Quantifying the Diffusion of Lipids in the Proximal/Distal Leaflets of a Supported Lipid Bilayer by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy

Diffusion of Multiple Species Resolved by Fluorescence Lifetime Recovery after Photobleaching (FLRAP)

Fluorescence recovery after photobleaching (FRAP) is now an indispensable tool to analyze the diffusion of molecules in vivo and in vitro. However, a conventional fluorescence intensity-based approach has difficulty in analyzing the diffusion of multiple species simultaneously. Here, we report fluorescence lifetime recovery after photobleaching (FLRAP) that incorporates fluorescence lifetime information into FRAP. By using FLRAP, the fluorescence intensity-recovery curves of each species can be successfully extracted from the ensemble photon data by utilizing their species-specific fluorescence decay curves, which are verified by applying FLRAP to two heterogeneous systems. Thus, FLRAP can be a powerful tool to quantitatively elucidate the molecular diffusion of multiple species in complex systems such as in living cells.

Peripheral adsorption of polylysine on one leaflet of a lipid bilayer reduces the lipid diffusion of both leaflets

Understanding polycation-lipid interaction is essential not only in molecular biology but also in the biomedical industry and pharmacology. However, the effect of the polycation-lipid interaction on the molecular properties of lipids in biomembranes remains elusive. Here, two fluorescence correlation spectroscopies (FCSs), pulse-interleaved excitation (PIE) FCS and lifetime-based FCS, were performed to elucidate the change in the lipid diffusion of a model biomembrane induced by polylysine (PLL) adsorption. The results of PIE-FCS showed that the diffusions of both anionic and zwitterionic lipids become slower in the presence of PLL but the mobility of the anionic lipids is much reduced, suggesting the preferential interaction between the PLL and the anionic lipids due to the electrostatic attraction. Furthermore, leaflet-specific lipid diffusion analysis by lifetime-based FCS clearly showed that PLL adsorption on one leaflet of the membrane reduces the lipid diffusion of both leaflets in the same manner. This clearly indicates that the interleaflet coupling is strong in the presence of PLL.

Sublytic gasdermin-D pores captured in atomistic molecular simulations

Gasdermin-D (GSDMD) is the ultimate effector of pyroptosis, a form of programmed cell death associated with pathogen invasion and inflammation. After proteolytic cleavage by caspases, the GSDMD N-terminal domain (GSDMDNT) assembles on the inner leaflet of the plasma membrane and induces the formation of membrane pores. We use atomistic molecular dynamics simulations to study GSDMDNT monomers, oligomers, and rings in an asymmetric plasma membrane mimetic. We identify distinct interaction motifs of GSDMDNT with phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) and phosphatidylserine (PS) headgroups and describe their conformational dependence. Oligomers are stabilized by shared lipid binding sites between neighboring monomers acting akin to double-sided tape. We show that already small GSDMDNT oligomers support stable, water-filled, and ion-conducting membrane pores bounded by curled beta-sheets. In large-scale simulations, we resolve the process of pore formation from GSDMDNT arcs and lipid efflux from partial rings. We find that high-order GSDMDNT oligomers can crack under the line tension of 86 pN created by an open membrane edge to form the slit pores or closed GSDMDNT rings seen in atomic force microscopy experiments. Our simulations provide a detailed view of key steps in GSDMDNT-induced plasma membrane pore formation, including sublytic pores that explain nonselective ion flux during early pyroptosis.

Atomic force microscopy for quantitative understanding of peptide-induced lipid bilayer remodeling

A number of peptides are known to bind lipid bilayer membranes and cause these natural barriers to leak in an uncontrolled manner. Though membrane permeabilizing peptides play critical roles in cellular activity and may have promising future applications in the therapeutic arena, significant questions remain about their mechanisms of action. The atomic force microscope (AFM) is a single molecule imaging tool capable of addressing lipid bilayers in near-native fluid conditions. The apparatus complements traditional assays by providing local topographic maps of bilayer remodeling induced by membrane permeabilizing peptides. The information garnered from the AFM includes direct visualization and statistical analyses of distinct bilayer remodeling modes such as highly localized pore-like voids in the bilayer and dispersed thinned membrane regions. Colocalization of distinct remodeling modes can be studied. Here we examine recent work in the field and outline methods used to achieve precise AFM image data. Experimental challenges and common pitfalls are discussed as well as techniques for unbiased analysis including the Hessian blob detection algorithm, bootstrapping, and the Bayesian information criterion. When coupled with robust statistical analyses, high precision AFM data is poised to advance understanding of an important family of peptides that cause poration of membrane bilayers.

Correlated diffusion in lipid bilayers

Dynamic processes on membrane surfaces are essential for biological function. Traditionally, quantitative measurements of lipid/protein motion have been interpreted in the framework of membrane hydrodynamics. However, some recent single-molecule tracking studies have proven difficult to interpret via hydrodynamic arguments. Does this suggest a failure of hydrodynamic theory or simply highlight the dangers in attempting to extend hydrodynamic arguments down to molecular scales? Intermolecular correlations are superior to single-molecule observations for studying hydrodynamics due to the longer length scales involved. The current work reports dynamic pair correlations of lipids in model membranes. Submicron distance-dependent correlations are well resolved, and complementary numerical calculations indicate that hydrodynamic theory can predict membrane dynamics over distances of tens of nanometers and longer.

Lipid membranes are complex quasi–two-dimensional fluids, whose importance in biology and unique physical/materials properties have made them a major target for biophysical research. Recent single-molecule tracking experiments in membranes have caused some controversy, calling the venerable Saffman–Delbrück model into question and suggesting that, perhaps, current understanding of membrane hydrodynamics is imperfect. However, single-molecule tracking is not well suited to resolving the details of hydrodynamic flows; observations involving correlations between multiple molecules are superior for this purpose. Here dual-color molecular tracking with submillisecond time resolution and submicron spatial resolution is employed to reveal correlations in the Brownian motion of pairs of fluorescently labeled lipids in membranes. These correlations extend hundreds of nanometers in freely floating bilayers (black lipid membranes) but are severely suppressed in supported lipid bilayers. The measurements are consistent with hydrodynamic predictions based on an extended Saffman–Delbrück theory that explicitly accounts for the two-leaflet bilayer structure of lipid membranes.

Advanced fluorescence correlation spectroscopy for studying biomolecular conformation

We present the recent developments and advances in fluorescence correlation spectroscopy (FCS) and their application to the investigation of biomolecular conformations. In particular, we present and discuss three techniques: multichannel nanosecond FCS, photo-induced electron transfer FCS, and fluorescence lifetime correlation spectroscopy. We briefly describe each method and discuss recent applications to diverse biophysical studies of biomolecular conformation.

Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces

The individual and collective structure and properties of biomolecules can change dramatically when they are localized at an interface. However, the small spatial extent of interfacial regions poses challenges to the detailed characterization of multiscale processes that dictate the structure and function of large biological units such as peptides, proteins, or nucleic acids. This Perspective surveys a broad set of tools that provide new opportunities to probe complex, dynamic interfaces across the vast range of temporal regimes that connect molecular-scale events to macroscopic observables. An emphasis is placed on the integration over multiple time scales, the use of complementary techniques, and the incorporation of external stimuli to control interfacial properties with spatial, temporal, and chemical specificity.

Microsecond Folding of preQ1 Riboswitch and Its Biological Significance Revealed by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy

Riboswitches are regulatory elements of bacterial mRNA which function with conformational switching upon binding of specific cellular metabolites. In particular, transcriptional riboswitches regulate gene expression kinetically through the conformational change of the aptamer domain. In this study, we investigate the conformational dynamics and ligand binding mechanisms of the aptamer domain of a transcriptional prequeuosine (preQ₁) riboswitch from Bacillus subtilis using two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS) with microsecond time resolution. The obtained time-resolved single-molecule data indicate that the aptamer domain undergoes folding/unfolding including three forms, which are attributed to hairpin (O), pseudoknot-like (pF), and H-type pseudoknot (fF) structures. It is found that a cofactor, Mg²⁺, binds only to the fF form with the conformational selection mechanism. In contrast, it is indicated that the ligand, preQ₁, binds to the O form with the induced-fit mechanism and significantly accelerates the microsecond O → pF folding process. It is also shown that the binding with preQ₁ substantially stabilizes the fF form that is generated from the pF form with a long time constant (>10 ms). Combining these results with the results of a former smFRET study on the slower time scale, we obtain an overall picture of the folding/unfolding dynamics of the aptamer domain as well as its energy landscape. On the basis of the picture obtained, we discuss the significance of the microsecond folding/unfolding of the aptamer domain for biological function of the riboswitch and propose the molecular mechanism of the gene expression controlled by the structural dynamics of the aptamer domain.

Effect of electrostatic interaction on the leaflet-specific diffusion in a supported lipid bilayer revealed by fluorescence lifetime correlation analysis

Lipid–support electrostatic interaction determines the lipid dynamics in the proximal leaflet of a SLB.

Reduction of glass-surface charge density slows the lipid diffusion in the proximal leaflet of a supported lipid bilayer

Understanding the effect of a solid support on the dynamical properties of a supported lipid bilayer (SLB) is a prerequisite for the applications of SLB as a model biomembrane. Here, we applied two-dimensional fluorescence lifetime correlation spectroscopy to examine the effect of solution pH on the diffusion of lipids in the proximal/distal leaflets of a zwitterionic SLB. Leaflet-specific diffusion analyses at various pH revealed that the diffusion of lipids in the proximal leaflet facing a glass surface becomes slower by decreasing pH with the transition pH of ∼7.4. We attributed it to the reduction of the surface charge density of a glass support. Furthermore, the data clearly showed that the lipid diffusion in the distal leaflet facing a bulk solution is insensitive to the change in the diffusion property of the proximal leaflet. This reflects a weak interleaflet coupling between the proximal and distal leaflets of the SLB.

Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy: Concepts and Applications

We review the basic concepts and recent applications of two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS), which is the extension of fluorescence correlation spectroscopy (FCS) to analyze the correlation of fluorescence lifetime in addition to fluorescence intensity. Fluorescence lifetime is sensitive to the microenvironment and can be a "molecular ruler" when combined with FRET. Utilization of fluorescence lifetime in 2D FLCS thus enables us to quantify the inhomogeneity of the system and the interconversion dynamics among different species with a higher time resolution than other single-molecule techniques. Recent applications of 2D FLCS to various biological systems demonstrate that 2D FLCS is a unique and promising tool to quantitatively analyze the microsecond conformational dynamics of macromolecules at the single-molecule level.