Rotational dynamics of surface probes in lipid vesicles

Single-Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes

In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm-2 ) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single-molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus "wobble") of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve nanodomains and enzyme-induced compositional heterogeneity within membranes, where NR within liquid-ordered vs. liquid-disordered domains shows a ≈4° difference in polar angle and a ≈0.3π sr difference in wobble angle. As a new type of imaging spectroscopy, SMOLM exposes the organizational and functional dynamics of lipid-lipid, lipid-protein, and lipid-dye interactions with single-molecule, nanoscale resolution.

Discerning Dynamic Signatures of Membrane-Bound α-Synuclein Using Site-Specific Fluorescence Depolarization Kinetics

α-Synuclein is an intrinsically disordered protein that adopts an α-helical structure upon binding to the negatively charged lipid membrane. Binding-induced conformational change of α-synuclein plays a crucial role in the regulation of synaptic plasticity. In this work, we utilized the fluorescence depolarization kinetics methodology to gain the site-specific dynamical insights into the membrane-bound α-synuclein. We took advantage of the nonoccurrence of Cys in α-synuclein and created single-Cys variants at different sites for us to be able to label it with a thiol-active fluorophore. Our fluorescence depolarization results reveal the presence of three dynamically distinct types of motions of α-synuclein on POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)) small unilamellar vesicles (SUVs): (i) the (local) wobbling-in-cone motion of the fluorophore on the subnanosecond timescale, (ii) the backbone segmental mobility on the nanosecond timescale, and (iii) a slow depolarization component with a characteristic long rotational correlation time (∼60 ns) that is independent of the residue position. This characteristic timescale could potentially arise due to global tumbling of the protein-membrane complex, the global reorientation of only the protein within the membrane, and/or the translation diffusion of the protein on the curved membrane surface that could result in fluorescence depolarization due to the angular displacement of the transition dipole. In order to discern the molecular origin of the characteristic long rotational correlation time, we then carried our depolarization experiments varying the curvature of the membrane and varying the binding affinity by changing the lipid headgroup. These experiments revealed that the long rotational correlation time primarily arises due to the translational diffusion of α-synuclein on the curved membrane surface with a diffusion coefficient of ∼8.7 × 10^-10 m²/s. The site-specific fluorescence depolarization methodology will find broad application in quantifying diffusion of a wide range of membrane-associated proteins involved in functions and diseases.

Membrane interactions of intrinsically disordered proteins: The example of alpha-synuclein

Peripheral membrane proteins associate reversibly with biological membranes that, compared to protein binding partners, are structurally labile and devoid of specific binding pockets. Membranes in different subcellular compartments vary primarily in their chemical composition and physical properties, and recognition of these features is therefore critical for allowing such proteins to engage their proper membrane targets. Intrinsically disordered proteins (IDPs) are well-suited to accomplish this task using highly specific and low- to moderate-affinity interactions governed by recognition principles that are both similar to and different from those that mediate the membrane interactions of rigid proteins. IDPs have also evolved multiple mechanisms to regulate membrane (and other) interactions and achieve their impressive functional diversity. Moreover, IDP-membrane interactions may have a kinetic advantage in fast processes requiring rapid control of such interactions, such as synaptic transmission or signaling. Herein we review the biophysics, regulation and functional implications of IDP-membrane interactions and include a brief overview of some of the methods that can be used to study such interactions. At each step, we use the example of alpha-synuclein, a protein involved in the pathogenesis of Parkinson's disease and one of the best characterized membrane-binding IDP, to illustrate some of the principles discussed.

Atomistic Picture of Fluorescent Probes with Hydrocarbon Tails in Lipid Bilayer Membranes: An Investigation of Selective Affinities and Fluorescent Anisotropies in Different Environmental Phases

By reverting to spectroscopy, changes in the biological environment of a fluorescent probe can be monitored and the presence of various phases of the surrounding lipid bilayer membranes can be detected. However, it is currently not always clear in which phase the probe resides. The well-known orange 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbo-cyanine perchlorate (DiI-C18(5)) fluorophore, for instance, and the new, blue BODIPY (4,4-difluoro-4-bora-3 a,4 a-diaza- s-indacene) derivative were experimentally seen to target and highlight identical parts of giant unilamellar vesicles of various compositions, comprising mixtures of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), sphingomyelin (SM), and cholesterol (Chol). However, it was not clear which of the coexisting membrane phases were visualized (Bacalum et al., Langmuir. 2016, 32, 3495). The present study addresses this issue by utilizing large-scale molecular dynamics simulations and the z-constraint method, which allows evaluating Gibbs free-energy profiles. The current calculations give an indication why, at room temperature, both BODIPY and DiI-C18(5) probes prefer the gel (S_o) phase in DOPC/DPPC (2:3 molar ratio) and the liquid-ordered (L_o) phase in DOPC/SM/Chol (1:2:1 molar ratio) mixtures. This study highlights the important differences in orientation and location and therefore in efficiency between the probes when they are used in fluorescence microscopy to screen various lipid bilayer membrane phases. Dependent on the lipid composition, the angle between the transition-state dipole moments of both probes and the normal to the membrane is found to deviate clearly from 90°. It is seen that the DiI-C18(5) probe is located in the headgroup region of the SM/Chol mixture, in close contact with water molecules. A fluorescence anisotropy study also indicates that DiI-C18(5) gives rise to a distinctive behavior in the SM/Chol membrane compared to the other considered membranes. The latter behavior has not been seen for the studied BODIPY probe, which is located deeper in the membrane.

How does the surface charge of ionic surfactant and cholesterol forming vesicles control rotational and translational motion of rhodamine 6G perchlorate (R6G ClO₄)?

The rotational dynamics and translational diffusion of a hydrophilic organic molecule, rhodamine 6G perchlorate (R6G ClO4) in small unilamellar vesicles formed by two different ionic surfactants, cetyltrimethylammonium bromide (CTAB) and sodium dodecyl sulfate (SDS), with cholesterol have been investigated using fluorescence spectroscopic methods. Moreover, in this article the formation of vesicle using anionic surfactant, SDS at different cholesterol-to-surfactant molar ratio (expressed by Q value (Q = [cholesterol]/[surfactant])) has also been reported. Visual observation, dynamic light scattering (DLS) study, turbidity measurement, steady state fluorescence anisotropy (r0) measurement, and eventually microscopic images reveal the formation of small unilamellar vesicles in aqueous solution. Also, in this study, an attempt has been made to observe whether the cationic probe molecule, rhodamine 6G (R6G) experiences similar or different microenvironment in cholesterol-SDS and cholesterol-CTAB assemblies with increase in cholesterol concentration. The influence of cholesterol on rotational and translational diffusion of R6G molecules has been investigated by monitoring UV-vis absorption, fluorescence, time-resolved fluorescence anisotropy, and finally fluorescence correlation spectroscopy (FCS) measurements. In cholesterol-SDS assemblies, due to the strong electrostatic attractive interaction between the negatively charged surface of vesicle and cationic R6G molecules, the rotational and diffusion motion of R6G becomes slower. However, in cholesterol-CTAB aggregates, the enhanced hydrophobicity and electrostatic repulsion induces the migration of R6G from vesicle bilayer to aqueous phase. The experimental observations suggest that the surface charge of vesicles has a stronger influence than the hydrophobicity of the vesicle bilayer on the rotational and diffusion motion of R6G molecules.

A method to map spatiotemporal pH changes inside living cells using a pH-triggered DNA nanoswitch

A few cellular compartments maintain acidic environments in their interiors that are crucial for their proper function. Alteration in steady state organelle pH is closely linked to several diseases. Although a few probes exist to measure pH of cell compartments, each has several associated limitations. We present a high-performance pH sensor, a DNA nanoswitch, a convenient method to map spatiotemporal pH changes in endocytic pathways. DNA has been used to make a variety of nanoswitches in vitro . However, the present DNA nanoswitch functions as a pH sensing device equally efficiently intracellularly as it does in vitro. This DNA nanoswitch functions as a FRET-based pH sensor in the pH regime of 5.5-7, with high dynamic range between pH 5.8 and 7. It is efficiently engulfed by Drosophila hemocytes through endocytosis and can be used to measure the acidity of the endocytic vesicles that it marks during their maturation till their lysosomal stage.

Membrane fluidity and lipid order in ternary giant unilamellar vesicles using a new bodipy-cholesterol derivative

Cholesterol-rich, liquid-ordered (L(o)) domains are believed to be biologically relevant, and yet detailed knowledge about them, especially in live cells under physiological conditions, is elusive. Although these domains have been observed in model membranes, understanding cholesterol-lipid interactions at the molecular level, under controlled lipid mixing, remains a challenge. Further, although there are a number of fluorescent lipid analogs that partition into liquid-disordered (L(d)) domains, the number of such analogs with a high affinity for biologically relevant L(o) domains is limited. Here, we use a new Bodipy-labeled cholesterol (Bdp-Chol) derivative to investigate membrane fluidity, lipid order, and partitioning in various lipid phases in giant unilamellar vesicles (GUVs) as a model system. GUVs were prepared from mixtures of various molar fractions of dioleoylphosphatidylcholine, cholesterol, and egg sphingomyelin. The L(d) phase domains were also labeled with 1,1'-didodecyl-3,3,3',3'-tetramethylindocarbocyanine (DiI-C(12)) for comparison. Two-photon fluorescence lifetime and anisotropy imaging of Bdp-Chol are sensitive to lipid phase domains in GUVs. The fluorescence lifetime of Bdp-Chol in liquid-disordered, single-phase GUVs is 5.50 +/- 0.08 ns, compared with 4.1 +/- 0.4 ns in the presence of DiI-C(12). The observed reduction of fluorescence lifetime is attributed to Förster resonance energy transfer between Bdp-Chol (a donor) and DiI-C(12) (an acceptor) with an estimated efficiency of 0.25 and donor-acceptor distance of 2.6 +/- 0.2 nm. These results also indicate preferential partitioning (K(p) = 1.88) of Bdp-Chol into the L(o) phase. One-photon, time-resolved fluorescence anisotropy of Bdp-Chol decays as a triexponential in the lipid bilayer with an average rotational diffusion coefficient, lipid order parameter, and membrane fluidity that are sensitive to phase domains. The translational diffusion coefficient of Bdp-Chol, as measured using fluorescence correlation spectroscopy, is (7.4 +/- 0.3) x 10(-8) cm(2)/s and (5.0 +/- 0.2) x 10(-8) cm(2)/s in the L(d) and L(o) phases, respectively. Experimental translational/rotational diffusion coefficient ratios are compared with theoretical predictions using the hydrodynamic model (Saffman-Delbrück). The results suggest that Bdp-Chol is likely to form a complex with other lipid molecules during its macroscopic diffusion in GUV lipid bilayers at room temperature. Our integrated, multiscale results demonstrate the potential of this cholesterol analog for studying lipid-lipid interactions, lipid order, and membrane fluidity of biologically relevant L(o) domains.

Molecular dynamics simulations of DiI-C18(3) in a DPPC lipid bilayer

We performed a 40 ns simulation of 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI-C18(3)) in a 1,2-dipalmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) bilayer in order to facilitate interpretation of lipid dynamics and membrane structure from fluorescence lifetime, anisotropy, and fluorescence correlations spectroscopy (FCS). Incorporation of DiI of 1.6 to 3.2 mol% induced negligible changes in area per lipid but detectable increases in bilayer thickness, each of which are indicators of membrane structural perturbation. The DiI chromophore angle was 77 +/- 17 degrees with respect to the bilayer normal, consistent with rotational diffusion inferred from polarization studies. The DiI headgroup was located 0.63 nm below the lipid head group-water interface, a novel result in contrast to some popular cartoon representations of DiI but consistent with DiI's increase in quantum yield when incorporated into lipid bilayers. Importantly, the fast component of rotational anisotropy matched published experimental results demonstrating that sufficient free volume exists at the sub-interfacial region to support fast rotations. Simulations with non-charged DiI head groups exhibited DiI flip-flop, demonstrating that the positively-charged chromophore stabilizes the orientation and location of DiI in a single monolayer. DiI induced detectable changes in interfacial properties of water ordering, electrostatic potential, and changes in P-N vector orientation of DPPC lipids. The diffusion coefficient of DiI (9.7 +/- 0.02 x 10(-8) cm2 s(-1)) was similar to the diffusion of DPPC molecules (10.7 +/- 0.04 x 10(-8) cm2 s(-1)), supporting the conclusion that DiI dynamics reflect lipid dynamics. These results provide the first atomistic level insight into DiI dynamics, results essential in elucidating lipid dynamics through single molecule fluorescence studies.

Precise positioning of myosin VI on endocytic vesicles in vivo

Myosin VI has been studied in both a monomeric and a dimeric form in vitro. Because the functional characteristics of the motor are dramatically different for these two forms, it is important to understand whether myosin VI heavy chains are brought together on endocytic vesicles. We have used fluorescence anisotropy measurements to detect fluorescence resonance energy transfer between identical fluorophores (homoFRET) resulting from myosin VI heavy chains being brought into close proximity. We observed that, when associated with clathrin-mediated endocytic vesicles, myosin VI heavy chains are precisely positioned to bring their tail domains in close proximity. Our data show that on endocytic vesicles, myosin VI heavy chains are brought together in an orientation that previous in vitro studies have shown causes dimerization of the motor. Our results are therefore consistent with vesicle-associated myosin VI existing as a processive dimer, capable of its known trafficking function.

Diffusion trajectory of an asymmetric object: information overlooked by the mean square displacement

Diffusion of an asymmetric object is characterized by its translational and rotational diffusion coefficients. Until now, anisotropic diffusion studies have been based on ensemble averages. Here we present a theoretical basis for the analysis of the trajectories of a single particle with anisotropic diffusion coefficients. We discuss the relevance of this method for motion of biomolecules in the membrane of living cells.

Discrete and heterogeneous rotational dynamics of single membrane probe dyes in gel phase supported lipid bilayer

In order to probe the local dynamics of lipid bilayers in the gel phase, we measured the rotational time trajectories of a membrane probe, diI(3), in supported bilayers of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) using single molecule fluorescence polarization imaging. diI(3) has two hydrocarbon tails that mimic phospholipid tails and has its transition dipole moment lying mostly on the plane of the membrane; hence it is an excellent probe for rotational dynamics in membranes. Above the transition temperature, the probes are laterally mobile and do not display polarized emission. In the gel phase below the transition temperature, lateral mobility is severely reduced and the emission becomes polarized with its polarization direction changing in the milliseconds time scale. Molecule by molecule analysis of the rotational time scales revealed significant heterogeneities among molecules, much larger than would be due to statistical noise. Control experiments using small unilamellar vesicles suggest that the heterogeneities are not caused by surface interactions and are intrinsic to the gel phase membrane. The rotational dynamics is strongly temperature dependent and the thermally activated state for the rotational motion has a large entropic barrier (> 30kB), indicating that relatively large local disorder is required for the rotational motion to occur. Rotational hopping between discrete angles has been observed at the lowest temperatures (approximately 10 degrees C). Our results suggest that the gel phase membrane is not uniform at the microscopic level but is highly dynamic with the rigidity of local environments constantly changing.

Dynamics imaging of lipid phases and lipid-marker interactions in model biomembranes

Biomembranes are complex systems that regulate numerous biological processes. Lipid phases that constitute these membranes influence their properties and transport characteristics. Here, we demonstrate the potential of short-range dynamics imaging (excited-state lifetime, rotational diffusion, and order parameter) as a sensitive probe of lipid phases in giant unilamellar vesicles (GUVs). Liquid-disordered and gel phases were labeled with Bodipy-PC at room temperature. Two-photon fluorescence lifetime imaging microscopy of single-phase GUVs reveals more heterogeneity in fluorescence lifetimes of Bodipy in the gel phase (DPPC: 3.8+/-0.6 ns) as compared with the fluid phase (DOPC: 5.2+/-0.2 ns). The phase-specificity of excited-state lifetime of Bodipy-PC is attributed to the stacking of ordered lipid molecules that possibly enhances homo-FRET. Fluorescence polarization anisotropy imaging also reveals distinctive molecular order that is phase specific. The results are compared with DiI-C12-labeled fluid GUVs to investigate the sensitivity of our fluorescence dynamics assay to different lipid-marker interactions. Our results provide a molecular perspective of lipid phase dynamics and the nature of their microenvironments that will ultimately help our understanding of the structure-function relationship of biomembranes in vivo. Furthermore, these ultrafast excited-state dynamics will be used for molecular dynamics simulation of lipid-lipid, lipid-marker and lipid-protein interactions.

Measuring diffusion in cell membranes by fluorescence correlation spectroscopy

Fluorescence Correlation Spectroscopy (FCS) can measure diffusion on the cell surface with unparalleled sensitivity. In appropriate situations, this can be the most sensitive and accurate method for measuring receptor interaction and oligomerization. Here we attempt to describe FCS in sufficient detail so that the reader is able to judge when there is a compelling reason to choose this technique, understand the basic theory behind it, construct a FCS spectrometer in the laboratory, and analyze the data to obtain a meaningful estimate of the physical parameters.