Conformational Dynamics of a Single Protein Monitored for 24 h at Video Rate

In Situ Photoreversible Tuning of Chemical Interface Damping in Single Gold Nanorods Through Cucurbit[8]uril-Based Host-Guest Interactions

Chemical interface damping (CID) is a recently proposed plasmon-damping pathway based on the interfacial hot-electron transfer from metal to adsorbate molecules. However, the in situ reversible tuning of CID in single gold nanorods (AuNRs) has remained a considerable challenge. In this study, we used total internal reflection scattering microscopy and spectroscopy to investigate the CID induced by p-aminoazobenzene (p-AAB), which has fast photoisomerization characteristics, attached to single AuNRs. We demonstrated the in situ reversible tuning of CID in single AuNRs by switching between ultraviolet (UV, 365 nm) and visible (vis, 465 nm) irradiation to induce photoresponsive structural conversions between the cis and trans forms of p-AAB in ethanol, leading to different lowest unoccupied molecular orbital (LUMO) energies for both forms. The localized surface plasmon resonance (LSPR) line width was wide under vis irradiation but narrow under UV irradiation, indicating that hot electrons are more efficiently transferred to trans-p-AAB with a low LUMO energy level. We further investigated the in situ photoreversible tuning of CID by manipulating supramolecular host-guest interactions between cucurbit[8]uril (CB[8]) and p-AAB in the single AuNRs. Additionally, real-time in situ reversible tuning of CID in single AuNRs was achieved through photonic switching of the cis-trans forms of p-AAB inside CB[8]. The LSPR line width was narrow under vis irradiation but gradually widened under UV irradiation before narrowing again upon returning to vis irradiation, unlike the case with p-AAB only. These results can be ascribed to the fact that cis-p-AAB completely encapsulated within CB[8] in water is thermodynamically more favorable than trans-p-AAB. Therefore, we have discovered a new strategy for tuning the CID by performing p-AAB photoisomerization and adjusting the wavelength of incident light in single AuNRs. In addition, this study demonstrates that CID can be effectively applied to the development of biosensors to detect guest molecules and their structural changes inside the cavity of CB[8] in single AuNRs.

Visualizing Single-Molecule Protein Conformational Transitions and Free Energy Landscape

Monitoring the conformational dynamics of individual proteins is essential to understand the relationship between structure and function in molecular regulatory mechanisms. However, the fast dynamics of single proteins remain poorly understood. Here, we construct a single-molecule sensing platform by introducing plasmonic imaging of single nanoparticles to sense and report the protein conformational changes at the single-molecule level. Tracking the fluctuations of individual nanoparticles with high resolution, we detect and characterize distinct conformational states of molecular chaperone heat shock protein 90 (Hsp90). We also explore the conformational changes of Hsp90 in situ under different nucleotide conditions. Analysis of the conformational fluctuations between the open and closed states of single Hsp90 provides important information on free energy profiles, effective spring constants, and multiphase behaviors. This method offers a strategy to visualize the conformational changes of single proteins in real-time and provides insights into the underlying molecular mechanisms.

Exploring Rotational Diffusion with Plasmonic Coupling

Measuring the orientation dynamics of nanoparticles and nonfluorescent molecules in real time with optical methods is still a challenge in nanoscience and biochemistry. Here, we examine optoplasmonic sensing taking the rotational diffusion of plasmonic nanorods as an experimental model. Our detection method is based on monitoring the dark-field scattering of a relatively large sensor gold nanorod (GNR) (40 nm in diameter and 112 nm in length) as smaller plasmonic nanorods cross its near field. We observe the rotational motion of single small gold nanorods (three samples with about 5 nm in diameter and 15.5, 19.1, and 24.6 nm in length) in real time with a time resolution around 50 ns. Plasmonic coupling enhances the signal of the diffusing gold nanorods, which are 1 order of magnitude smaller in volume (about 300 nm3) than those used in our previous rotational diffusion experiments. We find a better angular sensitivity with plasmonic coupling in comparison to the free diffusion in the confocal volume. Yet, the angle sensitivity we find with plasmonic coupling is reduced compared to the sensitivity expected from simulations at fixed positions due to the simultaneous translational and rotational diffusion of the small nanorods. To get a reliable plasmonic sensor with the full angular sensitivity, it will be necessary to construct a plasmonic assembly with positions and orientations nearly fixed around the optimum geometry.

The Onset of Molecule-Spanning Dynamics in Heat Shock Protein Hsp90

Protein dynamics have been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is largely unknown how fast (local) fluctuations can lead to slow global (allosteric) changes. Here, fast molecule-spanning dynamics on the 100 to 200 ns time scale in the heat shock protein 90 (Hsp90) are shown. Global real-space movements are assigned to dynamic modes on this time scale, which is possible by a combination of single-molecule fluorescence, quasi-elastic neutron scattering and all-atom molecular dynamics (MD) simulations. The time scale of these dynamic modes depends on the conformational state of the Hsp90 dimer. In addition, the dynamic modes are affected to various degrees by Sba1, a co-chaperone of Hsp90, depending on the location within Hsp90, which is in very good agreement with MD simulations. Altogether, this data is best described by fast molecule-spanning dynamics, which precede larger conformational changes in Hsp90 and might be the molecular basis for allostery. This integrative approach provides comprehensive insights into molecule-spanning dynamics on the nanosecond time scale for a multi-domain protein.

Single-Particle Plasmon Sensor to Monitor Proteolytic Activity in Real Time

We have established a label-free plasmonic platform that monitors proteolytic activity in real time. The sensor consists of a random array of gold nanorods that are functionalized with a design peptide that is specifically cleaved by thrombin, resulting in a blueshift of the longitudinal plasmon. By monitoring the plasmon of many individual nanorods, we determined thrombin's proteolytic activity in real time and inferred relevant kinetic parameters. Furthermore, a comparison to a kinetic model revealed that the plasmon shift is dictated by a competition between peptide cleavage and thrombin binding, which have opposing effects on the measured plasmon shift. The dynamic range of the sensor is greater than two orders of magnitude, and it is capable of detecting physiologically relevant levels of active thrombin down to 3 nM in buffered conditions. We expect these plasmon-mediated label-free sensors to open the window to a range of applications stretching from the diagnostic and characterization of bleeding disorders to fundamental proteolytic and pharmacological studies.

Plasmonic Nanostructure Biosensors: A Review

Plasmonic nanostructure biosensors based on metal are a powerful tool in the biosensing field. Surface plasmon resonance (SPR) can be classified into localized surface plasmon resonance (LSPR) and propagating surface plasmon polariton (PSPP), based on the transmission mode. Initially, the physical principles of LSPR and PSPP are elaborated. In what follows, the recent development of the biosensors related to SPR principle is summarized. For clarity, they are categorized into three groups according to the sensing principle: (i) inherent resonance-based biosensors, which are sensitive to the refractive index changes of the surroundings; (ii) plasmon nanoruler biosensors in which the distances of the nanostructure can be changed by biomolecules at the nanoscale; and (iii) surface-enhanced Raman scattering biosensors in which the nanostructure serves as an amplifier for Raman scattering signals. Moreover, the advanced application of single-molecule detection is discussed in terms of metal nanoparticle and nanopore structures. The review concludes by providing perspectives on the future development of plasmonic nanostructure biosensors.

Nonlocal Optical Response of Particle Plasmons in Single Gold Nanorods

The investigation of particle plasmons in metal nanoparticles has predominantly relied on local optical response approximations. However, as the nanoparticle size approaches the average distance of electrons to the metal surface, mesoscopic effects such as size-dependent plasmon line width broadening and resonance energy blue shifts are expected to become observable. In this work, we compared the experimental spectral characteristics with simulated values obtained by using a generalized nonlocal optical response theory-based local analogue model. Our results show that the nonlocal plasmon damping effects in single nanoparticles are less pronounced than those observed in plasmon-coupled systems. Furthermore, our research demonstrates that single-particle dark-field spectroscopy is an effective tool for investigating the nonlocal optical response of particle plasmons in single nanoparticles. These results have important implications for the rational design of novel nanophotonic devices.

Plasmonic Nanomaterials in Dark Field Sensing Systems

Plasma nanoparticles offer promise in data storage, biosensing, optical imaging, photoelectric integration, etc. This review highlights the local surface plasmon resonance (LSPR) excitation mechanism of plasmonic nanoprobes and its critical significance in the control of dark-field sensing, as well as three main sensing strategies based on plasmonic nanomaterial dielectric environment modification, electromagnetic coupling, and charge transfer. This review then describes the component materials of plasmonic nanoprobes based on gold, silver, and other noble metals, as well as their applications. According to this summary, researchers raised the LSPR performance of composite plasmonic nanomaterials by combining noble metals with other metals or oxides and using them in process analysis and quantitative detection.

Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics

Grp94, an ER-localized molecular chaperone, is required for the folding and activation of many membrane and secretory proteins. Client activation by Grp94 is mediated by nucleotide and conformational changes. In this work, we aim to understand how microscopic changes from nucleotide hydrolysis can potentiate large-scale conformational changes of Grp94. We performed all-atom molecular dynamics simulations on the ATP-hydrolysis competent state of the Grp94 dimer in four different nucleotide bound states. We found that Grp94 was the most rigid when ATP was bound. ATP hydrolysis or nucleotide removal enhanced mobility of the N-terminal domain and ATP lid, resulting in suppression of interdomain communication. In an asymmetric conformation with one hydrolyzed nucleotide, we identified a more compact state, similar to experimental observations. We also identified a potential regulatory role of the flexible linker, as it formed electrostatic interactions with the Grp94 M-domain helix near the region where BiP is known to bind. These studies were complemented with normal-mode analysis of an elastic network model to investigate Grp94's large-scale conformational changes. SPM analysis identified residues that are important in signaling conformational change, many of which have known functional relevance in ATP coordination and catalysis, client binding, and BiP binding. Our findings suggest that ATP hydrolysis in Grp94 alters allosteric wiring and facilitates conformational changes.

Multiple solution solving in plasmon sensing by deep learning: determination of layer refractive index and thickness in one experiment: comment

In a recent Letter [Opt. Lett.46, 5667 (2021)10.1364/OL.444442], Du et al. proposed a deep learning method for determining the refractive index (n) and thickness (d) of the surface layer on nanoparticles in a single-particle plasmon sensing experiment. This comment highlights the methodological issues arising in that Letter.

Dynamic Heterogeneity in the Optical Signals from Single Nano-Objects

In contrast to ensemble-averaged measurements, single-molecule experiments directly display the heterogeneity of molecular properties in space and time. In many complex systems, spatial heterogeneity is regularly accompanied by temporal or dynamic heterogeneity; if a property differs from molecule to molecule, it will often vary in time for one and the same molecule. In this short paper, we discuss a few examples of complex systems where dynamical heterogeneity was observed in single-molecule or single-particle optical signals. For single biomolecules, the first demonstration of dynamic heterogeneity in a single enzyme was provided by Xie and colleagues. Other examples are found in glassy systems, and very recently in the magnetic relaxation of single superparamagnetic nanoparticles. The ubiquity of this phenomenon suggests that, rather than an exception, dynamic heterogeneity is the rule in complex systems with multiple degrees of freedom.

Conformational Dynamics and Mechanisms of Client Protein Integration into the Hsp90 Chaperone Controlled by Allosteric Interactions of Regulatory Switches: Perturbation-Based Network Approach for Mutational Profiling of the Hsp90 Binding and Allostery

Understanding the allosteric mechanisms of the Hsp90 chaperone interactions with cochaperones and client protein clientele is fundamental to dissect activation and regulation of many proteins. In this work, atomistic simulations are combined with perturbation-based approaches and dynamic network modeling for a comparative mutational profiling of the Hsp90 binding and allosteric interaction networks in the three Hsp90 maturation complexes with FKBP51 and P23 cochaperones and the glucocorticoid receptor (GR) client. The conformational dynamics signatures of the Hsp90 complexes and dynamics fluctuation analysis revealed how the intrinsic plasticity of the Hsp90 dimer can be modulated by cochaperones and client proteins to stabilize the closed dimer state required at the maturation stage of the ATPase cycle. In silico deep mutational scanning of the protein residues characterized the hot spots of protein stability and binding affinity in the Hsp90 complexes, showing that binding hot spots may often coincide with the regulatory centers that modulate dynamic allostery in the Hsp90 dimer. We introduce a perturbation-based network approach for mutational scanning of allosteric residue potentials and characterize allosteric switch clusters that control mechanism of cochaperone-dependent client recognition and remodeling by the Hsp90 chaperone. The results revealed a conserved network of allosteric switches in the Hsp90 complexes that allow cochaperones and GR protein to become integrated into the Hsp90 system by anchoring to the conformational switch points in the functional Hsp90 regions. This study suggests that the Hsp90 binding and allostery may operate under a regulatory mechanism in which activation or repression of the Hsp90 activity can be pre-encoded in the allosterically regulated Hsp90 dimer motions. By binding directly to the conformational switch centers on the Hsp90, cochaperones and interacting proteins can efficiently modulate the allosteric interactions and long-range communications required for client remodeling and activation.

Molecular homogeneity of GB1 revealed by single molecule force spectroscopy

In single molecule studies, the ergodic hypothesis is inherently assumed, which states that the time average of a physical quantity of a single member of an ensemble is the same as the average of the same quantity on the whole ensemble at a given time. This hypothesis implies the homogeneity of a molecular ensemble of a system of interest. However, it is difficult to test the validity of the ergodic hypothesis experimentally. Recent theoretical work suggested that heterogeneity may be widely present in single molecule force spectroscopy studies. Here we used atomic force microscope based single molecule force spectroscopy to examine the molecular homogeneity/heterogeneity of a small globular protein GB1 in its mechanical unfolding reaction. Using a polyprotein (GB1)₄, we directly measured the ensemble average and time average for a single molecule of the mechanical unfolding force and kinetic parameters that characterize the mechanical unfolding free energy profile of GB1. Our results showed that the ensemble averages of these physical quantities are indeed the same as the time averages for single molecules, and individual molecules did not show any differences amongst them in these physical quantities. These results are consistent with the expectation of the ergodic hypothesis and indicate that GB1 is a homogeneous molecular ensemble in its mechanical unfolding reaction on the time scale of our force spectroscopy experiments.

Light Extinction by Agglomerates of Gold Nanoparticles: A Plasmon Ruler for Sub-10 nm Interparticle Distances

Plasmon rulers relate the shift of resonance wavelength, λ_l, of gold agglomerates to the average distance, s, between their constituent nanoparticles. These rulers are essential for monitoring the dynamics of biomolecules (e.g., proteins and DNA) by determining their small (<10 nm) coating thickness. However, existing rulers for dimers and chains estimate coating thicknesses smaller than 10 nm with rather large errors (more than 200%). Here, the light extinction of dimers, 7- and 15-mers of gold nanoparticles with diameter d_p = 20-80 nm and s = 1-50 nm is simulated. Such agglomerates shift λ_l up to 680 nm due to plasmonic coupling, in excellent agreement with experimental data by microscopy, dynamic light scattering, analytical centrifugation, and UV-visible spectroscopy. Subsequently, a new plasmon ruler is derived for gold nanoagglomerates that enables the accurate determination of sub-10 nm coating thicknesses, in excellent agreement also with tedious microscopy measurements.

Non-ergodicity of a globular protein extending beyond its functional timescale

Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble. Here, by performing single-molecule fluorescence resonance energy transfer (smFRET) experiments and molecular dynamics (MD) simulations of a multi-domain globular protein, cytoplasmic protein-tyrosine phosphatase (SHP2), we demonstrate that the functional inter-domain motion is observationally non-ergodic over the time spans 10⁻¹² to 10⁻⁷ s and 10⁻¹ to 10² s. The difference between observational non-ergodicity and simple non-convergence is discussed. In comparison, a single-strand DNA of similar size behaves ergodically with an energy landscape resembling a one-dimensional linear chain. The observed non-ergodicity results from the hierarchical connectivity of the high-dimensional energy landscape of the protein molecule. As the characteristic time for the protein to conduct its dephosphorylation function is ∼10 s, our findings suggest that, due to the non-ergodicity, individual, seemingly identical protein molecules can be dynamically and functionally different.

Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble.

Two-colour single-molecule photoinduced electron transfer fluorescence imaging microscopy of chaperone dynamics

Many proteins are molecular machines, whose function is dependent on multiple conformational changes that are initiated and tightly controlled through biochemical stimuli. Their mechanistic understanding calls for spectroscopy that can probe simultaneously such structural coordinates. Here we present two-colour fluorescence microscopy in combination with photoinduced electron transfer (PET) probes as a method that simultaneously detects two structural coordinates in single protein molecules, one colour per coordinate. This contrasts with the commonly applied resonance energy transfer (FRET) technique that requires two colours per coordinate. We demonstrate the technique by directly and simultaneously observing three critical structural changes within the Hsp90 molecular chaperone machinery. Our results reveal synchronicity of conformational motions at remote sites during ATPase-driven closure of the Hsp90 molecular clamp, providing evidence for a cooperativity mechanism in the chaperone’s catalytic cycle. Single-molecule PET fluorescence microscopy opens up avenues in the multi-dimensional exploration of protein dynamics and allosteric mechanisms.

Revealing mechanisms of complex protein machines requires simultaneous exploration of multiple structural coordinates. Here the authors report two-colour fluorescence microscopy combined with photoinduced electron transfer probes to simultaneously detect two structural coordinates in single protein molecules.

Multiple solution solving in plasmon sensing by deep learning: determination of a layer refractive index and thickness in one experiment

Plasmons have received intensive attention owing to their significant spectrum shift in environmental sensing. Experimentally, the same spectral shifts may be caused by different combinations of structural parameters of a plasmonic nanoparticle. This multi-parameter problem cannot be solved by just a single feature analysis, but requires using the full scattering spectrum containing all features of the parameters. In this Letter, a deep learning method for solving multi-parameter problems is proposed based on the layer refractive index (n) and layer thickness (d) sensing of different nanorods and nanospheres. The full scattering spectrum can be theoretically simulated, precisely predicted using a well-trained deep learning method, and experimentally obtained using a homemade dark-field microscope. An error analysis of the simulation and experimental results indicates that this method is a potential way to determine n and d and further solve multi-parameter in plasmon sensing.

4.9% Au stabilizes Ag in an atomically homogenous bimetallic alloy for anisotropic nanocrystals with enhanced stability under light irradiation

Instability problems encountered by Ag nanocrystals largely limit their use in practical applications. In AuAg bimetallic alloys, the stability of Ag can be greatly enhanced, whereas doping a high fraction of Au to the alloy usually leads to the loss of the superior properties of Ag and undesirable degradation of the quality factor of the plasmonic resonance. Herein, we provide experimental evidence that the atomically homogenous AuAg alloy nanocrystals with Au fraction as low as 4.9% (at%) possess comparable stability to pure Au, while the superior plasmonic properties of Ag are largely reserved. The study is based on the synthetic strategy developed for the overgrowth on the Au nanorods of atomically homogenous AuAg alloy shells with a tunable Au/Ag ratio but constant size and anisotropic shape. The stability of over 800 individual alloy nanocrystals in the absence of surfactants is simultaneously characterized at the single-particle level for over 10 h under light irradiation. The stability transition is explained in correlation with the charge redistribution of Ag occurring at the same critical Au fraction. We note that such bimetallic alloy nanocrystals with a low Au fraction possessing both high stability and high quality of resonance are preferred in fundamental researches and practical applications.

Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces

The individual and collective structure and properties of biomolecules can change dramatically when they are localized at an interface. However, the small spatial extent of interfacial regions poses challenges to the detailed characterization of multiscale processes that dictate the structure and function of large biological units such as peptides, proteins, or nucleic acids. This Perspective surveys a broad set of tools that provide new opportunities to probe complex, dynamic interfaces across the vast range of temporal regimes that connect molecular-scale events to macroscopic observables. An emphasis is placed on the integration over multiple time scales, the use of complementary techniques, and the incorporation of external stimuli to control interfacial properties with spatial, temporal, and chemical specificity.

Plasmonic Assemblies for Real-Time Single-Molecule Biosensing

Their tunable optical properties and versatile surface functionalization have sparked applications of plasmonic assemblies in the fields of biosensing, nonlinear optics, and photonics. Particularly, in the field of biosensing, rapid advances have occurred in the use of plasmonic assemblies for real-time single-molecule sensing. Compared to individual particles, the use of assemblies as sensors provides stronger signals, more control over the optical properties, and access to a broader range of timescales. In the past years, they have been used to directly reveal single-molecule interactions, mechanical properties, and conformational dynamics. This review summarizes the development of real-time single-molecule sensors built around plasmonic assemblies. First, a brief overview of their optical properties is given, and then recent applications are described. The current challenges in the field and suggestions to overcome those challenges are discussed in detail. Their stability, specificity, and sensitivity as sensors provide a complementary approach to other single-molecule techniques like force spectroscopy and single-molecule fluorescence. In future applications, the impact in real-time sensing on ultralong timescales (hours) and ultrashort timescales (sub-millisecond), time windows that are difficult to access using other techniques, is particularly foreseen.

Visualizing the Dynamics of a Protein Folding Machinery: The Mechanism of Asymmetric ATP Processing in Hsp90 and its Implications for Client Remodelling

The Hsp90 chaperone system interacts with a wide spectrum of client proteins, forming variable and dynamic multiprotein complexes that involve the intervention of cochaperone partners. Recent results suggest that the role of Hsp90 complexes is to establish interactions that suppress unwanted client activities, allow clients to be protected from degradation and respond to biochemical signals. Cryo-electron microscopy (cryoEM) provided the first key molecular picture of Hsp90 in complex with a kinase, Cdk4, and a cochaperone, Cdc37. Here, we use a combination of molecular dynamics (MD) simulations and advanced comparative analysis methods to elucidate key aspects of the functional dynamics of the complex, with different nucleotides bound at the N-terminal Domain of Hsp90. The results reveal that nucleotide-dependent structural modulations reverberate in a striking asymmetry of the dynamics of Hsp90 and identify specific patterns of long-range coordination between the nucleotide binding site, the client binding pocket, the cochaperone and the client. Our model establishes a direct atomic-resolution cross-talk between the ATP-binding site, the client region that is to be remodeled and the surfaces of the Cdc37-cochaperone.

Label-Free Plasmonic Detection of Untethered Nanometer-Sized Brownian Particles

Optical detection of individual nanometer-sized analytes, virus particles, and protein molecules holds great promise for understanding and control of biological samples and healthcare applications. As fluorescent labels impose restrictions on detection bandwidth and require lengthy and invasive processes, label-free optical techniques are highly desirable. Here, we introduce an optical technique capable of transforming gold nanorods commonly used as photostable labels into highly localized high-speed probes. Our method detects single untethered 5 nm diameter gold particles as they traverse subattoliter volumes in Brownian motion with a time resolution below microseconds.

Critical Review: digital resolution biomolecular sensing for diagnostics and life science research

One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.

Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques

Enhanced sampling techniques are a promising approach to obtain reliable binding free-energy profiles for flexible protein-ligand complexes from molecular dynamics (MD) simulations. To put four popular enhanced sampling techniques to a biologically relevant and challenging test, we studied the partial dissociation of an antigenic peptide from the Major Histocompatibility Complex I (MHC I) HLA-B*35:01 to systematically investigate the performance of umbrella sampling (US), replica exchange with solute tempering 2 (REST2), bias exchange umbrella sampling (BEUS, or replica-exchange umbrella sampling), and well-tempered metadynamics (MTD). With regard to the speed of sampling and convergence, the peptide-MHC I complex (pMHC I) under study showcases intrinsic strengths and weaknesses of the four enhanced sampling techniques used. We found that BEUS can best handle the sampling challenges that arise from the coexistence of an enthalpically and an entropically stabilized free-energy minimum in the pMHC I under study. These findings might also be relevant for other flexible biomolecular systems with competing enthalpically and entropically stabilized minima.

Plasmonic Nanosensors for the Label-Free Imaging of Dynamic Protein Patterns

We introduce a new approach to monitor the dynamics and spatial patterns of biological molecular assemblies. Our molecular imaging method relies on plasmonic gold nanoparticles as point-like detectors and requires no labeling of the molecules. We show spatial resolution of up to 5 μm and 30 ms temporal resolution, which is comparable to wide-field fluorescence microscopy, while requiring only readily available gold nanoparticles and a dark-field optical microscope. We demonstrate the method on MinDE proteins attaching to and detaching from lipid membranes of different composition for 24 h. We foresee our new imaging method as an indispensable tool in advanced molecular biology and biophysics laboratories around the world.

Detailed balance for diffusion in a potential with trapping and forward-backward symmetry of trapping time distributions

For particles diffusing in a potential, detailed balance guarantees the absence of net fluxes at equilibrium. Here, we show that the conventional detailed balance condition is a special case of a more general relation that works when the diffusion occurs in the presence of a distributed sink that eventually traps the particle. We use this relation to study the lifetime distribution of particles that start and are trapped at specified initial and final points. It turns out that when the sink strength at the initial point is nonzero, the initial and final points are interchangeable, i.e., the distribution is independent of which of the two points is initial and which is final. In other words, this conditional trapping time distribution possesses forward–backward symmetry.

Top-down machine learning approach for high-throughput single-molecule analysis

Single-molecule approaches provide enormous insight into the dynamics of biomolecules, but adequately sampling distributions of states and events often requires extensive sampling. Although emerging experimental techniques can generate such large datasets, existing analysis tools are not suitable to process the large volume of data obtained in high-throughput paradigms. Here, we present a new analysis platform (DISC) that accelerates unsupervised analysis of single-molecule trajectories. By merging model-free statistical learning with the Viterbi algorithm, DISC idealizes single-molecule trajectories up to three orders of magnitude faster with improved accuracy compared to other commonly used algorithms. Further, we demonstrate the utility of DISC algorithm to probe cooperativity between multiple binding events in the cyclic nucleotide binding domains of HCN pacemaker channel. Given the flexible and efficient nature of DISC, we anticipate it will be a powerful tool for unsupervised processing of high-throughput data across a range of single-molecule experiments.

Plasmonic thermochromism based on a reversible redox reaction of Ag+/Ag on Au nanorods

Reversible redox reaction-based thermochromism using plasmonic nanocrystals is challenging due to the requirements set based on the complexity of the reaction system where the oxidizing and reducing agents must not interfere with each other, and both should possess temperature sensitivity. Herein, we demonstrate plasmonic thermochromism based on a reversible redox reaction of Ag+/Ag on Au nanorods (AuNRs) by incorporating temperature-sensitive reducing and oxidizing agents into the same system. The competition between reduction and oxidation is solely dependent on temperature. When the temperature is above (below) the transition temperature, the reduction of Ag+ (oxidation of Ag) dominates on the surface of AuNRs, and the thermochromic nanostructure solution appears green (red). An experimental study on the mechanism reveals that HOCl produced at low concentrations by H2O2 is the source of the observed temperature dependence of the Ag oxidation. Rationally tuning the transition temperature in a range from 27 to 40 °C can be realized by changing the concentration of some key chemical compounds in the solution. The thermochromic solution can be standalone-functional within multiple cycles of heating and cooling and long-term storage without any additional reagents. Our study provides new insight into plasmonic thermochromism and may pave the way for fabricating smart thermochromic materials.

From Nonequilibrium Single-Molecule Trajectories to Underlying Dynamics

Single-molecule observations of biomolecular dynamics and folding are commonly rationalized using the model of diffusive dynamics on a free-energy landscape, which is inferred via the Boltzmann inversion of the equilibrium distribution of the experimental observable. Can the same model be applied to high-resolution single-molecule trajectories of molecular machines that lack thermal equilibrium so that the Boltzmann inversion method is inapplicable? In this Letter, we discuss two approaches to reconstructing the underlying free-energy landscape in such nonequilibrium systems and explore the performance of this model in application to trajectories with complex underlying dynamics.

Structural Consequences of Multisite Phosphorylation in the BAK1 Kinase Domain

Multisite phosphorylation is an important mechanism of post-translational control of protein kinases. The effects of combinations of possible phosphorylation states on protein kinase activity are difficult to study experimentally because of challenges in isolating a particular phosphorylation state; surprising little effort on this topic has been expended in computational studies. To understand the effects of multisite phosphorylation on the plant protein kinase brassinosteroid insensitive 1-associated kinase 1 (BAK1) conformational ensemble, we performed Gaussian accelerated molecular dynamics simulations on eight BAK1 mod-forms involving phosphorylation of the four activation-loop threonine residues and binding of ATP-Mg²⁺. We find that unphosphorylated BAK1 transitions into an inactive conformation with a "cracked" activation loop and with the αC helix swung away from the active site. T450 phosphorylation can prevent the activation loop from cracking and keep the αC helix in an active-like conformation, whereas phosphorylation of T455 only slightly stabilizes the activation loop. There is a general trend of reduced flexibility in interlobe motion with increased phosphorylation. Interestingly, the αC helix is destabilized when the activation loop is fully phosphorylated but is again stabilized with ATP-Mg²⁺ bound. Our results provide insight into the mechanism of phosphorylation-controlled BAK1 activation while at the same time represent the first, to our knowledge, comprehensive, comparative study of the effects of combinatorial phosphorylation states on protein kinase conformational dynamics.

Detection of tBid Oligomerization and Membrane Permeabilization by Graphene-Based Single-Molecule Surface-Induced Fluorescence Attenuation

The permeabilization of organelle membranes by BCL-2 family proteins is a pivotal step during the regulation of apoptosis; the underlying mechanisms remain unclear. Based on the fluorescence attenuation by graphene oxide, we developed a single-molecule imaging method termed surface-induced fluorescence attenuation (smSIFA), which enabled us to track both vertical and lateral kinetics of singly labeled BCL-2 family protein tBid during membrane permeabilization. We found that tBid monomers lie shallowly on the lipid bilayer, where they self-assemble to form oligomers. During the initiation phase of self-assembly, the two central hydrophobic helices (α₆ and α₇) of tBid insert halfway into the phospholipid core, while the other helices remain on the surface. In oligomerized tBid clusters, α₆ and α₇ prefer to float up, and the other helices may sink to the bottom of the membrane and cause the formation of transient two-dimensional, micelle-like pore structures, which are responsible for the permeabilization of membranes and the induction of apoptosis. Our results shed light on the understanding of tBid-induced apoptosis, and this nanotechnology-based smSIFA approach could be used to dissect the kinetic interaction between membrane protein and lipid bilayer at the single-molecule level with subnanometer precision.

Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein

The mammalian CLOCK:BMAL1 transcription factor complex and its coactivators CREB-binding protein (CBP)/p300 and mixed-lineage leukemia 1 (MLL1) critically regulate circadian transcription and chromatin modification. Circadian oscillations are regulated by interactions of BMAL1's C-terminal transactivation domain (TAD) with the KIX domain of CBP/p300 (activating) and with the clock protein CRY1 (repressing) as well as by the BMAL1 G-region preceding the TAD. Circadian acetylation of Lys⁵³⁷ within the G-region enhances repressive BMAL1-TAD-CRY1 interactions. Here, we characterized the interaction of the CBP-KIX domain with BMAL1 proteins, including the BMAL1-TAD, parts of the G-region, and Lys⁵³⁷ Tethering the small compound 1-10 in the MLL-binding pocket of the CBP-KIX domain weakened BMAL1 binding, and MLL1-bound KIX did not form a ternary complex with BMAL1, indicating that the MLL-binding pocket is important for KIX-BMAL1 interactions. Small-angle X-ray scattering (SAXS) models of BMAL1 and BMAL1:KIX complexes revealed that the N-terminal BMAL1 G-region including Lys⁵³⁷ forms elongated extensions emerging from the bulkier BMAL1-TAD:KIX core complex. Fitting high-resolution KIX domain structures into the SAXS-derived envelopes suggested that the G-region emerges near the MLL-binding pocket, further supporting a role of this pocket in BMAL1 binding. Additionally, mutations in the second CREB-pKID/c-Myb-binding pocket of the KIX domain moderately impacted BMAL1 binding. The BMAL1(K537Q) mutation mimicking Lys⁵³⁷ acetylation, however, did not affect the KIX-binding affinity, in contrast to its enhancing effect on CRY1 binding. Our results significantly advance the mechanistic understanding of the protein interaction networks controlling CLOCK:BMAL1- and CBP-dependent gene regulation in the mammalian circadian clock.

Nano-colorimetrically determined refractive index variation with ultra-high chromatic resolution

We develop a front-to-end solution where the shift of chromaticity from scattering of plasmonic nanoparticles is used as the reporter for nano-environmental refractive index variation. By co-projecting possible power combinations of RGB LEDs and digitized color grid density of CCD with various luminance onto the CIE 1931 chromaticity diagram, optimum condition for nanoenvironment sensing can be achieved. The highest resolution for local refractive index change is 0.0021 per distinguishable color, which is higher than that of a typical handheld spectrometer by 4.8 times. This result shows great potential in simplifying nano-environment sensing instruments and is particularly useful for multi-point dynamical process.

Plasmon Rulers as a Probe for Real-Time Microsecond Conformational Dynamics of Single Molecules

Biopolymers such as DNA, RNA, and proteins exploit conformational changes to modulate their function. Although state-of-the-art single-molecule approaches enable identification of conformational states, the transition path and metastable intermediates often remain elusive because they occur on microsecond time scales. Here we introduce a method to probe conformational dynamics with microsecond integration times based on a heterodimer of plasmonic particles. By combining Brownian dynamics and electromagnetic simulations, we find that integration times of 1 μs can be routinely achieved, providing the capability to identify short-lived intermediates and transition paths at the single-molecule level in real-time. Importantly, plasmon rulers require no specialized equipment but can be probed on existing fluorescence microscopes equipped with a fast camera. The approach combines the advantages of fluorescent probes (zero-force, parallelization) and mechanical probes such as optical tweezers (continuous microsecond integration times). They offer a unique opportunity to study conformational dynamics and compare measurements to full-atom simulations, where computational demands limit the simulation time.