Rotational diffusion of the α(2a) adrenergic receptor revealed by FlAsH labeling in living cells

Unraveling the hidden temporal range of fast β2-adrenergic receptor mobility by time-resolved fluorescence

G-protein-coupled receptors (GPCRs) are hypothesized to possess molecular mobility over a wide temporal range. Until now the temporal range has not been fully accessible due to the crucially limited temporal range of available methods. This in turn, may lead relevant dynamic constants to remain masked. Here, we expand this dynamic range by combining fluorescent techniques using a spot confocal setup. We decipher mobility constants of β₂-adrenergic receptor over a wide time range (nanosecond to second). Particularly, a translational mobility (10 µm²/s), one order of magnitude faster than membrane associated lateral mobility that explains membrane protein turnover and suggests a wider picture of the GPCR availability on the plasma membrane. And a so far elusive rotational mobility (1-200 µs) which depicts a previously overlooked dynamic component that, despite all complexity, behaves largely as predicted by the Saffman-Delbrück model.

The mobility of the β2-adrenergic receptor, from the nanosecond to the second range, is revealed by combining several fluorescent spectroscopy techniques. These data also show a previously hidden mobility of this GPCR.

Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook

Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.

Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags

Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.

Rotational Diffusion of Membrane Proteins in Crowded Membranes

Membrane proteins travel along cellular membranes and reorient themselves to form functional oligomers and protein-lipid complexes. Following the Saffman-Delbrück model, protein radius sets the rate of this diffusive motion. However, it is unclear how this model, derived for ideal and dilute membranes, performs under crowded conditions of cellular membranes. Here, we study the rotational motion of membrane proteins using molecular dynamics simulations of coarse-grained membranes and 2-dimensional Lennard-Jones fluids with varying levels of crowding. We find that the Saffman-Delbrück model captures the size-dependency of rotational diffusion under dilute conditions where protein-protein interactions are negligible, whereas stronger scaling laws arise under crowding. Together with our recent work on lateral diffusion, our results reshape the description of protein dynamics in native membrane environments: The translational and rotational motions of proteins with small transmembrane domains are rapid, whereas larger proteins or protein complexes display substantially slower dynamics.

Protein Rotational Dynamics in Aligned Lipid Membranes Probed by Anisotropic T1ρ NMR Relaxation

A membrane-bound form of Pf1 coat protein reconstituted in magnetically aligned DMPC/DHPC bicelles was used as a molecular probe to quantify for the viscosity of the lipid membrane interior by measuring the uniaxial rotational diffusion coefficient of the protein. Orientationally dependent ¹⁵N NMR relaxation times in the rotating frame, or T_1ρ, were determined by fitting individually the decay of the resolved NMR peaks corresponding to the transmembrane helix of Pf1 coat protein as a function of the spin-lock time incorporated into the 2D SAMPI4 pulse sequence. The T_1ρ relaxation mechanism was modeled by uniaxial rotational diffusion on a cone, which yields a linear correlation with respect to the bond factor sin⁴θ_B, where θ_B is the angle that the NH bond forms with respect to the axis of rotation. Importantly, the bond factors can be independently measured from the dipolar couplings in the separated local-field SAMPI4 spectra. From this dependence, the value of the diffusion coefficient D_|| = 8.0 × 10⁵ s^-1 was inferred from linear regression of the experimental T_1ρ data even without any spectroscopic assignment. Alternatively, a close value of D_|| = 7.7 × 10⁵ s^-1 was obtained by fitting the T_1ρ relaxation data for the assigned NMR peaks of the transmembrane domain of Pf1 to a wavelike pattern as a function of residue number. The method illustrates the use of single-helix transmembrane peptides as molecular probes to assess the dynamic parameters of biological membranes by NMR relaxation in oriented lipid bilayers.

Characterization of Fluorescein Arsenical Hairpin (FlAsH) as a Probe for Single-Molecule Fluorescence Spectroscopy

In recent years, new labelling strategies have been developed that involve the genetic insertion of small amino-acid sequences for specific attachment of small organic fluorophores. Here, we focus on the tetracysteine FCM motif (FLNCCPGCCMEP), which binds to fluorescein arsenical hairpin (FlAsH), and the ybbR motif (TVLDSLEFIASKLA) which binds fluorophores conjugated to Coenzyme A (CoA) via a phosphoryl transfer reaction. We designed a peptide containing both motifs for orthogonal labelling with FlAsH and Alexa647 (AF647). Molecular dynamics simulations showed that both motifs remain solvent-accessible for labelling reactions. Fluorescence spectra, correlation spectroscopy and anisotropy decay were used to characterize labelling and to obtain photophysical parameters of free and peptide-bound FlAsH. The data demonstrates that FlAsH is a viable probe for single-molecule studies. Single-molecule imaging confirmed dual labeling of the peptide with FlAsH and AF647. Multiparameter single-molecule Förster Resonance Energy Transfer (smFRET) measurements were performed on freely diffusing peptides in solution. The smFRET histogram showed different peaks corresponding to different backbone and dye orientations, in agreement with the molecular dynamics simulations. The tandem of fluorophores and the labelling strategy described here are a promising alternative to bulky fusion fluorescent proteins for smFRET and single-molecule tracking studies of membrane proteins.

Conformational Profiling of the AT1 Angiotensin II Receptor Reflects Biased Agonism, G Protein Coupling, and Cellular Context

Here, we report the design and use of G protein-coupled receptor-based biosensors to monitor ligand-mediated conformational changes in receptors in intact cells. These biosensors use bioluminescence resonance energy transfer with Renilla luciferase (RlucII) as an energy donor, placed at the distal end of the receptor C-tail, and the small fluorescent molecule FlAsH as an energy acceptor, its binding site inserted at different positions throughout the intracellular loops and C-terminal tail of the angiotensin II type I receptor. We verified that the modifications did not compromise receptor localization or function before proceeding further. Our biosensors were able to capture effects of both canonical and biased ligands, even to the extent of discriminating between different biased ligands. Using a combination of G protein inhibitors and HEK 293 cell lines that were CRISPR/Cas9-engineered to delete Gα_q, Gα₁₁, Gα₁₂, and Gα₁₃ or β-arrestins, we showed that Gα_q and Gα₁₁ are required for functional responses in conformational sensors in ICL3 but not ICL2. Loss of β-arrestin did not alter biased ligand effects on ICL2P2. We also demonstrate that such biosensors are portable between different cell types and yield context-dependent readouts of G protein-coupled receptor conformation. Our study provides mechanistic insights into signaling events that depend on either G proteins or β-arrestin.

Rotamer-Restricted Fluorogenicity of the Bis-Arsenical ReAsH

Fluorogenic dyes such as FlAsH and ReAsH are used widely to localize, monitor, and characterize proteins and their assemblies in live cells. These bis-arsenical dyes can become fluorescent when bound to a protein containing four proximal Cys thiols-a tetracysteine (Cys4) motif. Yet the mechanism by which bis-arsenicals become fluorescent upon binding a Cys4 motif is unknown, and this nescience limits more widespread application of this tool. Here we probe the origins of ReAsH fluorogenicity using both computation and experiment. Our results support a model in which ReAsH fluorescence depends on the relative orientation of the aryl chromophore and the appended arsenic chelate: the fluorescence is rotamer-restricted. Our results do not support a model in which fluorogenicity arises from the relief of ring strain. The calculations identify those As-aryl rotamers that support fluorescence and those that do not and correlate well with prior experiments. The rotamer-restricted model we propose is supported further by biophysical studies: the excited-state fluorescence lifetime of a complex between ReAsH and a protein bearing a high-affinity Cys4 motif is longer than that of ReAsH-EDT2, and the fluorescence intensity of ReAsH-EDT2 increases in solvents of increasing viscosity. By providing a higher resolution view of the structural basis for fluorogenicity, these results provide a clear strategy for the design of more selective bis-arsenicals and better-optimized protein targets, with a concomitant improvement in the ability to characterize previously invisible protein conformational changes and assemblies in live cells.

Time-resolved FRET reports FGFR1 dimerization and formation of a complex with its effector PLCγ1

In vitro and in vivo imaging of protein tyrosine kinase activity requires minimally invasive, molecularly precise optical probes to provide spatiotemporal mechanistic information of dimerization and complex formation with downstream effectors. We present here a construct with genetically encoded, site-specifically incorporated, bioorthogonal reporter that can be selectively labelled with exogenous fluorogenic probes to monitor the structure and function of fibroblast growth factor receptor (FGFR). GyrB.FGFR1KD.TC contains a coumermycin-induced artificial dimerizer (GyrB), FGFR1 kinase domain (KD) and a tetracysteine (TC) motif that enables fluorescent labelling with biarsenical dyes FlAsH-EDT2 and ReAsH-EDT2. We generated bimolecular system for time-resolved FRET (TR-FRET) studies, which pairs FlAsH-tagged GyrB.FGFR1KD.TC and N-terminal Src homology 2 (nSH2) domain of phospholipase Cγ (PLCγ), a downstream effector of FGFR1, fused to mTurquoise fluorescent protein (mTFP). We demonstrated phosphorylation-dependent TR-FRET readout of complex formation between mTFP.nSH2 and GyrB.FGFR1KD.TC. By further application of TR-FRET, we also demonstrated formation of the GyrB.FGFR1KD.TC homodimer by coumermycin-induced dimerization. Herein, we present a spectroscopic FRET approach to facilitate and propagate studies that would provide structural and functional insights for FGFR and other tyrosine kinases.

Coherent and stochastic averaging in solid-state NMR

A new approach for calculating solid-state NMR lineshapes of uniaxially rotating membrane proteins under the magic-angle spinning conditions is presented. The use of stochastic Liouville equation (SLE) allows one to account for both coherent sample rotation and stochastic motional averaging of the spherical dipolar powder patterns by uniaxial diffusion of the spin-bearing molecules. The method is illustrated via simulations of the dipolar powder patterns of rigid samples under the MAS conditions, as well as the recent method of rotational alignment in the presence of both MAS and rotational diffusion under the conditions of dipolar recoupling. It has been found that it is computationally more advantageous to employ direct integration over a spherical grid rather than to use a full angular basis set for the SLE solution. Accuracy estimates for the bond angles measured from the recoupled amide ¹H-¹⁵N dipolar powder patterns have been obtained at various rotational diffusion coefficients. It has been shown that the rotational alignment method is applicable to membrane proteins approximated as cylinders with radii of approximately 20Å, for which uniaxial rotational diffusion within the bilayer is sufficiently fast and exceeds the rate 2×10⁵s^-1.

Clustering of low-valence particles: structure and kinetics

We compute the structure and kinetics of two systems of low-valence particles with three or six freely oriented bonds in two dimensions. The structure of clusters formed by trivalent particles is complex with loops and holes, while hexavalent particles self-organize into regular and compact structures. We identify the elementary structures which compose the clusters of trivalent particles. At initial stages of clustering, the clusters of trivalent particles grow with a power-law time dependence. Yet at longer times fusion and fission of clusters equilibrates and clusters form a heterogeneous phase with polydispersed sizes. These results emphasize the role of valence in the kinetics and stability of finite-size clusters.

H-Ras forms dimers on membrane surfaces via a protein-protein interface

The lipid-anchored small GTPase Ras is an important signaling node in mammalian cells. A number of observations suggest that Ras is laterally organized within the cell membrane, and this may play a regulatory role in its activation. Lipid anchors composed of palmitoyl and farnesyl moieties in H-, N-, and K-Ras are widely suspected to be responsible for guiding protein organization in membranes. Here, we report that H-Ras forms a dimer on membrane surfaces through a protein-protein binding interface. A Y64A point mutation in the switch II region, known to prevent Son of sevenless and PI3K effector interactions, abolishes dimer formation. This suggests that the switch II region, near the nucleotide binding cleft, is either part of, or allosterically coupled to, the dimer interface. By tethering H-Ras to bilayers via a membrane-miscible lipid tail, we show that dimer formation is mediated by protein interactions and does not require lipid anchor clustering. We quantitatively characterize H-Ras dimerization in supported membranes using a combination of fluorescence correlation spectroscopy, photon counting histogram analysis, time-resolved fluorescence anisotropy, single-molecule tracking, and step photobleaching analysis. The 2D dimerization Kd is measured to be ∼1 × 10(3) molecules/µm(2), and no higher-order oligomers were observed. Dimerization only occurs on the membrane surface; H-Ras is strictly monomeric at comparable densities in solution. Analysis of a number of H-Ras constructs, including key changes to the lipidation pattern of the hypervariable region, suggest that dimerization is a general property of native H-Ras on membrane surfaces.

Kinetics and mechanism of G protein-coupled receptor activation

The activation of a G protein-coupled receptor is generally triggered by binding of an agonist to the receptor's binding pocket, or, in the case of rhodopsin, by light-induced changes of the pre-bound retinal. This is followed by a series of a conformational changes towards an active receptor conformation, which is capable of signalling to G proteins and other downstream proteins. In the past few years, a number of new techniques have been employed to analyze the kinetics of this activation process, including X-ray crystallographic three-dimensional structures of receptors in the inactive and the active states, NMR studies of labelled receptors, molecular simulations, and optical analyses with fluorescence resonance energy transfer (FRET). Here we review our current understanding of the activation process of GPCRs as well as open questions in the sequence of events ranging from (sub-)microsecond activation by light or agonist binding to millisecond activation of receptors by soluble ligands and the subsequent generation of an intracellular signal.

Synthesis of a targeted biarsenical Cy3-Cy5 affinity probe for super-resolution fluorescence imaging

Photoswitchable fluorescent probes capable of the targeted labeling of tagged proteins are of significant interest due to their ability to enable in situ imaging of protein complexes within native biomolecular assemblies. Here we describe the synthesis of a fluorescent probe (AsCy3Cy5) and demonstrate the targeted labeling and super-resolution imaging of a tagged protein within a supramolecular protein complex.

Surveying protein structure and function using bis-arsenical small molecules

Exploration across the fields of biology, chemical biology, and medicine has led to an increasingly complex, albeit incomplete, view of the interactions that drive life's processes. The ability to monitor and track the movement, activity, and interactions of biomolecules in living cells is an essential part of this investigation. In our laboratory, we have endeavored to develop tools that are capable not only of monitoring protein localization but also reporting on protein structure and function. Central to our efforts is a new strategy, bipartite tetracysteine display, that relies on the specific and high-affinity interaction between a fluorogenic, bis-arsenical small molecule and a unique protein sequence, conformation, or assembly. In 1998, a small-molecule analogue of fluorescein with two arsenic atoms, FlAsH, was shown by Tsien and coworkers to fluoresce upon binding to a linear amino acid sequence, Cys-Cys-Arg-Glu-Cys-Cys. Later work demonstrated that substituting Pro-Gly for Arg-Glu optimized both binding and fluorescence yield. Our strategy of bipartite tetracysteine display emanated from the idea that it would be possible to replace the intervening Pro-Gly dipeptide in this sequence with a protein or protein partnership, provided the assembled protein fold successfully reproduced the approximate placement of the two Cys-Cys pairs. In this Account, we describe our recent progress in this area, with an emphasis on the fundamental concepts that underlie the successful use of bis-arsenicals such as FlAsH and the related ReAsH for bipartite display experiments. In particular, we highlight studies that have explored how broadly bipartite tetracysteine display can be employed and that have navigated the conformational boundary conditions favoring success. To emphasize the utility of these principles, we outline two recently reported applications of bipartite tetracysteine display. The first is a novel, encodable, selective, Src kinase sensor that lacks fluorescent proteins but possesses a fluorescent readout exceeding that of most sensors based on Förster resonance energy transfer (FRET). The second is a unique method, called complex-edited electron microscopy (CE-EM), that facilitates visualization of protein-protein complexes with electron microscopy. Exciting as these applications may be, the continued development of small-molecule tools with improved utility in living cells, let alone in vivo, will demand a more nuanced understanding of the fundamental photophysics that lead to fluorogenicity, as well as creative approaches toward the synthesis and identification of new and orthogonal dye-tag pairs that can be applied facilely in tandem. We describe one example of a dye-sequence tag pair that is chemically distinct from bis-arsenical chemistry. Through further effort, we expect that that bipartite tetracysteine display will find successful use in the study of sophisticated biological questions that are essential to the fields of biochemistry and biology as well as to our progressive understanding of human disease.