimated from fluorescence spectra of pyrene-dicarboxylic acid conjugates. The localization of the pyrene moiety was modified by conjugation with succinic acid, suberic acid, or dodecanedioic acid, and the conjugates were evaluated in the shallow, middle, and deep regions of the aggregates. Span and Tween surfactants have been employed to prepare these aggregates, because they form various kinds of aggregates such as micelles and vesicles. It was realized that the hydrophobicity gradually increased from the interface to the hydrophobic core. Alternatively, a comparison of hydrophobicity within the aggregates showed no remarkable difference. Moreover, the analyses suggested that there are a few water molecules in the deep region. These results support the idea of the localization of embedded molecules in aggregates.

Computational and photophysical characterization of a Laurdan malononitrile derivative

The malononitrile group is considered one of the strongest natural electron-withdrawing groups in a chemist's arsenal. However, surprisingly little is known about how this group functions in push-pull fluorophores. In a recent computational study, we reported that replacing the ketone group of the traditional push-pull dye Laurdan with a malononitrile group significantly improves the optical properties while retaining the membrane behavior of the parent molecule Laurdan. Motivated by these results, we report here the synthesis and photophysical characterization of the said compound, 6-(1-undecyl-2,2-dicyanovinyl)-N,N-dimethyl-2-naphthylamine (CN-Laurdan). To our surprise, this new CN-Laurdan probe is found to be much less bright than the parent Laurdan due to a large drop in the fluorescence quantum yield. Using computational methods, we determine that the origin of this low quantum yield is related to the existence of a non-radiative decay pathway related to a rotation of the malononitrile moiety, suggesting that the molecule could nonetheless function very well as a molecular rotor. We confirm experimentally that CN-Laurdan functions as a molecular rotor by measuring the quantum yield in methanol/glycerol mixtures of increasing viscosity. Specifically, we found a consistent increase in the quantum yield across the entire range of tested viscosities.

Spectroscopic, molecular dynamics simulation and biological studies of Flavin MonoNucleotide and Flavin Adenine Dinucleotide in biomimetic systems

The present study describes a comprehensive investigation of the spectroscopic characteristics, stability and in vitro antioxidant and cytotoxic properties of the Flavin MonoNucleotide (FMN) and Flavin Adenine Dinucleotide (FAD) in Dextran70 (Dx70) and Dx70/phospatidylcholine (PC) biomimetic systems by means of the UV-Vis absorption, fluorescence spectroscopy, chemiluminescence and Neutral Red assay. The affinity of FMN, FAD and the precursor riboflavin (RF) to an unsaturated phospholipid bilayer model as well as the location of the probes within the lipid bilayer were assessed from united-atom molecular dynamics simulations carried out on an unsaturated phospholipid bilayer model system, and the theoretical and experimental characterization of the two probes within biomembranes was complemented with the light microscopy survey of the cell morphology of L929 fibroblast cells cultivated in the presence of various dosage of FAD/FMN. In lipid bilayers, FMN/FAD resulted in a noticeable improvement of the antioxidant activity (the scavenging of reactive oxygen species up to 40%) and a significant effect on cellular viability in the L929 fibroblast cells. The results are important in the oxidative stress process concerning the redox reactions of flavins in humans as well as in further studies on different systems belonging to the category of flavoenzymes/flavoproteins, required for cellular respiration.

Laurdan and Di-4-ANEPPDHQ Influence the Properties of Lipid Membranes: A Classical Molecular Dynamics and Fluorescence Study

Environmentally sensitive (ES) dyes have been used for many decades to study the lipid order of cell membranes, as different lipid phases play a crucial role in a wide variety of cell processes. Yet, the understanding of how ES dyes behave, interact, and affect membranes at the atomistic scale is lacking, partially due to the lack of molecular dynamics (MD) models of these dyes. Here, we present ground- and excited-state MD models of commonly used ES dyes, Laurdan and di-4-ANEPPDHQ, and use MD simulations to study the behavior of these dyes in a disordered and an ordered membrane. We also investigate the effect that these two dyes have on the hydration and lipid order of the membranes, where we see a significant effect on the hydration of lipids proximal to the dyes. These findings are combined with experimental fluorescence experiments of ordered and disordered vesicles and live HeLa cells stained by the aforementioned dyes, where the generalized polarization (GP) values were measured at different concentrations of the dyes. We observe a small but significant decrease of GP at higher Laurdan concentrations in vesicles, while the same effect is not observed in cell membranes. The opposite effect is observed with di-4-ANEPPDHQ where no significant change in GP is seen for vesicles but a very substantial and significant decrease is seen in cell membranes. Together, our results show the profound effect that ES dyes have on membranes, and the presented MD models will be important for further understanding of these effects.

The interaction of a thiosemicarbazone derived from R - (+) - limonene with lipid membranes

As a potential drug, 2-nitrobenzaldehyde-thiosemicarbazone (2-TSC), a thiosemicarbazone derived from the terpene R-(+)-limonene, was studied through calorimetric and spectroscopic techniques. Differential Scanning Calorimetry (DSC) data showed that 2-TSC causes structural changes in a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DMPC) membrane, strongly decreasing the cooperativity of the bilayer gel-fluid thermal transition. Optical absorption spectroscopy showed that 2-TSC is more soluble in ethanol and lipids than in water medium, and that the drug displays different structures in the different environments. Though 2-TSC displays no fluorescence, time resolved fluorescence showed that the drug is an effective quencher of the fluorescent probe 6-dodecanoyl-2-dimethylaminonaphthalene (Laurdan). As it is well accepted that Laurdan is positioned into the bilayer close to the membrane surface, that is possibly the localization of 2-TSC in a bilayer. Electron spin resonance (ESR) of the probe 1-palmitoyl-2-stearoyl-(14-doxyl)-sn-glycero-3-phosphocholine (14-PCSL) revealed that 2-TSC is inserted into the hydrocarbon part of the bilayer, fluidizing the lipid bilayer gel phase and rigidifying or organizing the bilayer fluid phase. Similar effects are found for other lipophilic molecules, including cholesterol. These results are useful to improve the understanding of the processes that govern the interaction of thiosemicarbazones with cell membranes, related to the activity of the drugs and their cytotoxicity.

Computational Characterization of Novel Malononitrile Variants of Laurdan with Improved Photophysical Properties for Sensing in Membranes

Fluorescent probes are powerful tools for improving our understanding of cellular membranes and other complex biological environments. Using simulations, we gain atomistic and electronic insights into the effectiveness of the probes. In the current work, we have used various computational approaches to comprehensively investigate the properties of the fluorescent probe Laurdan and two Laurdan-like probes: AADAL and ECL. In addition, we propose the development of their corresponding novel malononitrile variants, which are computationally characterized herein. For the candidate probes, electronic structure calculations were used to rationalize their optical properties, including their ability for two-photon activation, and molecular dynamics simulations were used to unravel atomistic details of their functioning within lipid bilayers. While Laurdan, AADAL, and ECL were found to have very similar optical and membrane partitioning profiles, their malononitrile variants were found to show significantly improved optical properties, especially in regard to two-photon cross sections, and they appear to retain the desired membrane characteristics of the parent Laurdan molecule.

The influence of lipid membranes on fluorescent probes' optical properties

BACKGROUND

Organic fluorophores embedded in lipid bilayers can nowadays be described by a multiscale computational approach. Combining different length and time scales, a full characterization of the probe localization and optical properties led to novel insight into the effect of the environments.

SCOPE OF REVIEW

Following an introduction on computational advancements, three relevant probes are reviewed that delineate how a multiscale approach can lead to novel insight into the probes' (non) linear optical properties. Attention is paid to the quality of the theoretical description of the optical techniques.

MAJOR CONCLUSIONS

Computation can assess a priori novel probes' optical properties and guide the analysis and interpretation of experimental data in novel studies. The properties can be used to gain information on the phase and condition of the surrounding biological environment.

GENERAL SIGNIFICANCE

Computation showed that a canonical view on some of the probes should be revisited and adapted.

Influence of Membrane Phase on the Optical Properties of DPH

The fluorescent molecule diphenylhexatriene (DPH) has been often used in combination with fluorescence anisotropy measurements, yet little is known regarding the non-linear optical properties. In the current work, we focus on them and extend the application to fluorescence, while paying attention to the conformational versatility of DPH when it is embedded in different membrane phases. Extensive hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the influence of the phase- and temperature-dependent lipid environment on the probe. Already, the transition dipole moments and one-photon absorption spectra obtained in the liquid ordered mixture of sphingomyelin (SM)-cholesterol (Chol) (2:1) differ largely from the ones calculated in the liquid disordered DOPC and solid gel DPPC membranes. Throughout the work, the molecular conformation in SM:Chol is found to differ from the other environments. The two-photon absorption spectra and the ones obtained by hyper-Rayleigh scattering depend strongly on the environment. Finally, a stringent comparison of the fluorescence anisotropy decay and the fluorescence lifetime confirm the use of DPH to gain information upon the surrounding lipids and lipid phases. DPH might thus open the possibility to detect and analyze different biological environments based on its absorption and emission properties.

The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations

Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.