Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances

Voltage-dependent G-protein regulation of CaV2.2 (N-type) channels

How G proteins inhibit N-type, voltage-gated, calcium-selective channels (CaV2.2) during presynaptic inhibition is a decades-old question. G proteins Gβγ bind to intracellular CaV2.2 regions, but the inhibition is voltage dependent. Using the hybrid electrophysiological and optical approach voltage-clamp fluorometry, we show that Gβγ acts by selectively inhibiting a subset of the four different CaV2.2 voltage-sensor domains (VSDs I to IV). During regular "willing" gating, VSD-I and -IV activations resemble pore opening, VSD III activation is hyperpolarized, and VSD II appears unresponsive to depolarization. In the presence of Gβγ, CaV2.2 gating is "reluctant": pore opening and VSD I activation are strongly and proportionally inhibited, VSD IV is modestly inhibited, while VSD III is not. We propose that Gβγ inhibition of VSDs I and IV underlies reluctant CaV2.2 gating and subsequent presynaptic inhibition.

One-step detection of procollagen type III N-terminal peptide as a fibrosis biomarker using fluorescent immunosensor (quenchbody)

BACKGROUND

Procollagen type III N-terminal peptide (P-III-NP) is a fibrosis biomarker associated with liver and cardiac fibrosis. Despite the value of P-III-NP as a biomarker, its analysis currently relies on enzyme-linked immunosorbent assays (ELISA) and radioimmunoassays (RIA), which require more than 3 h. To facilitate early diagnosis and treatment through rapid biomarker testing, we developed a one-step immunoassay for P-III-NP using a quenchbody, which is a fluorescence-labeled immunosensor for immediate signal generation.

RESULTS

To create quenchbodies, the total mRNA of P-III-NP antibodies was extracted from early-developed hybridoma cells, and genes of variable regions were obtained through cDNA synthesis, inverse PCR, and sequencing. A single-chain variable fragment (scFv) with an N-terminal Cys-tag was expressed in E. coli Shuffle T7, resulting in a final yield of 9.8 mg L-1. The fluorescent dye was labeled on the Cys-tag of the anti-P-III-NP scFv using maleimide-thiol click chemistry, and the spacer arm lengths between the maleimide-fluorescent dyes were compared. Consequently, a TAMRA-C6-labeled quenchbody exhibited antigen-dependent fluorescence signals and demonstrated its ability to detect P-III-NP at concentrations as low as 0.46 ng mL-1 for buffer samples, 1.0 ng mL-1 for 2 % human serum samples.

SIGNIFICANCE

This one-step P-III-NP detection method provides both qualitative and quantitative outcomes within a concise 5-min timeframe. Furthermore, its application can be expanded using a 96-well platform and human serum, making it a high-throughput and sensitive method for testing fibrotic biomarkers.

Electrical and G-protein Regulation of CaV2.2 (N-type) Channels

How G-proteins inhibit N-type, voltage-gated, calcium-selective channels (Ca V 2.2) during presynaptic inhibition is a decades-old question. G-proteins Gβγ bind to intracellular Ca V 2.2 regions, but the inhibition is voltage-dependent. Using the hybrid electrophysiological and optical approach voltage-clamp fluorometry, we show that Gβγ acts by selectively inhibiting a subset of the four different Ca V 2.2 voltage-sensor domains (VSDs I-IV). During regular "willing" gating, VSDs I and IV activation resemble pore opening, VSD III activation is hyperpolarized, and VSD II appears unresponsive to depolarization. In the presence of Gβγ, Ca V 2.2 gating is "reluctant": pore opening and VSD-I activation are strongly and proportionally inhibited, VSD IV is modestly inhibited while VSD III is not. We propose that Gβγ inhibition of VSD-I and -IV underlies reluctant Ca V 2.2 gating and subsequent presynaptic inhibition.

A synthetic flavonoid derivate in the plasma membrane transforms the voltage-clamp fluorometry signal of CiHv1

Voltage-clamp fluorometry (VCF) enables the study of voltage-sensitive proteins through fluorescent labeling accompanied by ionic current measurements for voltage-gated ion channels. The heterogeneity of the fluorescent signal represents a significant challenge in VCF. The VCF signal depends on where the cysteine mutation is incorporated, making it difficult to compare data among different mutations and different studies and standardize their interpretation. We have recently shown that the VCF signal originates from quenching amino acids in the vicinity of the attached fluorophores, together with the effect of the lipid microenvironment. Based on these, we performed experiments to test the hypothesis that the VCF signal could be altered by amphiphilic quenching molecules in the cell membrane. Here we show that a phenylalanine-conjugated flavonoid (4-oxo-2-phenyl-4H-chromene-7-yl)-phenylalanine, (later Oxophench) has potent effects on the VCF signals of the Ciona intestinalis HV1 (CiHv1) proton channel. Using spectrofluorimetry, we showed that Oxophench quenches TAMRA (5(6)-carboxytetramethylrhodamine-(methane thiosulfonate)) fluorescence. Moreover, Oxophench reduces the baseline fluorescence in oocytes and incorporates into the cell membrane while reducing the membrane fluidity of HEK293 cells. Our model calculations confirmed that Oxophench, a potent membrane-bound quencher, modifies the VCF signal during conformational changes. These results support our previously published model of VCF signal generation and point out that a change in the VCF signal may not necessarily indicate an altered conformational transition of the investigated protein.

Conformational Dynamic Studies of Prokaryotic Potassium Channels Explored by Homo-FRET Methodologies

Fluorescence techniques have been widely used to shed light over the structure-function relationship of potassium channels for the last 40-50 years. In this chapter, we describe how a Förster resonance energy transfer between identical fluorophores (homo-FRET) approach can be applied to study the gating behavior of the prokaryotic channel KcsA. Two different gates have been described to control the K+ flux across the channel's pore, the helix-bundle crossing and the selectivity filter, located at the opposite sides of the channel transmembrane section. Both gates can be studied individually or by using a double-reporter system. Due to its homotetrameric structural arrangement, KcsA presents a high degree of symmetry that fulfills the first requisite to calculate intersubunit distances through this technique. The results obtained through this work have helped to uncover the conformational plasticity of the selectivity filter under different experimental conditions and the importance of its allosteric coupling to the opening of the activation (inner) gate. This biophysical approach usually requires low protein concentration and presents high sensitivity and reproducibility, complementing the high-resolution structural information provided by X-ray crystallography, cryo-EM, and NMR studies.

Insight into the Sensing Behavior of DNA Probes Based on MOF-Nucleic Acid Interaction for Bioanalysis

Adsorption of DNA probes onto nanomaterials is a promising strategy for bioassay establishment typically using fluorescence or catalytic activities to generate signals. Albeit important, there is currently a lack of systematic understanding of the sensing behaviors building on nanomaterial-DNA interactions, which greatly limits the rational method design and their subsequent applications. Herein, the issue was investigated by employing multifunctional metal-organic frameworks (MOFs) (FeTCPP⊂UiO-66) as a model that was synthesized via integrating heme-like ligand FeTCPP into commonly used MOFs (UiO-66). Our results demonstrated that the fluorescently labeled DNA adsorbed onto FeTCPP⊂UiO-66 was quenched through photoinduced electron transfer, fluorescence resonance energy transfer, and the internal filtration effect. Among different DNA structures, double-stranded DNA and hybridization chain reaction products largely retained their fluorescence due to desorption and conformational variation, respectively. In addition, ssDNA could maximally inhibit the peroxidase activity of FeTCPP⊂UiO-66, and this inhibition was strongly dependent on the strand length but independent of base composition. On the basis of these discoveries, a fluorescence/colorimetric dual-modal detection was designed against aflatoxin B1 with satisfactory performances obtained to further verify our results. This study provided some new insights into the sensing behaviors based on MOF-DNA interactions, indicating promising applications for rational bioassay design and its performance improvement.

Multiple mechanisms contribute to fluorometry signals from the voltage-gated proton channel

Voltage-clamp fluorometry (VCF) supplies information about the conformational changes of voltage-gated proteins. Changes in the fluorescence intensity of the dye attached to a part of the protein that undergoes a conformational rearrangement upon the alteration of the membrane potential by electrodes constitute the signal. The VCF signal is generated by quenching and dequenching of the fluorescence as the dye traverses various local environments. Here we studied the VCF signal generation, using the Hv1 voltage-gated proton channel as a tool, which shares a similar voltage-sensor structure with voltage-gated ion channels but lacks an ion-conducting pore. Using mutagenesis and lipids added to the extracellular solution we found that the signal is generated by the combined effects of lipids during movement of the dye relative to the plane of the membrane and by quenching amino acids. Our 3-state model recapitulates the VCF signals of the various mutants and is compatible with the accepted model of two major voltage-sensor movements.

Fluorometry signals indicating conformational change in an ion channel are generated by quenching amino acids and lipid effects during movement of the dye relative to the plane of the membrane.

Characterising ion channel structure and dynamics using fluorescence spectroscopy techniques

Ion channels undergo major conformational changes that lead to channel opening and ion conductance. Deciphering these structure-function relationships is paramount to understanding channel physiology and pathophysiology. Cryo-electron microscopy, crystallography and computer modelling provide atomic-scale snapshots of channel conformations in non-cellular environments but lack dynamic information that can be linked to functional results. Biophysical techniques such as electrophysiology, on the other hand, provide functional data with no structural information of the processes involved. Fluorescence spectroscopy techniques help bridge this gap in simultaneously obtaining structure-function correlates. These include voltage-clamp fluorometry, Förster resonance energy transfer, ligand binding assays, single molecule fluorescence and their variations. These techniques can be employed to unearth several features of ion channel behaviour. For instance, they provide real time information on local and global rearrangements that are inherent to channel properties. They also lend insights in trafficking, expression, and assembly of ion channels on the membrane surface. These methods have the advantage that they can be carried out in either native or heterologous systems. In this review, we briefly explain the principles of fluorescence and how these have been translated to study ion channel function. We also report several recent advances in fluorescence spectroscopy that has helped address and improve our understanding of the biophysical behaviours of different ion channel families.

Identification and quantification of within-burst dynamics in singly labeled single-molecule fluorescence lifetime experiments

Single-molecule spectroscopy has revolutionized molecular biophysics and provided means to probe how structural moieties within biomolecules spatially reorganize at different timescales. There are several single-molecule methodologies that probe local structural dynamics in the vicinity of a single dye-labeled residue, which rely on fluorescence lifetimes as readout. Nevertheless, an analytical framework to quantify dynamics in such single-molecule single dye fluorescence bursts, at timescales of microseconds to milliseconds, has not yet been demonstrated. Here, we suggest an analytical framework for identifying and quantifying within-burst lifetime-based dynamics, such as conformational dynamics recorded in single-molecule photo-isomerization-related fluorescence enhancement. After testing the capabilities of the analysis on simulations, we proceed to exhibit within-burst millisecond local structural dynamics in the unbound α-synuclein monomer. The analytical framework provided in this work paves the way for extracting a full picture of the energy landscape for the coordinate probed by fluorescence lifetime-based single-molecule measurements.

Acid responsiveness of emissive morpholinyl aminoquinolines and their use for cell fluorescence imaging

Herein, we report emissive aminoquinoline derivatives (TFMAQ) containing alkylmorpholine and arylmorpholine groups and their photophysical properties, acid-responsiveness, and organelle targeting. The alkylmorpholine group is well-known to favour accumulation in lysosomes and be acid-responsive, but, counterintuitively, the TFMAQ derivatives containing ethylmorpholine groups showed limited accumulation in lysosomes and, instead, preferential accumulation in lipid droplets. The findings reported here will aid the development of organelle/tissue specific dyes for cell imaging and diagnosis.

Gold Nanocluster-Based Fluorometric Banoxantrone Assay Enabled by Photoinduced Electron Transfer

Monitoring the blood concentration of banoxantrone (AQ4N) is important to evaluate the therapeutic efficacy and side effects of this new anticancer prodrug during its clinical applications. Herein, we report a fluorescence method for AQ4N detection through the modulation of the molecule-like photoinduced electron transfer (PET) behavior of gold nanoclusters (AuNCs). AQ4N can electrostatically bind to the surface of carboxylated chitosan (CC) and dithiothreitol (DTT) co-stabilized AuNCs and quench their fluorescence via a Coulomb interaction-accelerated PET process. Under optimized experimental conditions, the linear range of AQ4N is from 25 to 200 nM and the limit of detection is as low as 5 nM. In addition, this assay is confirmed to be reliable based on its successful use in AQ4N determination in mouse plasma samples. This work offers an effective strategy for AQ4N sensing based on fluorescent AuNCs and widens the application of AuNCs in clinical diagnosis and pharmaceutical analysis.

Measuring Membrane Penetration Depths and Conformational Changes in Membrane Peptides and Proteins

The structural organization and dynamic nature of the biomembrane components are important determinants for numerous cellular functions. Particularly, membrane proteins are critically important for various physiological functions and are important drug targets. The mechanistic insights on the complex functionality of membrane lipids and proteins can be elucidated by understanding the interplay between structure and dynamics. In this regard, membrane penetration depth represents an important parameter to obtain the precise depth of membrane-embedded molecules that often define the conformation and topology of membrane probes and proteins. In this review, we discuss about the widely used fluorescence quenching-based methods (parallax method, distribution analysis, and dual-quencher analysis) to accurately determine the membrane penetration depths of fluorescent probes that are either membrane-embedded or attached to lipids and proteins. Further, we also discuss a relatively novel fluorescence quenching method that utilizes tryptophan residue as the quencher, namely the tryptophan-induced quenching, which is sensitive to monitor small-scale conformational changes (short distances of < 15 Å) and useful in mapping distances in proteins. We have provided numerous examples for the benefit of readers to appreciate the importance and applicability of these simple yet powerful methods to study membrane proteins.

Cucurbit[n]uril Supramolecular Assemblies-Regulated Charge Transfer for Luminescence Switching of Gold Nanoclusters

Host-guest molecular assemblies are highly desirable for precisely controlling the luminescence properties of nanomaterials. Unfortunately, the design of high-quality luminescent nanoswitches is still very challenging due to the low affinity of traditional macrocyclic molecules (e.g., cyclodextrin) and inherently sophisticated electronic structures of nanoemitters. The current work represents the first to fabricate a luminescent nanoswitch using cucurbit[n]uril supramolecular assemblies-regulated luminescence of gold nanoclusters (AuNCs). It is found that, similar to a small-molecule fluorophore-based system, the luminescence of fabricated AuNC-cationic quencher nanohybrids can be reversibly manipulated by cucurbit[7]uril through altering the key parameters of the charge transfer process including the reorganization energy and electronic coupling between charge-transfer reactants. This study demonstrates the crucial role of cucurbit[n]uril host-guest assemblies in modulating the luminescence of AuNCs and their application in luminescence switching, thus offering new avenues for the fabrication and development of optical devices and smart materials.

Bz-8HQ: a novel supramolecular fluorochrome exhibiting multiple stimuli-responsiveness

A novel multifunctional fluorescent molecule (Bz-8HQ) was synthesized from the linkage of benzimidazole (Bz) and 8-hydroxyquinoline (8HQ) molecules and its response to multiple stimuli was investigated spectroscopically.

Monitoring protein conformational changes using fluorescent nanoantennas

Understanding the relationship between protein structural dynamics and function is crucial for both basic research and biotechnology. However, methods for studying the fast dynamics of structural changes are limited. Here, we introduce fluorescent nanoantennas as a spectroscopic technique to sense and report protein conformational changes through noncovalent dye-protein interactions. Using experiments and molecular simulations, we detect and characterize five distinct conformational states of intestinal alkaline phosphatase, including the transient enzyme-substrate complex. We also explored the universality of the nanoantenna strategy with another model protein, Protein G and its interaction with antibodies, and demonstrated a rapid screening strategy to identify efficient nanoantennas. These versatile nanoantennas can be used with diverse dyes to monitor small and large conformational changes, suggesting that they could be used to characterize diverse protein movements or in high-throughput screening applications.

Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements

The allosteric coupling between activation and inactivation processes is a common feature observed in K⁺ channels. Particularly, in the prokaryotic KcsA channel the K⁺ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pK_a of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.

BK Channel Gating Mechanisms: Progresses Toward a Better Understanding of Variants Linked Neurological Diseases

The large conductance Ca2+-activated potassium (BK) channel is activated by both membrane potential depolarization and intracellular Ca2+ with distinct mechanisms. Neural physiology is sensitive to the function of BK channels, which is shown by the discoveries of neurological disorders that are associated with BK channel mutations. This article reviews the molecular mechanisms of BK channel activation in response to voltage and Ca2+ binding, including the recent progress since the publication of the atomistic structure of the whole BK channel protein, and the neurological disorders associated with BK channel mutations. These results demonstrate the unique mechanisms of BK channel activation and that these mechanisms are important factors in linking BK channel mutations to neurological disorders.

Linear-Response and Nonlinear-Response Formulations of the Instantaneous Marcus Theory for Nonequilibrium Photoinduced Charge Transfer

Instantaneous Marcus theory (IMT) offers a way for capturing the time-dependent charge transfer (CT) rate coefficient in nonequilibrium photoinduced CT processes, where the system was photoexcited from its equilibrated ground state vertically to the excitonic state, followed by an electronic transition to the CT state. As derived from the linearized semiclassical nonequilibrium Fermi's golden rule (LSC NE-FGR), the original IMT requires expensive all-atom nonequilibrium molecular dynamics (NEMD) simulations. In this work, we propose computationally efficient linear-response and nonlinear-response formulations for IMT rate calculations, which only require equilibrium molecular dynamics simulations. The linear- and nonlinear-response IMT methods were tested to predict the transient behavior in the photoinduced CT dynamics of the carotenoid-porphyrin-C₆₀ molecular triad solvated in explicit tetrahydrofuran. Our result demonstrated that the nonlinear-response IMT is in excellent agreement with the benchmark NEMD for all cases investigated here, whereas the linear-response IMT predicts the correct trend for all cases but overestimates the transient CT rate in one case involving a significant nonequilibrium relaxation. This mild breakdown of linear-response IMT is due to neglecting the higher-order terms in the exact nonlinear-response IMT. Taking advantage of time translational symmetry, the linear- and nonlinear-response approaches were demonstrated to be able to reduce the computational cost by 80% and 60% compared with NEMD simulations, respectively. Thus, we highly recommend the readily applicable and accurate nonlinear-response IMT approach for simulating nonequilibrium CT processes in complex molecular systems in the condensed phase.

Kinetic analysis of ASIC1a delineates conformational signaling from proton-sensing domains to the channel gate

Acid-sensing ion channels (ASICs) are neuronal Na⁺ channels that are activated by a drop in pH. Their established physiological and pathological roles, involving fear behaviors, learning, pain sensation, and neurodegeneration after stroke, make them promising targets for future drugs. Currently, the ASIC activation mechanism is not understood. Here, we used voltage-clamp fluorometry (VCF) combined with fluorophore-quencher pairing to determine the kinetics and direction of movements. We show that conformational changes with the speed of channel activation occur close to the gate and in more distant extracellular sites, where they may be driven by local protonation events. Further, we provide evidence for fast conformational changes in a pathway linking protonation sites to the channel pore, in which an extracellular interdomain loop interacts via aromatic residue interactions with the upper end of a transmembrane helix and would thereby open the gate.

Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes

The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.

Redesigning Solvatochromic Probe Laurdan for Imaging Lipid Order Selectively in Cell Plasma Membranes

Imaging of biological membranes by environmentally sensitive solvatochromic probes, such as Laurdan, provides information about the organization of lipids, their ordering, and their uneven distribution. To address a key drawback of Laurdan linked to its rapid internalization and subsequent labeling of internal membranes, we redesigned it by introducing a membrane anchor group based on negatively charged sulfonate and dodecyl chain. The obtained probe, Pro12A, stains exclusively the outer leaflet of lipid bilayers of liposomes, as evidenced by leaflet-specific fluorescence quenching with a viologen derivative, and shows higher fluorescence brightness than Laurdan. Pro12A also exhibits stronger spectral change between liquid-ordered and liquid-disordered phases in model membranes and distinguishes better lipid domains in giant plasma membrane vesicles (GPMVs) than Laurdan. In live cells, it stains exclusively the cell plasma membranes, in contrast to Laurdan and its carboxylate analogue C-Laurdan. Owing to its outer leaflet binding, Pro12A is much more sensitive to cholesterol extraction than Laurdan, which is redistributed within both plasma membrane leaflets and intracellular membranes. Finally, its operating range in the blue spectral region ensures the absence of crosstalk with a number of orange/red fluorescent proteins and dyes. Thus, Pro12A will enable accurate multicolor imaging of lipid organization of cell plasma membranes in the presence of fluorescently tagged proteins of interest, which will open new opportunities in biomembrane research.

Micellization-induced amplified fluorescence response for highly sensitive detection of heparin in serum

Fluorescence-based assays should be feasible in aqueous media for effectively detecting the biological factors. However, numerous sensors have limited signal transductions and low fluorescence quantum yields due to the ingerently reduced excited state energy of fluorophores in aqueous solution, which reduces their sensitivity. This necessitates a smart sensing approach with an amplified fluorescence response for analytes in aqueous solution. Herein, a new building block which self-assembles in aqueous media, giving a micellar sturcuture with the hydrophobic π-extended conjugated system at the core and hydrophilic groups at the periphery, was devised for the first time. We demonstrated that the aggregated fluorophores in a micelle induce amplified fluorescence quenching, in which the excited electron efficiently migrates through π-extended conjugated system in a micelle, as in a polymeric system. Such feature differentiates this sensing approach from the numerous fluorescence-based tools previously developed for sensitive detection. This new system exhibited highly sensitive signal transduction for specific analytes even under actual bioanalytical conditions.