Probing orientations of single fluorescent labels on a peptide reversibly binding to the human delta-opioid receptor

Fluorescent approaches for understanding interactions of ligands with G protein coupled receptors

G protein coupled receptors are responsible for a wide variety of signaling responses in diverse cell types. Despite major advances in the determination of structures of this class of receptors, the underlying mechanisms by which binding of different types of ligands specifically elicits particular signaling responses remain unclear. The use of fluorescence spectroscopy can provide important information about the process of ligand binding and ligand dependent conformational changes in receptors, especially kinetic aspects of these processes that can be difficult to extract from X-ray structures. We present an overview of the extensive array of fluorescent ligands that have been used in studies of G protein coupled receptors and describe spectroscopic approaches for assaying binding and probing the environment of receptor-bound ligands with particular attention to examples involving yeast pheromone receptors. In addition, we discuss the use of fluorescence spectroscopy for detecting and characterizing conformational changes in receptors induced by the binding of ligands. Such studies have provided strong evidence for diversity of receptor conformations elicited by different ligands, consistent with the idea that GPCRs are not simple on and off switches. This diversity of states constitutes an underlying mechanistic basis for biased agonism, the observation that different stimuli can produce different responses from a single receptor. It is likely that continued technical advances will allow fluorescence spectroscopy to play an important role in continued probing of structural transitions in G protein coupled receptors. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.

Correlative optical and scanning probe microscopies for mapping interactions at membranes

Innovative approaches for real-time imaging on molecular-length scales are providing researchers with powerful strategies for characterizing molecular and cellular structures and dynamics. Combinatorial techniques that integrate two or more distinct imaging modalities are particularly compelling as they provide a means for overcoming the limitations of the individual modalities and, when applied simultaneously, enable the collection of rich multi-modal datasets. Almost since its inception, scanning probe microscopy has closely associated with optical microscopy. This is particularly evident in the fields of cellular and molecular biophysics where researchers are taking full advantage of these real-time, in situ, tools to acquire three-dimensional molecular-scale topographical images with nanometer resolution, while simultaneously characterizing their structure and interactions though conventional optical microscopy. The ability to apply mechanical or optical stimuli provides an additional experimental dimension that has shown tremendous promise for examining dynamic events on sub-cellular length scales. In this chapter, we describe recent efforts in developing these integrated platforms, the methodology for, and inherent challenges in, performing coupled imaging experiments, and the potential and future opportunities of these research tools for the fields of molecular and cellular biophysics with a specific emphasis on the application of these coupled approaches for the characterization of interactions occurring at membrane interfaces.

Biophysical characterization of G-protein coupled receptor-peptide ligand binding

G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular responses to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GPCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques that have been successfully used for structural and biophysical characterization of peptide ligands binding to their cognate GPCRs. The techniques reviewed include solution-state nuclear magnetic resonance (NMR) spectroscopy, solid-state NMR, X-ray diffraction, fluorescence spectroscopy and single-molecule fluorescence methods, flow cytometry, surface plasmon resonance, isothermal titration calorimetry, and atomic force microscopy. The goal herein is to provide a cohesive starting point to allow selection of techniques appropriate to the elucidation of a given GPCR-peptide interaction.

Escaping the flatlands: new approaches for studying the dynamic assembly and activation of GPCR signaling complexes

Despite significant recent advances in molecular and structural studies of G protein-coupled receptors (GPCRs), an understanding of transmembrane signal transduction with chemical precision requires new approaches. Simple binary receptor-ligand or receptor-G protein complex models cannot adequately describe the relevant macromolecular signaling machineries. GPCR signalosomes undergo complex dynamic assembly-disassembly reactions to create allosteric signaling conduits whose properties cannot necessarily be predicted from individual elements alone. The combinatorial possibilities inherent in a system with hundreds of potential components suggest that high-content miniaturized experimental platforms and computational approaches will be required. To study allosteric effects involved in signalosome reaction pathways, a bottom-up approach using multicolor single-molecule detection fluorescence experiments in biochemically defined systems and complemented by molecular dynamics models of macromolecular complexes is proposed. In bridging the gap between molecular and systems biology, this synthetic approach suggests a way forward from the flatlands to multi-dimensional data collection.

Lipid bilayer blanketing versus penetrating silica colloidal crystals

Fluorescence intensities and diffusion coefficients were measured for a labeled lipid in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers deposited by vesicle fusion on two types of silica colloidal crystals, one made from 145 nm particles and the other from 490 nm particles. The bilayer is shown to blanket the top of the silica colloidal crystal for the 145 nm case and to coat the entire surface area for the 450 nm case. The diffusion coefficient of the labeled lipid is shown to be the same in both cases, showing that the diffusion coefficient is not an indicator of bilayer penetration.

Biotin-avidin binding kinetics measured by single-molecule imaging

The high affinity of avidin for biotin has made it useful for many bioanalytical applications involving the immobilization of proteins, vesicles, and other biomolecules to surfaces. To understand the formation and stability of the resulting biotin-avidin complex, it is useful to know the kinetics of the binding reaction, especially for situations where the complex is formed at a liquid-solid interface typically used in sensor or separation applications. In this work, a single-molecule fluorescence method is developed for measuring the kinetics and affinity constant for the binding of neutravidin, a deglycosylated variant of avidin, to surface-immobilized biotin. Biotin was immobilized using succinimidyl ester chemistry onto amine sites on glass surfaces. The surface density of biotin was controlled by the extreme dilution of 3-aminopropyltriethoxysilane into a monolayer of 2-cyanoethyltriethoxysilane. The resulting biotin binding sites are spaced apart by micrometer distances, and this avoids crowding effects and makes the resolution of single molecules possible. The binding and unbinding of individual tetramethylrhodamine-labeled neutravidin molecules is measured in situ by total-internal-reflection fluorescence (TIRF) microscopy imaging. Single-molecule detection and counting is readily achieved by this measurement, where quantitative control is established by determining the probabilities of false positive and negative events based on the intensity distributions of background and single-molecule spots and by comparing the bound molecule populations with the independently measured density of binding sites on the surface. The kinetics of binding and unbinding are evaluated by intermittent imaging and counting the number of bound neutravidin molecules versus time, following introduction of a neutravidin solution or its replacement by buffer over the low-density biotinylated surface. The neutravidin binding kinetics were found to be fast, essentially diffusion-controlled, while the stability of the complex and its dissociation rate appear to be influenced by the chemistry of biotin immobilization.

Combined scanning probe and total internal reflection fluorescence microscopy

Combining scanning probe and optical microscopy represents a powerful approach for investigating structure-function relationships and dynamics of biomolecules and biomolecular assemblies, often in situ and in real-time. This platform technology allows us to obtain three-dimensional images of individual molecules with nanometer resolution, while simultaneously characterizing their structure and interactions though complementary techniques such as optical microscopy and spectroscopy. We describe herein the practical strategies for the coupling of scanning probe and total internal reflection fluorescence microscopy along with challenges and the potential applications of such platforms, with a particular focus on their application to the study of biomolecular interactions at membrane surfaces.

Silica colloidal crystals as porous substrates for total internal reflection fluorescence microscopy of live cells

Total internal reflection fluorescence (TIRF) microscopy is a powerful means of probing biological cells because it reduces autofluorescence, but the need for direct contact between the cell surface and the microscope slide hinders chemical access to the cell surface. In this work, a submicrometer crystalline layer of colloidal silica on the microscope coverslip is shown to allow TIRF microscopy while also allowing chemical access to the cell surface. A 750 nm layer of 165 nm silica colloidal crystals was sintered onto a fused silica coverslip, and Chinese hamster ovary cells were successfully grown on this surface. This cell line over-expresses the human delta-opioid receptor, which enabled probing of the binding of a labeled ligand to the receptors on the cell surface. Total internal reflection and chemical access to the cell surface are demonstrated. The range of angles for total internal reflection is reduced only by 1/3 due to the lower index of refraction of the colloidal multilayer relative to fused silica.