Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay

Amyloid-beta ( A β 42 ) aggregates are characteristic signatures of Alzheimer's disease, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to A β 42 fibrils. We quantify correlations between fibril architectures, measured by SMOLM, and their growth and decay visualized by single-molecule localization microscopy (SMLM). We discover that stable A β 42 fibrils tend to be well-ordered, signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying A β 42 fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve β -sheet organization. SMOLM reveals that increased heterogeneity in fibril architectures is correlated with more dynamic remodeling and that large-scale fibril remodeling tends to originate from local regions that exhibit strong heterogeneity.

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.

Burst-by-Burst Measurement of Rotational Diffusion at Nanosecond Resolution Reveals Hot-Brownian Motion and Single-Chain Binding

We record dark-field scattering bursts of individual gold nanorods, 52 × 15 nm² in average size, freely diffusing in water suspension. We deduce their Brownian rotational diffusion constant from autocorrelation functions on a single-event basis. Due to spectral selection by the plasmonic resonance with the excitation laser, the distribution of rotational diffusion constants is much narrower than expected from the size distribution measured by TEM. As rotational diffusion depends on particle hydrodynamic volume, viscosity, and temperature, it can sense those parameters at the single-particle level. We demonstrate measurements of hot Brownian rotational diffusion of nanorods in temperature and viscosity gradients caused by plasmonic heating. Further, we monitor hydrodynamic volumes of gold nanorods upon addition of very low concentrations of the water-soluble polymer PVA, which binds to the particles, leading to measurable changes in their diffusion constant corresponding to binding of one to a few polymer coils. We propose this analysis technique for very low concentrations of biomolecules in solution.

Molecular Rotational Correlation Times and Nanoviscosity Determined by 111m Cd Perturbed Angular Correlation (PAC) of γ-rays Spectroscopy

The nanoviscosity experienced by molecules in solution may be determined through measurement of the molecular rotational correlation time, τ_c , for example, by fluorescence and NMR spectroscopy. With this work, we apply PAC spectroscopy to determine the rate of rotational diffusion, λ=1/τ_c , of a de novo designed protein, TRIL12AL16C, in solutions with viscosities, ξ, from 1.7 to 88 mPa⋅s. TRIL12AL16C was selected as molecular probe because it exhibits minimal effects due to intramolecular dynamics and static line broadening, allowing for exclusive elucidation of molecular rotational diffusion. Diffusion rates determined by PAC data agree well with literature data from fluorescence and NMR spectroscopy, and scales linearly with 1/ξ in agreement with the Stokes-Einstein-Debye model. PAC experiments require only trace amounts (∼10¹¹ ) of probe nuclei and can be conducted over a broad range of sample temperatures and pressures. Moreover, most materials are relatively transparent to γ-rays. Thus, PAC spectroscopy could find applications under circumstances where conventional techniques cannot be applied, spanning from the physics of liquids to in-vivo biochemistry.

Sharp turns and gyrotaxis modulate surface accumulation of microorganisms

Populations of swimming microorganisms are ubiquitous in aqueous environments from blood vessels to oceans and from biofilms to biotechnological industries, where they routinely encounter solid boundaries. This paper explores experimentally how the presence of boundaries influences the behavior of a marine alga (Heterosigma akashiwo), whose normal trajectories exhibit both random sharp turns and gravitational reorientation (gyrotaxis). Proximity to a plane boundary strongly increases the probability of sharp turns and thereby influences the distributions of swimming speed, angular velocity and, unexpectedly, rotational diffusivity as functions of distance from the boundary and of swimming orientation. These variations all contribute to enhancing accumulation beneath an upper boundary much more than gyrotaxis alone.

The accumulation of swimming microorganisms at surfaces is an essential feature of various physical, chemical, and biological processes in confined spaces. To date, this accumulation is mainly assumed to depend on the change of swimming speed and angular velocity caused by cell-wall contact and hydrodynamic interaction. Here, we measured the swimming trajectories of Heterosigma akashiwo (a biflagellate marine alga) near vertical and horizontal rigid boundaries. We observed that the probability of sharp turns is greatly increased near a vertical wall, resulting in significant changes in the distributions of average swimming speed, angular velocity, and rotational diffusivity near the wall (a quantity that has not previously been investigated) as functions of both distance from the wall and swimming orientation. These cannot be satisfactorily explained by standard hydrodynamic models. Detailed examination of an individual cell trajectory shows that wall contact by the leading flagellum triggers complex changes in the behavior of both flagella that cannot be incorporated in a mechanistic model. Our individual-based model for predicting cell concentration using the measured distributions of swimming speed, angular velocity, and rotational diffusivity agrees well with the experiment. The experiments and model are repeated for a cell suspension in a vertical plane, bounded above by a horizontal wall. The cell accumulation beneath the wall, expected from gyrotaxis, is considerably amplified by cell-wall interaction. These findings may shed light on the prediction and control of cell distribution mediated by gyrotaxis and cell-wall contact.

Revealing heterogeneity in correlation times of EGFP encapsulated in complex coacervate core micelles by analysis of fluorescence anisotropies

Encapsulation of enhanced green fluorescent protein (EGFP) in complex coacervate core micelles (C3Ms) can be established by mixing EGFP with diblock polymers at equal charge ratio. It has previously been shown that this encapsulation system is highly dynamic, implying existence of different populations; GFP free in solution or complexed with polymers (small complexes) and EGFP encapsulated in C3Ms. We performed time resolved fluorescence anisotropy experiments to determine the relative populations of EGFP encapsulated in C3Ms using three different fluorescence anisotropy decay analysis methods. First, Maximum Entropy Method (MEM) data analysis was employed for five different EGFP concentrations in C3Ms that were mixed with dark fluorescent proteins (10, 20, 30, 40 and 50% EGFP, respectively). In all cases, correlation-time distributions between 0.1 and 100 ns (on a logarithmic timescale) are clearly visible showing bimodal distribution. The distribution between 0.1 and 2.0 ns is due to homo-FRET between EGFP molecules packed in micelles and the distribution between 8 and 30 ns coincides with the correlation-time distribution of free EGFP in solution. The fraction of homo-FRET distribution linearly increases with increase of relative micellar EGFP concentrations. These MEM results were corroborated by two different analysis methods: global population analysis of all five fluorescence anisotropy decays arising from EGFP in micelles together with the one of free EGFP (direct analysis of anisotropies) and global associative population analysis of anisotropies by fitting parallel and perpendicular fluorescence decay components. In contrast to global analyses approaches, the MEM method directly reveals distributions of correlation times without any prior information about the sample. However, global associative analysis of anisotropies by fitting parallel and perpendicular fluorescence decay components is the only method that allows to estimate accurately fractions of free fluorophores in solution and encapsulated fluorophores.

Competing effects of rotational diffusivity and activity on finite-sized clusters

Colloidal particles interacting via short-range attraction and long-range repulsion are known to stabilize finite-sized clusters under equilibrium conditions. In this work, the effect of self-propulsion speed (activity) and rotational diffusivity (D_r) on the phase behavior of such particles is investigated using Brownian dynamics simulations. The system exhibits rich phase behavior consisting of clusters of different kinds. The cluster size varies non-monotonically with activity: increasing first and decreasing at higher activity, thus driving cluster-to-fluid phase transition. Rotational diffusivity also facilitates the formation of clusters. Larger clusters could be stabilized at lowD_rvalues while at highD_rvalues, clusters are stable even at higher activities. The analysis of the static structure factor of the system confirms that rotational diffusivity delays the cluster-to-fluid transition driven by activity.

Resolving the Three-Dimensional Rotational and Translational Dynamics of Single Molecules Using Radially and Azimuthally Polarized Fluorescence

We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR's orientational diffusion to be dramatically reduced, but curiously NR's median lateral displacements drastically increase from 20.8 to 75.5 nm (200 ms time lag). These jump diffusion events overwhelmingly originate from cholesterol-rich nanodomains within the SLB. These detailed measurements of single-molecule rotational and translational dynamics are made possible by raPol's high measurement precision and are not detectable in standard SMLM.

Cross-correlation analysis of X-ray photon correlation spectroscopy to extract rotational diffusion coefficients

X-ray photon correlation spectroscopy (XPCS) is a powerful technique that can probe a broad range of space and time scales and will become increasingly powerful due to coming advancements in coherence. Assessing translational and rotational diffusion is a key quantity in analyzing material structures and dynamics, with applications across molecular biology, drug discovery, and materials science. While methods for estimating translational diffusion coefficients from XPCS data are well-developed, there are no algorithms for measuring the rotational diffusion. Here, we present a mathematical formulation and algorithm based on angular-temporal cross-correlations for extracting this rotational information, providing tools for data analysis of XPCS. Although we focus on XPCS, the proposed method can be applied to other experimental techniques due to its generality.

Coefficients for translational and rotational diffusion characterize the Brownian motion of particles. Emerging X-ray photon correlation spectroscopy (XPCS) experiments probe a broad range of length scales and time scales and are well-suited for investigation of Brownian motion. While methods for estimating the translational diffusion coefficients from XPCS are well-developed, there are no algorithms for measuring the rotational diffusion coefficients based on XPCS, even though the required raw data are accessible from such experiments. In this paper, we propose angular-temporal cross-correlation analysis of XPCS data and show that this information can be used to design a numerical algorithm (Multi-Tiered Estimation for Correlation Spectroscopy [MTECS]) for predicting the rotational diffusion coefficient utilizing the cross-correlation: This approach is applicable to other wavelengths beyond this regime. We verify the accuracy of this algorithmic approach across a range of simulated data.

Ultrahigh-Speed Imaging of Rotational Diffusion on a Lipid Bilayer

We studied the rotational and translational diffusion of a single gold nanorod linked to a supported lipid bilayer with ultrahigh temporal resolution of two microseconds. By using a home-built polarization-sensitive dark-field microscope, we recorded particle trajectories with lateral precision of 3 nm and rotational precision of 4°. The large number of trajectory points in our measurements allows us to characterize the statistics of rotational diffusion with unprecedented detail. Our data show apparent signatures of anomalous diffusion such as sublinear scaling of the mean-squared angular displacement and negative values of angular correlation function at small lag times. However, a careful analysis reveals that these effects stem from the residual noise contributions and confirms normal diffusion. Our experimental approach and observations can be extended to investigate diffusive processes of anisotropic nanoparticles in other fundamental systems such as cellular membranes or other two-dimensional fluids.

Single-Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes

In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm-2 ) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single-molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus "wobble") of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve nanodomains and enzyme-induced compositional heterogeneity within membranes, where NR within liquid-ordered vs. liquid-disordered domains shows a ≈4° difference in polar angle and a ≈0.3π sr difference in wobble angle. As a new type of imaging spectroscopy, SMOLM exposes the organizational and functional dynamics of lipid-lipid, lipid-protein, and lipid-dye interactions with single-molecule, nanoscale resolution.

Single-Particle Dynamic Light Scattering: Shapes of Individual Nanoparticles

Metallic nanoparticles (MNPs) are prevalent in modern nanotechnologies due to their unique optical properties, chemical and photostability, and ease of manipulation. In particular, many recent advances have highlighted the importance of fundamentally understanding dynamic reconfiguration in MNP morphologies and compositions. Techniques to measure the shape of a single particle are lacking, however, often requiring immobilization, extensive numerical simulations, and irreversible alterations of the particle or its environment. In this work, we introduce "single-particle dynamic light scattering" (SP-DLS) as a far-field technique capable of analyzing the shape of individual, freely diffusing MNPs. Assuming symmetric-top rotors for MNPs and passively confining them to the focal volume of a dark-field microscope for long-term observation, we directly relate polarization dynamic fluctuations in the scattered light to the relative difference between the nondegenerate axes of individual particles. Our results show remarkable agreement with transmission electron microscopy analyses of the same population and allow for unprecedented measurements of the extent of prolate or oblate asphericity of nominally spherical MNPs in solution where the current implementation affords an asphericity detection limit of ∼2.5% assuming a 10% relative error. SP-DLS should serve as a powerful, nondestructive technique for characterizing the shapes of individual MNPs and other nanostructures.

Direct Observations of the Rotation and Translation of Anisotropic Nanoparticles Adsorbed at a Liquid-Solid Interface

We can learn about the interactions between nanoparticles (NPs) in solution and solid surfaces by tracking how they move. Here, we use liquid cell transmission electron microscopy (TEM) to follow directly the translation and rotation of Au nanobipyramids (NBPs) and nanorods (NRs) adsorbed onto a SiN _x surface at a rate of 300 frames per second. This study is motivated by the enduring need for a detailed description of NP motion on this common surface in liquid cell TEM. We will show that NPs move intermittently on the time scales of milliseconds. First, they rotate in two ways: (1) rotation around the center of mass and (2) pivoted rotation at the tips. These rotations also lead to different modes of translation. A NP can move through small displacements in the direction roughly parallel to its body axis (shuffling) or with larger steps via multiple tip-pivoted rotations. Analysis of the trajectories indicates that both displacements and rotation angles follow heavy-tailed power law distributions, implying anomalous diffusion. The spatial and temporal resolution afforded by our approach also revealed differences between the different NPs. The 50 nm NRs and 100 nm NBPs moved with a combination of shuffles and rotation-mediated displacements after illumination by the electron beam. With increasing electron fluence, 50 nm NRs also started to move via desorption-mediated jumps. The 70 nm NRs did not exhibit translational motion and only made small rotations. These results describe how NP dynamics evolve under the electron beam and how intermittent pinning and release at specific adsorption sites on the solid surface control NP motion at the liquid-solid interface. We also discuss the effect of SiN _x surface treatment on NP motion, demonstrating how our approach can provide broader insights into interfacial transport.

Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity

Studies of protein-ligand binding often rely on dissolving the ligand in dimethyl sulfoxide (DMSO) to achieve sufficient solubility, and then titrating the ligand solution into the protein solution. As a result, the final protein-ligand solution contains small amounts of DMSO in the buffer. Here we report how the addition of DMSO impacts studies of protein conformational dynamics. We used 15 N NMR relaxation to compare the rotational diffusion correlation time (τC ) of proteins in aqueous buffer with and without DMSO. We found that τC scales with the viscosity of the water-DMSO mixture, which depends sensitively on the amount of DMSO and varies by a factor of 2 across the relevant concentration range. NMR relaxation studies of side chains dynamics are commonly interpreted using τC as a fixed parameter, obtained from backbone 15 N relaxation data acquired on a separate sample. Model-free calculations show that errors in τC , arising from mismatched DMSO concentration between samples, lead to significant errors in order parameters. Our results highlight the importance of determining τC for each sample or carefully matching the DMSO concentrations between samples.

Resolving Mixtures in Solution by Single-Molecule Rotational Diffusivity

Sensing the size of individual molecules in an ensemble has proven to be a powerful tool to investigate biomolecular interactions and association-dissociation processes. In biologically relevant solution environments, molecular size is often sensed by translational or rotational diffusivity. The rotational diffusivity is more sensitive to the size and conformation of the molecules as it is inversely proportional to the cube of the hydrodynamic radius, as opposed to the inverse linear dependence of the translational diffusion coefficient. Single-molecule rotational diffusivity has been measured with time-resolved fluorescence anisotropy decay, but the ability to sense different sizes has been restricted by the limited number of photons available or has required surface attachment to observe each molecule longer, and the attachment may be perturbative. To address these limitations, we show how to measure and monitor single-molecule rotational diffusivity by combining the solution-phase Anti-Brownian ELectrokinetic (ABEL) trap and maximum likelihood analysis of time-resolved fluorescence anisotropy based on the information inherent in each detected photon. We demonstrate this approach by resolving a mixture of single- and double-stranded fluorescently labeled DNA molecules at equilibrium, freely rotating in a native solution environment. The rotational diffusivity, fluorescence brightness and lifetime, and initial and steady-state anisotropy are simultaneously determined for each trapped single DNA molecule. The time resolution and precision of this method are analyzed using statistical signal analysis and simulations. We present key parameters that define the usefulness of a particular fluorescent label for extracting molecular size information from single-molecule rotational diffusivity measurements.

Investigating molecular crowding within nuclear pores using polarization-PALM

The key component of the nuclear pore complex (NPC) controlling permeability, selectivity, and the speed of nucleocytoplasmic transport is an assembly of natively unfolded polypeptides, which contain phenylalanine-glycine (FG) binding sites for nuclear transport receptors. The architecture and dynamics of the FG-network have been refractory to characterization due to the paucity of experimental methods able to probe the mobility and density of the FG-polypeptides and embedded macromolecules within intact NPCs. Combining fluorescence polarization, super-resolution microscopy, and mathematical analyses, we examined the rotational mobility of fluorescent probes at various locations within the FG-network under different conditions. We demonstrate that polarization PALM (p-PALM) provides a rich source of information about low rotational mobilities that are inaccessible with bulk fluorescence anisotropy approaches, and anticipate that p-PALM is well-suited to explore numerous crowded cellular environments. In total, our findings indicate that the NPC’s internal organization consists of multiple dynamic environments with different local properties.

Most of the genetic material inside an animal cell is enclosed within a compartment called the nucleus. This compartment is separated from the rest of the cell by the nuclear envelope, a double-membrane structure containing thousands of pores that selectively allow certain molecules (collectively referred to as cargo) to enter and exit the nucleus.

The movement of cargo through the pores is controlled by large groups of proteins called nuclear pore complexes. The pore is at the center of the complex and is filled by a selective barrier made of an extensive network of flexible proteins known as the FG-network. Other proteins known as nuclear transport receptors bind to the proteins in the FG-network and carry cargos through the barrier.

The properties of the nuclear pore barrier and how it rapidly selects the right cargos have been difficult to study, in part, because the barrier network is constantly changing and is crowded with hundreds of transport receptors. New techniques are needed to investigate such highly crowded environments inside cells. Now, Fu et al. use a technique called polarization photoactivated localization microscopy (p-PALM) to explore the molecular crowding within the nuclear pore barrier in human cells. This technique measures the freedom with which a single molecule embedded in the network can rotate, providing information about the local environment. In a crowded environment, it is harder for the probe molecule to rotate as it is more likely to bump into other molecules.

Fu et al. found that there are different levels of crowding within the barrier. This is consistent with previous ideas of how the pore barrier could work, which propose that the nuclear transport receptors are less tightly packed in the center of the FG-network. This enables transport receptor and cargo complexes to move more rapidly through the center of the pore. The molecular crowding in the barrier of nuclear pores parallels that observed in other cellular compartments that also rely on assemblies of proteins with flexible structures. Thus, future work using p-PALM is expected to reveal more details about the biophysical properties of nuclear pores as well as those of other structures inside cells.

Diffusive Motion of Linear Microgel Assemblies in Solution

Due to the ability of microgels to rapidly contract and expand in response to external stimuli, assemblies of interconnected microgels are promising for actuation applications, e.g., as contracting fibers for artificial muscles. Among the properties determining the suitability of microgel assemblies for actuation are mechanical parameters such as bending stiffness and mobility. Here, we study the properties of linear, one-dimensional chains of poly(N-vinylcaprolactam) microgels dispersed in water. They were fabricated by utilizing wrinkled surfaces as templates and UV-cross-linking the microgels. We image the shapes of the chains on surfaces and in solution using atomic force microscopy (AFM) and fluorescence microscopy, respectively. In solution, the chains are observed to execute translational and rotational diffusive motions. Evaluation of the motions yields translational and rotational diffusion coefficients and, from the translational diffusion coefficient, the chain mobility. The microgel chains show no perceptible bending, which yields a lower limit on their bending stiffness.

ESR study of molecular orientation and dynamics of TEMPO derivatives in CLPOT 1D nanochannels

The molecular orientations and dynamics of 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) radical derivatives with large substituent groups at the 4-position (4-X-TEMPO) in the organic one-dimensional nanochannels within the nanosized molecular template 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) were examined using ESR. The concentrations of guest radicals, including 4-methoxy-TEMPO (MeO-TEMPO) or 4-oxo-TEMPO (TEMPONE), in the CLPOT nanochannels in each inclusion compound (IC) were reduced by co-including 4-substituted-2,2,6,6-tetramethylpiperidine (4-R-TEMP) compounds at a ratio of 1 : 30-1 : 600. At higher temperatures, the guest radicals in each IC underwent anisotropic rotational diffusion in the CLPOT nanochannels. The rotational diffusion activation energy, Ea , associated with MeO-TEMPO or TEMPONE in the CLPOT nanochannels (6-7 kJ mol(-1) ), was independent of the size and type of substituent group and was similar to the Ea values obtained for TEMPO and 4- hydroxy-TEMPO (TEMPOL) in our previous study. However, in the case in which TEMP was used as a guest compound for dilution (spacer), the tilt of the rotational axis to the principal axis system of the g-tensor, and the rotational diffusion correlation time, τR , of each guest radical in the CLPOT nanochannels were different from the case with other 4-R-TEMP. These results indicate the possibility of controlling molecular orientation and dynamics of guest radicals in CLPOT ICs through the appropriate choice of spacer. Copyright © 2016 John Wiley & Sons, Ltd.

Hydrodynamic Radii of Ranibizumab, Aflibercept and Bevacizumab Measured by Time-Resolved Phosphorescence Anisotropy

PURPOSE

To measure the hydrodynamic radii of intravitreal anti-VEGF drugs ranibizumab, aflibercept and bevacizumab with μs time-resolved phosphorescence anisotropy.

METHODS

Ruthenium-based dye Ru(bpy)2(mcbpy - O - Su - ester)(PF6)2, whose lifetime of several hundred nanoseconds is comparable to the rotational correlation time of these drugs in buffer, was used as a label. The hydrodynamic radii were calculated from the rotational correlation times of the Ru(bpy)2(mcbpy - O - Su - ester)(PF6)2-labelled drugs obtained with time-resolved phosphorescence anisotropy measurements in buffer/glycerol solutions of varying viscosity.

RESULTS

The measured radii of 2.76±0.04 nm for ranibizumab, 3.70±0.03 nm for aflibercept and 4.58±0.01 nm for bevacizumab agree with calculations based on molecular weight and other experimental measurements.

CONCLUSIONS

Time-resolved phosphorescence anisotropy is a relatively simple and straightforward method that allows experimental measurement of the hydrodynamic radius of individual proteins, and is superior to theoretical calculations which cannot give the required accuracy for a particular protein.

Sucralose Destabilization of Protein Structure

Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein model. For sucralose solutions, however, the diffusion is dependent on the concentration, strongly diverging from the viscosity predictions, and results in heterogeneous rotational diffusion.

DNA origami nanoneedles on freestanding lipid membranes as a tool to observe isotropic-nematic transition in two dimensions

We introduce a simple experimental system to study dynamics of needle-like nanoobjects in two dimensions (2D) as a function of their surface density close to the isotropic-nematic transition. Using fluorescence correlation spectroscopy, we find that translational and rotational diffusion of rigid DNA origami nanoneedles bound to freestanding lipid membranes is strongly suppressed upon an increase in the surface particle density. Our experimental observations show a good agreement with results of Monte Carlo simulations of Brownian hard needles in 2D.

Modelling and analysis of bacterial tracks suggest an active reorientation mechanism in Rhodobacter sphaeroides

Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly understood reorientation mechanism in the monoflagellate species Rhodobacter sphaeroides. The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable reorientation. When rotation restarts the cell body usually points in a new direction. It has been assumed that the new direction is simply the result of Brownian rotation. We consider three variants of a self-propelled particle model of bacterial motility. The first considers rotational diffusion only, corresponding to a non-chemotactic mutant strain. Two further models incorporate stochastic reorientations, describing 'run-and-tumble' motility. We derive expressions for key summary statistics and simulate each model using a stochastic computational algorithm. We also discuss the effect of cell geometry on rotational diffusion. Working with a previously published tracking dataset, we compare predictions of the models with data on individual stopping events in R. sphaeroides. This provides strong evidence that this species undergoes some form of active reorientation rather than simple reorientation by Brownian rotation.

Rotational mobility of single molecules affects localization accuracy in super-resolution fluorescence microscopy

The asymmetric nature of single-molecule (SM) dipole emission patterns limits the accuracy of position determination in localization-based super-resolution fluorescence microscopy. The degree of mislocalization depends highly on the rotational mobility of SMs; only for SMs rotating within a cone half angle α > 60° can mislocalization errors be bounded to ≤10 nm. Simulations demonstrate how low or high rotational mobility can cause resolution degradation or distortion in super-resolution reconstructions.

Gold nanorods as probes in two-photon fluorescence correlation spectroscopy: emerging applications and potential artifacts

Owing to the highly efficient two-photon fluorescence of gold nanorods and very short fluorescence lifetime compared with the rotational correlation time, the rotation and diffusion of a single gold nanorod can be easily observed by two-photon fluorescence correlation spectroscopy (TP-FCS). This property, along with the previous successful use as a contrast agent in two-photon fluorescence imaging, suggests a potential application in TP-FCS as well. Although the FCS measurement becomes highly efficient with gold nanorods as probes, the amplitude and temporal decay of the measured correlation functions depend critically on excitation power. Here, we investigate various photophysical processes of gold nanorods to determine the cause of such a sensitive power dependency. This understanding provides a basis for choosing appropriate FCS models to recover reasonable physical parameters. Although the correlation function amplitude G(0) is 32 times lower when the excitation power increases from 20 µW to 1.12 mW, the application of a saturation-modified FCS model yields very good fit to each data set and the fitted concentration of 0.64 nM is comparable to the 0.7 nM given by the inductively coupled plasma mass spectrometry measurement. The FCS assay appears to be an efficient method for the quantification of gold nanorods when correctly interpreted. However, even with the saturation considered in the fitting model, the fitted rotational and translational diffusion rates are getting faster as the power increases. This indicates that other effects such as photothermal effects may raise the local temperature, and thus increasing the rotational and translational diffusion rate.

Fast Crystal Growth Induces Mobility and Tension in Supercooled o-Terphenyl

A photobleaching method was used to measure the reorientation of dilute probes in liquid o-terphenyl near a crystal growth front. Near the glass-transition temperature Tg, mobility in the supercooled liquid was enhanced within ∼10 μm of the crystal growth front, by as much as a factor of 4. This enhanced mobility appears to be caused by tension created in the sample as a result of the density difference between the supercooled liquid and crystal. The maximum observed mobility enhancement corresponds to a tension of about -8 MPa, close to the cavitation limit for liquid o-terphenyl. Whereas the observed mobility near the growing crystal is not large enough to explain the extraordinary fast crystal growth observed near Tg in o-terphenyl and some other low-molecular-weight glassformers, these observations suggest that cavitation or fracture plays a key role in releasing tension and allowing fast crystal growth to occur at a steady rate.

Theory of nonrigid rotational motion applied to NMR relaxation in RNA

Solution NMR spectroscopy can elucidate many features of the structure and dynamics of macromolecules, yet relaxation measurements, the most common source of experimental information on dynamics, can sample only certain ranges of dynamic rates. A complete characterization of motion of a macromolecule thus requires the introduction of complementary experimental approaches. Solid-state NMR spectroscopy successfully probes the time scale of nanoseconds to microseconds, a dynamic window where solution NMR results have been deficient, and probes conditions where the averaging effects of rotational diffusion of the molecule are absent. Combining the results of the two distinct techniques within a single framework provides greater insight into dynamics, but this task requires the common interpretation of results recorded under very different experimental conditions. Herein, we provide a unified description of dynamics that is robust to the presence of large-scale conformational exchange, where the diffusion tensor of the molecule varies on a time scale comparable to rotational diffusion in solution. We apply this methodology to the HIV-1 TAR RNA molecule, where conformational rearrangements are both substantial and functionally important. The formalism described herein is of greater generality than earlier combined solid-state/solution NMR interpretations, if detailed molecular structures are available, and can offer a more complete description of RNA dynamics than either solution or solid-state NMR spectroscopy alone.

Anisotropic Picosecond X-ray Solution Scattering from Photo-selectively Aligned Protein Molecules

Anisotropic X-ray scattering patterns of transiently aligned protein molecules in solution are measured by using pump-probe X-ray solution scattering. When a linearly polarized laser pulse interacts with an ensemble of molecules, the population of excited molecules is created with their transition dipoles preferentially aligned along the laser polarization direction. We measured the X-ray scattering from the myoglobin protein molecules excited by a linearly polarized, short laser pulse and obtained anisotropic scattering patterns on 100 ps time scale. An anisotropic scattering pattern contains higher structural information content than a typical isotropic pattern available from randomly oriented molecules. In addition, multiple independent diffraction patterns measured by using various laser polarization orientations will give substantially increased amount of structural information compared with a single isotropic pattern. By monitoring the temporal change of the anisotropic scattering pattern from 100 ps to 1 μs, we observed the orientational dynamics of photo-generated myoglobin with the rotational diffusion time of ∼15 ns.

Slow exchange model of nonrigid rotational motion in RNA for combined solid-state and solution NMR studies

Functional RNA molecules are conformationally dynamic and sample a multitude of dynamic modes over a wide range of frequencies. Thus, a comprehensive description of RNA dynamics requires the inclusion of a broad range of motions across multiple dynamic rates which must be derived from multiple spectroscopies. Here we describe a slow conformational exchange theoretical approach to combining the description of local motions in RNA that occur in the nanosecond to microsecond window and are detected by solid-state NMR with nonrigid rotational motion of the HIV-1 transactivation response element (TAR) RNA in solution as observed by solution NMR. This theoretical model unifies the experimental results generated by solution and solid-state NMR and provides a comprehensive view of the dynamics of HIV-1 TAR RNA, a well-known paradigm of an RNA where function requires extensive conformational rearrangements. This methodology provides a quantitative atomic level view of the amplitudes and rates of the local and collective displacements of the TAR RNA molecule and provides directly motional parameters for the conformational capture hypothesis of this classical RNA-ligand interaction.

The Triple Axis and SPINS Spectrometers

In this paper are described the triple axis and spin polarized inelastic neutron scattering (SPINS) spectrometers which are installed at the NIST Cold Neutron Research Facility (CNRF). The general principle of operation of these two instruments is described in sufficient detail to allow the reader to make an informed decision as to their usefulness for his needs. However, it is the intention of the staff at the CNRF to provide the expert resources for their efficient use in any given situation. Thus, this work is not intended as a user manual but rather as a guide into the range of applicability of the two instruments.

Dynamics of fluorescence polarization in macromolecules

Reexamination of the theory of fluorescence time dependence owing to rotational diffusion of rigid macromolecules reveals deficiencies or hidden restrictions in each of the previous treatments. The correct master equation has five exponential decay terms, with preexponential factors that depend upon the diffusion constants and, in a completely symmetrical fashion, upon the orientations of absorbing and emitting dipoles.