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Spectroscopic single‐molecule localization microscopy (SMLM) has revolutionized the visualization and analysis of molecular structures and dynamics at the nanoscale level. The technique of combining high spatial resolution of SMLM with spectral information, enables multicolor super‐resolution imaging and provides insights into the local chemical environment of individual molecules. However, spectroscopic SMLM faces significant challenges, including limited spectral resolution and compromised localization precision because of signal splitting and the difficulties in analyzing complex, multidimensional datasets, that limit its application in studying intricate biological systems and materials. The recent integration of artificial intelligence (AI) with spectroscopic SMLM has emerged as a powerful approach for addressing these challenges. Here, it is reviewed how AI‐based methods applied to spectroscopic SMLM enhance and expand the capabilities of these applications. Recent advancements in AI‐driven data analysis for spectroscopic SMLM, including improved spectral classification, localization precision, and extraction of rich spectral information from unmodified point‐spread functions are discussed, further examining their applications in biological studies, materials science, and single‐molecule reaction analysis, which highlight how AI provides new insights into molecular behavior and interactions. The AI‐empowered approach adds new dimensions of information and provides new opportunities and insights into the nanoscale world of rapidly evolving field of spectroscopic SMLM. [ABSTRACT FROM AUTHOR]

Phycobilisomes (PBs) play an important role in cyanobacterial photosynthesis. They capture light and transfer excitation energy to the photosynthetic reaction centres. PBs are also central to some photoprotective and photoregulatory mechanisms that help sustain photosynthesis under non-optimal conditions. Amongst the mechanisms involved in excitation energy dissipation that are activated in response to excessive illumination is a recently discovered light-induced mechanism that is intrinsic to PBs and has been the least studied. Here, we used single-molecule spectroscopy and developed robust data analysis methods to explore the role of a terminal emitter subunit, ApcE, in this intrinsic, light-induced mechanism. We isolated the PBs from WT Synechocystis PCC 6803 as well as from the ApcE-C190S mutant of this strain and compared the dynamics of their fluorescence emission. PBs isolated from the mutant (i.e., ApcE-C190S-PBs), despite not binding some of the red-shifted pigments in the complex, showed similar global emission dynamics to WT-PBs. However, a detailed analysis of dynamics in the core revealed that the ApcE-C190S-PBs are less likely than WT-PBs to enter quenched states under illumination but still fully capable of doing so. This result points to an important but not exclusive role of the ApcE pigments in the light-induced intrinsic excitation energy dissipation mechanism in PBs. [ABSTRACT FROM AUTHOR]

By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information—such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond—for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit. [ABSTRACT FROM AUTHOR]

Highly disordered complexes between oppositely charged intrinsically disordered proteins present a new paradigm of biomolecular interactions. Here, we investigate the driving forces of such interactions for the example of the highly positively charged linker histone H1 and its highly negatively charged chaperone, prothymosin α (ProTα). Temperature-dependent single-molecule Förster resonance energy transfer (FRET) experiments and isothermal titration calorimetry reveal ProTα-H1 binding to be enthalpically unfavorable, and salt-dependent affinity measurements suggest counterion release entropy to be an important thermodynamic driving force. Using single-molecule FRET, we also identify ternary complexes between ProTα and H1 in addition to the heterodimer at equilibrium and show how they contribute to the thermodynamics observed in ensemble experiments. Finally, we explain the observed thermodynamics quantitatively with a mean-field polyelectrolyte theory that treats counterion release explicitly. ProTα-H1 complex formation resembles the interactions between synthetic polyelectrolytes, and the underlying principles are likely to be of broad relevance for interactions between charged biomolecules in general. [ABSTRACT FROM AUTHOR]

Free- living bacteria have regulatory systems that can quickly reprogram gene transcrip- tion in response to changes in the cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryotic Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so are unclear. We used multiwavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the Escherichia coli transcription cycle. In our experiments, RapA at <5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post termination complex (PTC)—consisting of core RNA polymerase (RNAP)- bound sequence nonspecifically to double-stranded DNA—and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis- dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription reinitiation in proteobacterial genomes. [ABSTRACT FROM AUTHOR]

Short-wave infrared (SWIR) emitters are at the center of ground-breaking applications in biomedical imaging, next-generation optoelectronic devices, and optical communications. Colloidal nanocrystals based on indium arsenide are some of the most promising SWIR emitters to date. However, the lack of single-particle spectroscopic methods accessible in the SWIR has prevented advances in both nanocrystal synthesis and fundamental characterization of emitters. Here, we demonstrate an implementation of a solution photon correlation Fourier spectroscopy (s-PCFS) experiment utilizing the SWIR sensitivity and time resolution of superconducting nanowire single-photon detectors to extract single-particle emission linewidths from colloidal indium arsenide/cadmium selenide (InAs/CdSe) core/shell nanocrystals emissive from 1.2 to 1.6 μm. We show that the average single InAs/CdSe nanocrystal fluorescence linewidth is, remarkably, as narrow as 52 meV, similar to what has been observed in some of the most narrowband nanostructured emitters in the visible region. Additionally, the single nanocrystal fluorescence linewidth increases with increasing shell thickness, suggesting exciton-phonon coupling as the dominant emission line-broadening mechanism in this system. The development of the SWIR s-PCFS technique has enabled measurements of spectral linewidths of colloidal SWIR-emissive NCs in solution and provides a platform to study the single NC spectral characteristics of SWIR emitters.

Abstract An azo-clamped nanoscale bichromophoric cyclophane is synthesized by the intramolecular Pd(II)-catalyzed coupling of the corresponding bisacetylenic precursor. The two azo moieties in the latter can adopt cis and trans configurations. Thin-layer chromatography shows only two spots, and by scanning tunneling microscopy the trans/trans and cis/cis isomers are found. The final cyclophane does not show any switching behavior at all, but dense and wide structures are visualized after adsorption to highly oriented pyrolytic graphite. Photophysical investigations of the cyclophane show that most of the fluorescence is quenched, most likely due to the azo clamp. However, bright molecules show nearly perfect single-photon emission, meaning that efficient energy transfer between the two chromophores takes place within the molecule.

Sample preparation is a crucial step in single-molecule experiments and involves passivating the microfluidic sample chamber, immobilizing the molecules, and setting experimental buffer conditions. The efficiency of the experiment depends on the quality and speed of sample preparation, which is often performed manually and relies on the experience of the experimenter. This can result in inefficient use of single-molecule samples and time, especially for high-throughput applications. To address this, a pressure-controlled microfluidic system is proposed to automate single-molecule sample preparation. The hardware is based on microfluidic components from ElveFlow and is designed to be cost-effective and adaptable to various microscopy applications. The system includes a reservoir pressure adapter and a reservoir holder designed for additive manufacturing. Two flow chamber designs Ibidi µ-slide and Grace Bio-Labs HybriWell chamber are characterized, and the flow characteristics of the liquid at different volume flow rates V̇ are simulated using CFD-simulations and compared to experimental and theoretical values. The goal of this work is to establish a straightforward and robust system for single-molecule sample preparation that can increase the efficiency of experiments and reduce the bottleneck of manual sample preparation, particularly for high-throughput applications.

Signal recognition particle (SRP) is a universally conserved targeting machine that mediates the targeted delivery of ∼30% of the proteome. The molecular mechanism by which eukaryotic SRP achieves efficient and selective protein targeting remains elusive. Here, we describe quantitative analyses of completely reconstituted human SRP (hSRP) and SRP receptor (SR). Enzymatic and fluorescence analyses showed that the ribosome, together with a functional signal sequence on the nascent polypeptide, are required to activate SRP for rapid recruitment of the SR, thereby delivering translating ribosomes to the endoplasmic reticulum. Single-molecule fluorescence spectroscopy combined with cross-complementation analyses reveal a sequential mechanism of activation whereby the ribosome unlocks the hSRP from an autoinhibited state and primes SRP to sample a variety of conformations. The signal sequence further preorganizes the mammalian SRP into the optimal conformation for efficient recruitment of the SR. Finally, the use of a signal sequence to activate SRP for receptor recruitment is a universally conserved feature to enable efficient and selective protein targeting, and the eukaryote-specific components confer upon the mammalian SRP the ability to sense and respond to ribosomes.

Proper localization of proteins to target membranes is a fundamental cellular process. How the nature and dynamics of the targeting complex help guide substrate proteins to the target membrane is not understood for most pathways. Here, we address this question for the conserved ATPase guided entry of tail-anchored protein 3 (Get3), which targets the essential class of tail-anchored proteins (TAs) to the endoplasmic reticulum (ER). Single-molecule fluorescence spectroscopy showed that, contrary to previous models of a static closed Get3•TA complex, Get3 samples open conformations on the submillisecond timescale upon TA binding, generating a fluctuating "protean clamp" that stably traps the substrate. Point mutations at the ATPase site bias Get3 toward closed conformations, uncouple TA binding from induced Get3•Get4/5 disassembly, and inhibit the ER targeting of the Get3•TA complex. These results demonstrate an essential role of substrate-induced Get3 dynamics in driving TA targeting to the membrane, and reveal a tightly coupled channel of communication between the TA-binding site, ATPase site, and effector interaction surfaces of Get3. Our results provide a precedent for large-scale dynamics in a substrate-bound chaperone, which provides an effective mechanism to retain substrate proteins with high affinity while also generating functional switches to drive vectorial cellular processes.

Detection of single molecules or particles avoids ensemble averaging and thus is able to provide a very local heterogeneous information which is not available from an ensemble measurement. Single molecules or particles can be detected based on their three characteristic optical properties, absorption, scattering and fluorescence/photoluminescence, in addition to their label-free detection. This short review focuses on our group’s research towards understanding and imaging the above three kinds of optical signals from single molecules and particles. [ABSTRACT FROM AUTHOR]

Polymorphism in the structure of amyloid fibrils suggests the existence of many different assembly pathways. Characterization of this heterogeneity is the key to understanding the aggregation mechanism and toxicity, but in practice it is extremely difficult to probe individual aggregation pathways in a mixture. Here, we present development of a method combining single-molecule fluorescence lifetime imaging and deep learning for monitoring individual fibril formation in real time and their high-throughput analysis. A deep neural network (FNet) separates an image of highly overlapping fibrils into single fibril images, which allows for tracking the growth and changes in characteristics of individual fibrils. Using this method, we investigated aggregation of the 42-residue amyloid-β peptide (Aβ42). We demonstrate that highly heterogeneous fibril formation can be quantitatively characterized in terms of the number of cross-β subunits, elongation speed, growth polarity, and conformation of fibrils. Tracking individual fibril formation and growth also leads to the discovery of a general nucleation mechanism (termed heterogeneous secondary nucleation), where a fibril is formed on the surface of an oligomer with a different structure. Our development will be broadly applicable to characterization of heterogeneous aggregation processes of other proteins. [ABSTRACT FROM AUTHOR]

The rise of super‐resolution fluorescence microscopy (SRM) has revolutionized our understanding of the nanoscale world. SRM has recently been correlated with spectroscopy techniques to obtain rich spectral information of individual molecules in addition to localization information. This technique ultimately provides multidimensional and functional information of single molecules, which is generally masked in the ensemble averages of previous bulk measurements and creates exciting new opportunities and challenges for single‐molecule spectroscopic imaging. We review the recent developments in single‐molecule spectroscopic imaging technique and how the challenges are addressed to effectively obtain single‐molecule spectroscopic information. Particular attention has been devoted to the applications of this method, including single‐molecule chemical kinetic studies and single‐molecule polarity sensing. Finally, we address the possible future enhancements and applications. Thus, we demonstrate how a single‐molecule spectroscopic imaging technique adds new dimensions of information to the SRM, providing new opportunities in a wide range of research fields. [ABSTRACT FROM AUTHOR]

Plasmonic nanostructures have immense potentials for extreme concentration of light into deep‐subwavelength spaces with giant local field intensity, which can be exploited for novel applications including nanoscale optical trapping, biosensing, and enhanced spectroscopy. Herein, a succinct overview of the potentials of engineered plasmonic nanoarchitectures of various geometries including nanoparticles, nanodimers, nanoapertures, nanoporous surfaces, and picometer‐scale gap systems for single‐molecule analysis is provided. In particular, the potentials of single plasmonic nanoparticles for single‐molecule sensing, coupled plasmonic nanodimers for few‐molecule strong coupling, metallic nanocavities for optical manipulation of single molecules, nanoporous metasurfaces for enhanced single‐molecule spectroscopy, and plasmonic picocavities for single‐molecule optomechanics are extensively discussed. Finally, as an outlook, exploiting such novel nanoarchitectures for developing innovative biosensing platforms that will be able to trap and detect objects at the single‐molecule level is forwarded.

Multicolor fluorescence microscopy is an essential tool to visualize structures and dynamics in the life and materials sciences. However, the near-simultaneous acquisition of labels differing in excitation spectrum is difficult and renders such measurements prone to artifacts. We present a simple strategy to provide quasi-simultaneous fluorescence imaging with multiple excitation wavelengths by using an optical element to displace the sample image on the sensor at a rate that is much faster than the image acquisition rate and synchronizing this with the illumination. The emission elicited by the different wavelengths can then be encoded into the point-spread function of the imaging or visualized as multiple distinct images. In doing so, our approach can eliminate or mitigate artifacts caused by temporal aliasing in conventional sequential imaging. We demonstrate the use of our system to uncover hidden emissive states in single quantum dots and for the imaging of Ca 2+ signaling in neurons.

• Single-molecule fluoresence spectroscopy is a key approach for the study of IDRs. • Molecular simulations provide atomistic insight into IDR conformation and dynamics. • Despite their importance, both sets of techniques have a number of limitations. • When combined they offer complimentary insight with largely orthogonal weaknesses. Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms. [ABSTRACT FROM AUTHOR]

Acquiring events massively from single-molecule force spectroscopy (SMFS) experiments, which is crucial for revealing important biophysical information, is usually not straightforward. A significant amount of human labor is usually required to identify events in the measured force spectrum during measuring or before performing further data analysis. This prevents the experiment from being done in a fully-automated manner or scaling with the throughput of the measuring setup. In this work, we attempt to tackle this problem with a deep learning approach. A deep neural network model is developed to infer the occurrence of the events using the data stream from the measuring setup. We demonstrated that the proposed method could achieve high accuracy with force spectrums of a variety of samples from both optical tweezers and AFMs by learning from user-given samples instead of complicated manual algorithm designing or parameter tuning. Furthermore, we found that the trained model can be used to perform event detection on datasets measured from a different optical tweezer setup, showing the potential of being leveraged in more complex deep learning schemes. • This work proposed a user-friendly approach to massively locate the events of interest from experimental SMFS data streams. • To our best knowledge, this work is the first attempt to adopt deep learning methods to locate events in SMFS experiments. • It is demonstrated that the proposed method could learn to locate events for a variety of samples from different instruments including optical tweezers and AFMs. • This method could help to achieve automated measuring on SMFS high-throughput platforms or other deep-learning based SMFS signal analysis. [ABSTRACT FROM AUTHOR]

The ATP-binding cassette transporter GlnPQ is an essential uptake system that transports glutamine, glutamic acid and asparagine in Gram-positive bacteria. It features two extra-cytoplasmic substrate-binding domains (SBDs) that are linked in tandem to the transmembrane domain of the transporter. The two SBDs differ in their ligand specificities, binding affinities and their distance to the transmembrane domain. Here, we elucidate the effects of the tandem arrangement of the domains on the biochemical, biophysical and structural properties of the protein. For this, we determined the crystal structure of the ligand-free tandem SBD1-2 protein from Lactococcus lactis in the absence of the transporter and compared the tandem to the isolated SBDs. We also used isothermal titration calorimetry to determine the ligand-binding affinity of the SBDs and single-molecule Förster resonance energy transfer (smFRET) to relate ligand binding to conformational changes in each of the domains of the tandem. We show that substrate binding and conformational changes are not notably affected by the presence of the adjoining domain in the wild-type protein, and changes only occur when the linker between the domains is shortened. In a proof-of-concept experiment, we combine smFRET with protein-induced fluorescence enhancement (PIFE–FRET) and show that a decrease in SBD linker length is observed as a linear increase in donor-brightness for SBD2 while we can still monitor the conformational states (open/closed) of SBD1. These results demonstrate the feasibility of PIFE–FRET to monitor protein–protein interactions and conformational states simultaneously.

Recent advances in single‐molecule spectroscopic imaging techniques, such as spectrally resolved stochastic optical reconstruction microscopy (SR‐STORM), have been effective for obtaining detailed spectral information at the molecular level. However, its application for single‐molecule sensing is highly challenging owing to its complicated configuration and limited spectral information. In this study, we demonstrated single‐molecule polarity sensing by combining grating‐based SR‐STORM with the solvatochromic dye, Nile red. The spatial and spectral resolutions of the custom‐built grating‐based SR‐STORM were examined for various color ranges of fluorescent dyes, and this approach was successfully applied for sensing nanoscale local polarity of various organic solvent molecules and surfactant molecules. Furthermore, we demonstrated that the proposed method effectively distinguished the different polarities of functional groups within surfactant molecules at the single‐molecule level. We anticipate that the proposed approach can be combined with other chromic molecules for application to many other chemical systems. [ABSTRACT FROM AUTHOR]

Conjugated donor-acceptor copolymers hold great potential as materials for high-performance organic photovoltaics, organic transistors and organic thermoelectric devices. Their low optical bandgap is achieved by alternation of donor and acceptor moieties along the polymer chain, leading to a pronounced charge-transfer character of electronic excitations. However, the influence of appended side chains and of chemical defects of the backbone on their photophysical and conformational properties remains largely unexplored on the level of individual chains. Here, we employ room temperature single-molecule photoluminescence spectroscopy on four compounds based on the prototypical copolymer PCDTBT with systematically changed chemical structure. Our results show that an increasing density of statistically added hexyl chains to the TBT comonomer distorts the molecular conformation, likely through the increase of average dihedral angles along the backbone. We find that, although the conformation becomes more twisted with high hexyl density, the side chains appear to stabilize the backbone in this twisted conformation. In addition, we demonstrate that homocoupling defects along the backbone barely influence the PL spectra of single chains, and thus intra-chain electronic properties., (© 2024 The Authors. ChemPhysChem published by Wiley-VCH GmbH.)

Deinococcus radiodurans (DR) survives in the presence of hundreds of double-stranded DNA (dsDNA) breaks by efficiently repairing such breaks. RecO, a protein that is essential for the extreme radioresistance of DR, is one of the major recombination mediator proteins in the RecA-loading process in the RecFOR pathway. However, how RecO participates in the RecA-loading process is still unclear. In this work, we investigated the function of drRecO using single-molecule techniques. We found that drRecO competes with the ssDNA-binding protein (drSSB) for binding to the freely exposed ssDNA, and efficiently displaces drSSB from ssDNA without consuming ATP. drRecO replaces drSSB and dissociates it completely from ssDNA even though drSSB binds to ssDNA approximately 300 times more strongly than drRecO does. We suggest that drRecO facilitates the loading of RecA onto drSSB-coated ssDNA by utilizing a small drSSB-free space on ssDNA that is generated by the fast diffusion of drSSB on ssDNA.

We have measured the polarizabilities of four families of molecules adsorbed to Au{111} surfaces, with structures ranging from fully saturated to fully conjugated, including single-molecule switches. Measured polarizabilities increase with increasing length and conjugation in the adsorbed molecules and are consistent with theoretical calculations. For single-molecule switches, the polarizability reflects the difference in substrate-molecule electronic coupling in the ON and OFF conductance states. Calculations suggest that the switch between the two conductance states is correlated with an oxidation state change in a nitro functional group in the switch molecules.

Fundamental understanding of chemistry and physical properties at the nanoscale enables the rational design of interface-based systems. Surface interactions underlie numerous technologies ranging from catalysis to organic thin films to biological systems. Since surface environments are especially prone to heterogeneity, it becomes crucial to characterize these systems with spatial resolution sufficient to localize individual active sites or defects. Spectroscopy presents as a powerful means to understand these interactions, but typical light-based techniques lack sufficient spatial resolution. This review describes the growing number of applications for the nanoscale spectroscopic technique, tip-enhanced Raman spectroscopy (TERS), with a focus on developments in areas that involve measurements in new environmental conditions, such as liquid, electrochemical, and ultrahigh vacuum. The expansion into unique environments enables the ability to spectroscopically define chemistry at the spatial limit. Through the confinement and enhancement of light at the apex of a plasmonic scanning probe microscopy tip, TERS is able to yield vibrational fingerprint information of molecules and materials with nanoscale resolution, providing insight into highly localized chemical effects. [ABSTRACT FROM AUTHOR]

Single-molecule fluorescence resonance energy transfer (smFRET) is used to investigate the movement of the γ-subunit within the H+-ATPsynthase from chloroplasts during proton transport-coupled ATP synthesis. The FRET donor fluorophore is attached to residue γC322 and the FRET acceptor is non-covalently bound to a non-catalytic nucleotide binding site. The labeled enzyme is integrated into liposomes and ATP synthesis is started by an acid-base transition. A custom-built confocal microscope with two spectral detection channels is used to measure smFRET with freely diffusing proteoliposomes. Analysis of the smFRET time traces reveals stepwise distance changes between the two fluorophores. During catalysis the γ-subunit interacts with equal probability with each αβ-pair. In ADP-inhibited enzymes, the γ-subunit interacts with only one specific αβ-pair. Comparison of the smFRET data with cryo-EM data (Hahn, Vonck, Mills, Meier, & Kühlbrandt, 2018, Science, 360, pp. 620-628) indicated that the transition from the ADP-inhibited state to the active state is accompanied by a large rotational movement of the γ-subunit. [ABSTRACT FROM AUTHOR]

Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of macromolecular crowding on the interactions of IDPs with their cellular targets. Here, we investigate the influence of crowding on the interaction between two IDPs that fold upon binding, with polyethylene glycol as a crowding agent. Single-molecule spectroscopy allows us to quantify the effects of crowding on a comprehensive set of observables simultaneously: the equilibrium stability of the complex, the association and dissociation kinetics, and the microviscosity, which governs translational diffusion. We show that a quantitative and coherent explanation of all observables is possible within the framework of depletion interactions if the polymeric nature of IDPs and crowders is incorporated based on recent theoretical developments. The resulting integrated framework can also rationalize important functional consequences, for example, that the interaction between the two IDPs is less enhanced by crowding than expected for folded proteins of the same size. [ABSTRACT FROM AUTHOR]

An often limiting factor for studying protein folding by single-molecule fluorescence resonance energy transfer (FRET) is the ability to site-specifically introduce a photostable organic FRET donor (D) and a complementary acceptor (A) into a polypeptide chain. Using alternating-laser excitation and chymotrypsin inhibitor 2 as a model, we show that chemical labeling of a unique cysteine, followed by enzymatic modification of a reactive glutamine in an N-terminally appended substrate sequence recognition tag for transglutaminase (TGase) affords stoichiometrically D-/A-labeled protein suitable for single-molecule FRET experiments. Thermodynamic data indicate that neither the presence of the TGase tag nor D/A labeling perturbs protein stability. As the N terminus in proteins is typically solvent accessible, a TGase tag can (in principle) be appended to any protein of interest by genetic engineering. Two-step chemical/enzymatic labeling may thus represent a simple, low-cost, and widely available strategy for DIA labeling of proteins for FRET-based single-molecule protein folding studies, even for non-protein-experts laboratories.

The conversion of solar radiation to chemical energy in plants and green algae takes place in the thylakoid membrane. This amphiphilic environment hosts a complex arrangement of light-harvesting pigment-protein complexes that absorb light and transfer the excitation energy to photochemically active reaction centers. This efficient light-harvesting capacity is moreover tightly regulated by a photoprotective mechanism called non-photochemical quenching to avoid the stress-induced destruction of the catalytic reaction center. In this review we provide an overview of single-molecule fluorescence measurements on plant light-harvesting complexes (LHCs) of varying sizes with the aim of bridging the gap between the smallest isolated complexes, which have been well-characterized, and the native photosystem. The smallest complexes contain only a small number (10–20) of interacting chlorophylls, while the native photosystem contains dozens of protein subunits and many hundreds of connected pigments. We discuss the functional significance of conformational dynamics, the lipid environment, and the structural arrangement of this fascinating nano-machinery. The described experimental results can be utilized to build mathematical-physical models in a bottom-up approach, which can then be tested on larger in vivo systems. The results also clearly showcase the general property of biological systems to utilize the same system properties for different purposes. In this case it is the regulated conformational flexibility that allows LHCs to switch between efficient light-harvesting and a photoprotective function.

Fluorescence resonance energy transfer in single enzyme molecules (smFRET, single-molecule measurement) allows the measurement of multicomponent distance distributions in complex biomolecules similar to pulsed electron–electron double resonance (PELDOR, ensemble measurement). Both methods use reporter groups: FRET exploits the distance dependence of the electric interaction between electronic transition dipole moments of the attached fluorophores, whereas PELDOR spectroscopy uses the distance dependence of the interaction between the magnetic dipole moments of attached spin labels. Such labels can be incorporated easily to cysteine residues in the protein. Comparison of distance distributions obtained with both methods was carried out with the H+-ATPase from Escherichia coli (EF0F1). The crystal structure of this enzyme is known. It contains endogenous cysteines, and as an internal reference two additional cysteines were introduced (EF0F1–γT106C–εH56C). These positions were chosen to allow application of both methods under optimal conditions. Both methods yield very similar multicomponent distance distributions. The dominating distance distribution (> 50%) is due to the two cysteines introduced by site-directed mutagenesis and the distance is in agreement with the crystal structure. Two additional distance distributions are detected with smFRET and with PELDOR. These can be assigned by comparison with the structure to labels at endogenous cysteines. One additional distribution is detected only with PELDOR. The comparison indicates that under optimal conditions smFRET and PELDOR result in the same distance distributions. PELDOR has the advantage that different distributions can be obtained with ensemble measurements, whereas FRET requires single-molecule techniques. [ABSTRACT FROM AUTHOR]

Strong dipole–dipole coupling within and between π‐conjugated segments shifts electronic transitions, and modifies vibronic coupling and excited‐state lifetimes. Since J‐type coupling between monomers along the conjugated‐polymer (CP) chain and H‐type coupling of chromophores between chains of a CP compete, a superposition of the spectral modifications arising from each type of coupling emerges, making the two couplings hard to discern in the ensemble. We introduce a single‐molecule H‐type aggregate of fixed spacing and variable length of up to 10 nm. HJ‐type aggregate formation is visualized intuitively in the scatter of single‐molecule spectra. [ABSTRACT FROM AUTHOR]

The photophysical properties of chromophores react very sensitively upon changes of their electrostatic environment. This allows conformational fluctuations of a protein to be monitored by optical spectroscopy via the fluctuations of the spectral signatures of chromophores that are embedded in the protein's matrix. However, to be successful as an approach this requires that the structural fluctuations within the proteins would occur synchronously. This restriction can be overcome by studying the proteins on an individual basis. In this contribution, we illustrate this approach on the example of the peripheral light-harvesting complexes from photosynthetic purple bacteria that contain bacteriochlorophyll a as natural cofactors. [ABSTRACT FROM AUTHOR]

Experiments carried out in recent years using single-molecule spectroscopy to study the low-temperature dynamics of some molecular solid-state media with a disordered internal structure made it possible to obtain new information on the dynamics of such media at the local level. In some substances, the time-dependent behavior of the majority of individual spectra of single fluorescent molecules introduced into the studied medium as a local spectral probe corresponded to the predictions of the standard model of tunneling two-level systems. In others, the behavior of most of the spectra of single molecules was more complicated, which it is difficult to describe in the framework of the standard model. This paper is devoted to the analysis of the results of studies of low-temperature spectral dynamics of single fluorescent molecules in a number of disordered molecular systems (amorphous polyisobutylene, toluene, cumene, propylene carbonate). The observed deviations from the predictions of the theory are associated with the microstructure of the systems under study and the sample shape. Possible reasons for the deviations of the observed local spectral dynamics from the predictions of the standard model of tunneling two-level systems are discussed. Inadequately. [ABSTRACT FROM AUTHOR]

The fluorescence of photosystem I (PSI) trimers in proximity to bimetallic plasmonic nanostructures have been explored by single-molecule spectroscopy (SMS) at cryogenic temperature (1.6 K). PSI serves as a model for biological multichromophore-coupled systems with high potential for biotechnological applications. Plasmonic nanostructures are fabricated by thermal annealing of thin metallic films. The fluorescence of PSI has been intensified due to the coupling with plasmonic nanostructures. Enhancement factors up to 22.9 and 5.1 are observed for individual PSI complexes coupled to Au/Au and Ag/Au samples, respectively. Additionally, a wavelength dependence of fluorescence enhancement is observed, which can be explained by the multichromophoric composition of PSI.

Abstract Efficient light harvesting in a photosynthetic antenna system is disturbed by a ragged and fluctuating energy landscape of the antenna pigments in response to the conformation dynamics of the protein. This situation is especially pronounced in Photosystem I (PSI) containing red shifted chlorophylls (red Chls) with the excitation energy much lower than the primary donor. The present study was conducted to clarify light-harvesting dynamics of PSI isolated from Synechocystis sp. PCC6803 by using single-molecule spectroscopy at liquid‑nitrogen temperatures. Fluorescence emission at around 720 nm from the red Chls in single PSI trimers was monitored at 80–100 K. Intermittent variations in the emission intensities, so-called blinking, were frequently observed. Its time scale lay in several tens of seconds. The blinking amplitude depended on the redox state of the phylloquinone (A 1). Electrochromic shifts of Chls induced by the negative charge on A 1 were calculated based on the X-ray crystallographic structure. A Chl molecule, Chl-A839 (numbering according to PDB 5OY0), bound near A 1 was found to have a large electrochromic shift. This Chl has strong exciton coupling with neighboring Chl (A838) whose site energy was predicted to be determined by interaction with an arginine residue (ArgF84) [Adolphs et al., 2010]. A possible scenario of the blinking was proposed. Conformational fluctuations of ArgF84 seesaw the excitation-energy of Chl-A838, which perturbs the branching ratio of excitation-energy between the red Chl and the cationic form of P700 as a quencher. The electrochromic shift of Chl-A839 enhances the effect of the conformation dynamics of ArgF84. Highlights • Single PSI trimers show fluorescence blinking but rarely shows spectral diffusion at 80 K • Blinking is enhanced upon pre-oxidation of P700 containing neutral phylloquinone • Excitation energy of Chl-A839 is blue shifted upon photo-reduction of phylloquinone • Chl-A838 near Chl-A839 is proposed to be the key pigment for the blinking [ABSTRACT FROM AUTHOR]

The existence of fluorescent impurities has been a long-standing obstacle in single-molecule imaging, which results in sample misidentification and higher localization uncertainty. Spectroscopic single-molecule localization microscopy can record the full fluorescent spectrum of every stochastic single-molecule emission event. This capability allows us to quantify the spatial and spectral characteristics of fluorescent impurities introduced by sample preparation steps, based on which we developed a method to effectively separate fluorescent impurities from target molecules. [ABSTRACT FROM AUTHOR]

The recent surge in spectroscopic Single-Molecule Localization Microscopy (sSMLM) offers exciting new capabilities for combining single molecule imaging and spectroscopic analysis. Through the synergistic integration of super-resolution optical microscopy and single-molecule spectroscopy, sSMLM offers combined strengths from both fields. By capturing the full spectra of single molecule fluorescent emissions, sSMLM can distinguish minute spectroscopic variations from individual fluorescent molecules while preserving nanoscopic spatial localization precision. It can significantly extend the coding space for multi-molecule super-resolution imaging. Furthermore, it has the potential to detect spectroscopic variations in fluorescence emission associated with molecular interactions, which further enables probing local chemical and biochemical inhomogeneities of the nano-environments. In this review, we seek to explain the working principle of sSMLM technologies and the status of sSMLM techniques towards new super-resolution imaging applications. [ABSTRACT FROM AUTHOR]