Quantifying lipid-protein interaction by fluorescence correlation spectroscopy (FCS)

Requirements for efficient endosomal escape by designed mini-proteins

ZF5.3 is a compact, rationally designed mini-protein that escapes efficiently from the endosomes of multiple cell types. Despite its small size (27 amino acids), ZF5.3 can be isolated intact from the cytosol of treated cells and guides multiple classes of proteins into the cytosol and/or nucleus. In the best cases, delivery efficiencies reach or exceed 50% to establish nuclear or cytosolic concentrations of 500 nM or higher. But other than the requirement for unfoldable cargo and an intact HOPS complex, there is little known about how ZF5.3 traverses the limiting endocytic membrane. Here we delineate the attributes of ZF5.3 that enable efficient endosomal escape. We confirm that ZF5.3 is stable at pH values between 5.5 and 7.5, with no evidence of unfolding even at temperatures as high as 95 °C. The high-resolution NMR structure of ZF5.3 at pH 5.5, also reported here, shows a canonical p zinc-finger fold with the penta-arg motif integrated seamlessly into the C-terminal α-helix. At lower pH, ZF5.3 unfolds cooperatively as judged by both circular dichroism and high-resolution NMR. Unfolding occurs upon protonation of a single Zn(II)-binding His side chain whose pKa corresponds almost exactly to that of the late endosomal lumen. pH-induced unfolding is essential for endosomal escape, as a ZF5.3 analog that remains folded at pH 4.5 fails to efficiently reach the cytosol, despite high overall uptake. Finally, using reconstituted liposomes, we identify a high-affinity interaction of ZF5.3 with a specific lipid-BMP-that is selectively enriched in the inner leaflet of late endosomal membranes. This interaction is 10-fold stronger at low pH than neutral pH, providing a molecular picture for why escape occurs preferentially and in a HOPS-dependent manner from late endosomal compartments. The requirements for programmed endosomal escape identified here should aid and inform the design of proteins, peptidomimetics, and other macromolecules that reach cytosolic or nuclear targets intact and at therapeutically relevant concentrations.

Integrated approaches to unravel the impact of protein lipoxidation on macromolecular interactions

Protein modification by lipid derived reactive species, or lipoxidation, is increased during oxidative stress, a common feature observed in many pathological conditions. Biochemical and functional consequences of lipoxidation include changes in the conformation and assembly of the target proteins, altered recognition of ligands and/or cofactors, changes in the interactions with DNA or in protein-protein interactions, modifications in membrane partitioning and binding and/or subcellular localization. These changes may impact, directly or indirectly, signaling pathways involved in the activation of cell defense mechanisms, but when these are overwhelmed they may lead to pathological outcomes. Mass spectrometry provides state of the art approaches for the identification and characterization of lipoxidized proteins/residues and the modifying species. Nevertheless, understanding the complexity of the functional effects of protein lipoxidation requires the use of additional methodologies. Herein, biochemical and biophysical methods used to detect and measure functional effects of protein lipoxidation at different levels of complexity, from in vitro and reconstituted cell-like systems to cells, are reviewed, focusing especially on macromolecular interactions. Knowledge generated through innovative and complementary technologies will contribute to comprehend the role of lipoxidation in pathophysiology and, ultimately, its potential as target for therapeutic intervention.

Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins

Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.

Using Synchronous Fluorescence to Investigate Chemical Interactions Influencing Foam Characteristics in Sparkling Wines

The appearance of bubbles and foam can influence the likeability of a wine even before its consumption. Since foams are essential to visual and taste attributes of sparkling wines, it is of great importance to understand which compounds affect bubbles and foam characteristics. The aim of this work was to investigate the effect of interactions among proteins, amino acids, and phenols on the characteristics of foam in sparkling wines by using synchronous fluorescence spectroscopy techniques. Results have shown that several compounds present in sparkling wines influence foam quality differently, and importantly, highlighted how the interaction of those compounds might result in different effects on foam parameters. Amongst the results, mannoproteins were found to be most likely to promote foam and collar stability, while phenols were likely to increase the small bubbles and collar height in the foam matrix. In summary, this work contributes to a better understanding of the effect of wine compounds on foam quality as well as the effect of the interactions between those compounds.

Detection of long-range electrostatic interactions between charged molecules by means of fluorescence correlation spectroscopy

In the present paper, an experimental feasibility study on the detection of long-range intermolecular interactions through three-dimensional molecular diffusion in solution is performed. This follows recent theoretical and numerical analyses reporting that long-range electrodynamic forces between biomolecules could be identified through deviations from Brownian diffusion. The suggested experimental technique was fluorescence correlation spectroscopy (FCS). By considering two oppositely charged molecular species in aqueous solution, namely, lysozymes and fluorescent dye molecules (Alexa488), the diffusion coefficient of the dyes has been measured for different values of the concentration of lysozyme, that is, for different average distances between the oppositely charged molecules. For our model, long-range interactions are of electrostatic origin, suggesting that their action radius can be varied by changing the ionic strength of the solution. The experimental outcomes clearly prove the detectability of long-range intermolecular interactions by means of the FCS technique. Molecular dynamics simulations provide a clear and unambiguous interpretation of the experimental results.

Measuring Protein Binding to Lipid Vesicles by Fluorescence Cross-Correlation Spectroscopy

Fluorescence correlation spectroscopy has been previously used to investigate peptide and protein binding to lipid membranes, as it allows for very low amounts of sample, short measurement times and equilibrium binding conditions. Labeling only one of the binding partners, however, comes with certain drawbacks, as it relies on identifying binding events by a change in diffusion coefficient. Since peptide and protein aggregation can obscure specific binding, and since non-stoichiometric binding necessitates the explicit choice of a statistical distribution for the number of bound ligands, we additionally label the liposomes and perform dual-color fluorescence cross-correlation spectroscopy (dcFCCS). We develop a theoretical framework showing that dcFCCS amplitudes allow calculation of the degree of ligand binding and the concentration of unbound ligand, leading to a model-independent binding curve. As the degree of labeling of the ligands does not factor into the measured quantities, it is permissible to mix labeled and unlabeled ligand, thereby extending the range of usable protein concentrations and accessible dissociation constants, K_D. The total protein concentration, but not the fraction of labeled protein, needs to be known. In this work, we apply our dcFCCS analysis scheme to Sar1p, a protein of the COPII complex, which binds "major-minor-mix" liposomes. A Langmuir isotherm model yields K_D=(2.1±1.1)μM as the single-site dissociation constant. The dcFCCS framework presented here is highly versatile for biophysical analysis of binding interactions. It may be applied to many types of fluorescently labeled ligands and small diffusing particles, including nanodiscs and liposomes containing membrane protein receptors.

Applying Fluorescence Correlation Spectroscopy to Investigate Peptide-Induced Membrane Disruption

There is considerable interest in understanding the interactions of antimicrobial peptides with phospholipid membranes. Fluorescence correlation spectroscopy (FCS) is a powerful experimental technique that can be used to gain insight into these interactions. Specifically, FCS can be used to quantify leakage of fluorescent molecules of different sizes from large unilamellar lipid vesicles, thereby providing a tool for estimating the size of peptide-induced membrane disruptions. If fluorescently labeled lipids are incorporated into the membranes of the vesicles, FCS can also be used to obtain information about whether leakage occurs due to localized membrane perturbations or global membrane destabilization. Here, we outline a detailed step-by-step protocol on how to optimally implement an FCS-based leakage assay. To make the protocol easily accessible to other researchers, it has been supplemented with a number of practical tips and tricks.

Electrostatically driven lipid-protein interaction: Answers from FRET

Electrostatics govern the association of a large number of proteins with cellular membranes. In some cases, these proteins present specialized lipid-binding modules or membrane targeting domains while in other cases association is achieved through nonspecific interaction of unstructured clusters of basic residues with negatively charged lipids. Given its spatial resolution in the nanometer range, Förster resonance energy transfer (FRET) is a powerful tool to give insight into protein-lipid interactions and provide molecular level information which is difficult to retrieve with other spectroscopic techniques. In this review we present and discuss the basic formalisms of both hetero- and homo-FRET pertinent to the most commonly encountered problems in lipid-protein interaction studies and highlight some examples of implementations of different FRET methodologies to characterize lipid/protein systems in which electrostatic interactions play a crucial role. This article is part of a Special Issue entitled: Lipid-protein interactions.