Coiled-coil tag-probe labeling methods for live-cell imaging of membrane receptors

Noncanonical Amino Acid Tools and Their Application to Membrane Protein Studies

Methods rooted in chemical biology have contributed significantly to studies of integral membrane proteins. One recent key approach has been the application of genetic code expansion (GCE), which enables the site-specific incorporation of noncanonical amino acids (ncAAs) with defined chemical properties into proteins. Efficient GCE is challenging, especially for membrane proteins, which have specialized biogenesis and cell trafficking machinery and tend to be expressed at low levels in cell membranes. Many eukaryotic membrane proteins cannot be expressed functionally in E. coli and are most effectively studied in mammalian cell culture systems. Recent advances have facilitated broader applications of GCE for studies of membrane proteins. First, AARS/tRNA pairs have been engineered to function efficiently in mammalian cells. Second, bioorthogonal chemical reactions, including cell-friendly copper-free "click" chemistry, have enabled linkage of small-molecule probes such as fluorophores to membrane proteins in live cells. Finally, in concert with advances in GCE methodology, the variety of available ncAAs has increased dramatically, thus enabling the investigation of protein structure and dynamics by multidisciplinary biochemical and biophysical approaches. These developments are reviewed in the historical framework of the development of GCE technology with a focus on applications to studies of membrane proteins.

Elucidation of Complex Dynamic Intermolecular Interactions in Membranes

Biomembranes composed of various proteins and lipids play important roles in cellular functions, such as signal transduction and substance transport. In addition, some bioactive peptides and pathogenic proteins target membrane proteins and lipids to exert their effects. Therefore, an understanding of dynamic and complex intermolecular interactions among these membrane constituents is needed to elucidate their mechanisms. This review summarizes the major research carried out in the author's laboratory on how lipids and their inhomogeneous distributions regulate the structures and functions of antimicrobial peptides and Alzheimer's amyloid β-protein. Also, how to detect transmembrane helix-helix and membrane protein-protein interactions and how they are modulated by lipids are discussed.

Complementary leucine zippering system for effective intracellular delivery of proteins by cell-penetrating peptides

A heterodimeric leucine zipper composed of a pair of leucine zipper peptides containing acidic or basic amino acid residues at appropriate positions in each peptide was used as a molecular glue to connect protein cargos to a cell-penetrating peptide (CPP) carrier. To investigate the hybridization properties by fluorescence experiments, we prepared an enhanced green fluorescent protein (EGFP) fused with an acidic leucine zipper (LzK), EGFP-LzK, and a basic leucine zipper (LzE) modified with a CPP, LzE-CPP. The LzK and LzE formed a 1:1 hybrid when EGFP-LzK and LzE-CPP were mixed in phosphate buffer saline, thereby conjugating the EGFP with the CPP. The formation of the 1:1 hybrid was confirmed by fluorescence spectra and fluorescence titration curves. Results from fluorescence microscopy experiments showed that EGFP was successfully delivered into cells by conjugating with the CPP via formation of the LzK/LzE hybrid. We also fused the apoptotic protein p53 with LzK (p53-LzK) and investigated the inhibition of cell proliferation of various cell lines by incubation with the p53-LzK/LzE-CPP hybrid. This hybrid was found to localize in nuclei and successfully inhibited cell-specific proliferation. The LzE/LzK zipper system inhibited cell proliferation more efficiently than the directly fused conjugate, p53-CPP. Our method will be a useful drug delivery system for delivering bioactive proteins to treat various diseases.

Live-cell imaging of membrane proteins by a coiled-coil labeling method-Principles and applications

In situ investigations in living cell membranes are important to elucidate the dynamic behaviors of membrane proteins in complex biomembrane environments. Protein-specific labeling is a key technique for the detection of a target protein by fluorescence imaging. The use of post-translational labeling methods using a genetically encodable tag and synthetic probes targeting the tag offer a smaller label size, labeling with synthetic fluorophores, and precise control of the labeling ratio in multicolor labeling compared with conventional genetic fusions with fluorescent proteins. This review focuses on tag-probe labeling studies for live-cell analysis of membrane proteins based on heterodimeric peptide pairs that form coiled-coil structures. The robust and simple peptide-peptide interaction enables not only labeling of membrane proteins by noncovalent interactions, but also covalent crosslinking and acyl transfer reactions guided by coiled-coil assembly. A number of studies have demonstrated that membrane protein behaviors in live cells, such as internalization of receptors and the oligomeric states of various membrane proteins (G-protein-coupled receptors, epidermal growth factor receptors, influenza A M2 channel, and glycopholin A), can be precisely analyzed using coiled-coil labeling, indicating the potential of this labeling method in membrane protein research.

[Fluorescent Peptide Tools for Studying the Self-association of Membrane Proteins]

Detecting the behaviors of proteins in membranes is often challenging; we need to develop new methods to better understand the mechanisms involved. We have developed two types of peptide-based experimental systems that can detect the self-association of proteins in bilayer environments: 1) a single-pair fluorescence detection system for studying the self-association of transmembrane helices in model membranes; and 2) live-cell fluorescence labeling and analysis of the oligomeric state of membrane proteins using a coiled-coil labeling method. By using these methods, we show that membrane cholesterol significantly affects the self-association of transmembrane helices.

Single-molecule labeling for studying trafficking of renal transporters

The ability to detect and track single molecules presents the advantage of visualizing the complex behavior of transmembrane proteins with a time and space resolution that would otherwise be lost with traditional labeling and biochemical techniques. Development of new imaging probes has provided a robust method to study their trafficking and surface dynamics. This mini-review focuses on the current technology available for single-molecule labeling of transmembrane proteins, their advantages, and limitations. We also discuss the application of these techniques to the study of renal transporter trafficking in light of recent research.

Stoichiometric analysis of oligomeric states of three class-A GPCRs, chemokine-CXCR4, dopamine-D2, and prostaglandin-EP1 receptors, on living cells

G-protein-coupled receptors (GPCRs) form the largest family of transmembrane receptors, and their oligomerization has been suggested to be related to their functions. Despite extensive studies, their oligomeric states are highly controversial. One of the reasons is the overestimation of oligomerization by conventional methods. We recently established a stoichiometric analysis method for precisely determining the oligomeric state of membrane proteins on living cells with the combined use of the coiled-coil labeling method and a spectral imaging technique and showed that the prototypical class-A GPCR β₂ -adrenergic receptor (β₂ AR) did not form functional oligomers. In this study, we expanded our study to three well-studied class-A GPCRs: C-X-C chemokine receptor of stromal cell-derived factor-1α (CXCR4), dopamine receptor D2 short isotype (D2R), and prostaglandin E receptor subtype 1 (EP1R). We found that these receptors did not form constitutive homooligomers. The receptors exhibited calcium signaling upon agonist stimulation as monomers, although CXCR4 and EP1R gradually clustered after fast signaling. We conclude that homooligomerization is not necessary for the signal transductions of these four class-A GPCRs. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Selective amine labeling of cell surface proteins guided by coiled-coil assembly

Covalent labeling of target proteins in living cells is useful for both fluorescence live-cell imaging and the subsequent biochemical analyses of the proteins. Here, we report an efficient method for the amine labeling of membrane proteins on the cell surface, guided by a noncovalent coiled-coil interaction. A carboxyl sulfosuccinimidyl ester introduced at the C-terminus of the coiled-coil probe reacted with target proteins under mild labeling conditions ([probe] = 150 nM, pH 7.4, 25°C) for 20 min. Various fluorescent moieties with different hydrophobicities are available for covalent labeling with high signal/background labeling ratios. Using this method, oligomeric states of glycophorin A (GpA) were compared in mammalian CHO-K1 cells and sodium dodecyl sulfate (SDS) micelles. In the cell membranes, no significant self-association of GpA was detected, whereas SDS-PAGE suggested partial dimerization of the proteins. Membrane cholesterol was found to be an important factor that suppressed the dimerization of GpA. Thus, the covalent functionality enables direct comparison of the oligomeric state of membrane proteins under various conditions. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 484-490, 2016.

Measuring receptor recycling in polarized MDCK cells

Recycling of proteins such as channels, pumps, and receptors is critical for epithelial cell function. In this chapter we present a method to measure receptor recycling in polarized Madin-Darby canine kidney cells using an iodinated ligand. We describe a technique to iodinate transferrin (Tf), we discuss how (125)I-Tf can be used to label a cohort of endocytosed Tf receptor, and then we provide methods to measure the rate of recycling of the (125)I-Tf-receptor complex. We also show how this approach, which is easily adaptable to other proteins, can be used to simultaneously measure the normally small amount of (125)I-Tf transcytosis and degradation.

[Stoichiometric analysis of oligomerization of membrane proteins using coiled-coil labeling and in-cell spectroscopy]

Many membrane proteins are responsible for signaling and ionic transport necessary to maintain biological functions in vivo. Recently, not only conformational changes but also oligomerization have been proposed to regulate protein activation. Thus, the study of membrane protein oligomerization is crucial for new drug development. The existing destructive methodologies such as immunoprecipitation, however, are not suitable to determine oligomeric states precisely because of the artificial aggregation of proteins after detergent solubilization. In the present study, the coiled-coil tag-probe labeling method and spectral imaging were first combined to establish a new methodology based on fluorescence resonance energy transfer (FRET) for stoichiometric analysis of the oligomeric states of membrane proteins on living cells. After validating the method for mono-, di-, and tetrameric standard membrane proteins, the oligomeric state of β₂-adrenergic receptors (β₂ARs) was examined to clarify its functional significance. It was found that β2ARs could transduce cyclic adenosine 5'-monophosphate (cAMP) signals and internalize them upon treatment with ligands without showing any FRET signals. Thus, β₂ARs do not form constitutive homooligomers, and homooligomerization is not necessary for the receptor function of β₂ARs. Finally, the oligomeric state of full-length M2 proton-selective channels of influenza A virus was investigated. Although the results of X-ray crystallography and NMR studies using fragment peptides suggested that M2 stably forms a tetrameric channel, the full-length M2 proteins formed proton-conducting dimers at neutral pH and these dimers were converted to tetramers at acidic pH, indicating that the minimal functional unit of the M2 channel is a dimer.

[A visualization tool for oligomerization and internalization of membrane proteins in living cells: coiled-coil labeling method]

Genetic fusion of fluorescent/luminescent proteins to a target protein for specific labeling in living cells has been widely used to investigate the intracellular trafficking and oligomerization of the proteins. However, several limitations of fluorescent/luminescent proteins, such as considerable size, difficulty in controlling labeling ratio in multicolor labeling, can obscure true behaviors of the target proteins. To overcome these difficulties, post-translational labeling methods using pairs of small genetically-encodable 'tags' and synthetic 'probes' targeting the tags have been widely studied in recent years. We have developed a quick tag-probe labeling method using a high-affinity heterodimeric coiled-coil formation between the E3 tag (EIAALEK)3 attached to the target protein and the K4 probe (KIAALKE)4 labeled with a fluorophore. The labeling is cell-surface-specific and completed within 1 min, therefore suitable for monitoring oligomerization/internalization of membrane proteins on living cell surface. Taking advantage of easiness in multicolor labeling, we show that the oligomeric state of membrane proteins can be precisely analyzed based on fluorescence resonance energy transfer. By using this method, we found that β2 adrenergic receptors do not form constitutive homooligomers, and homooligomerization is not necessary for the receptor function. Furthermore, the degree of internalization of the β2 receptors following agonist stimulation was evaluated by ratiometric detection of pH decrease in endosomes.

Stoichiometric analysis of oligomerization of membrane proteins on living cells using coiled-coil labeling and spectral imaging

Many membrane proteins are proposed to work as oligomers; however, the conclusion is sometimes controversial, as for β2-adorenergic receptor (β2AR), which is one of the best-studied family A G-protein-coupled receptors. This is due to the lack of methods for easy and precise detection of the oligomeric state of membrane proteins on living cells. Here, we show that a combination of the coiled-coil tag-probe labeling method and spectral imaging enable a stoichiometric analysis of the oligomeric state of membrane proteins on living cells using monomeric, dimeric, and tetrameric standard membrane proteins. Using this method, we found that β2ARs do not form constitutive homooligomers, while they exhibit their functions such as the cyclic adenosine 5'-monophosphate (cAMP) signaling and internalization upon agonist stimulation.

Improvement of probe peptides for coiled-coil labeling by introducing phosphoserines

We have developed a method of rapidly labeling membrane proteins in living cells using a high-affinity heterodimeric coiled-coil construct containing an E3 tag (EIAALEK)(3) genetically fused to the target protein and a K4 probe (KIAALKE)(4) labeled with a fluorophore such as tetramethylrhodamine (TMR) at its N-terminus (TMR-K4). However, coiled-coil labeling cannot be applied to highly negatively charged cell lines such as HEK293, because of the nonspecific adsorption of the positively charged K4 probes to cell membranes. To reduce the net positive charge, we synthesized new probes that include phosphoserine residues (pSer) between the K4 sequence and TMR fluorophore (TMR-(pSer)(n)-K4, [n = 1-3]). The affinity of the pSer-introduced probes was comparable to that of the TMR-K4 probe. However, the TMR-(pSer)(2)-K4 and TMR-(pSer)(3)-K4 probes tended to aggregate during labeling. In contrast, TMR-pSer-K4, which was as soluble as TMR-K4, achieved higher signal/background ratios (30-100) for four host cell lines (HEK293, HeLa, SH-SY5Y, and PC12) than did TMR-K4 (~10 for HEK293 cells), demonstrating that the improved probe can be used for various types of cells.

Smart self-assembled hybrid hydrogel biomaterials

Hybrid biomaterials are systems created from components of at least two distinct classes of molecules, for example, synthetic macromolecules and proteins or peptide domains. The synergistic combination of two types of structures may produce new materials that possess unprecedented levels of structural organization and novel properties. This Review focuses on biorecognition-driven self-assembly of hybrid macromolecules into functional hydrogel biomaterials. First, basic rules that govern the secondary structure of peptides are discussed, and then approaches to the specific design of hybrid systems with tailor-made properties are evaluated, followed by a discussion on the similarity of design principles of biomaterials and macromolecular therapeutics. Finally, the future of the field is briefly outlined.