The effects of allosteric and competitive inhibitors on ZIKV protease conformational dynamics explored through smFRET, nanoDSF, DSF, and F NMR.

Zika and dengue viruses cause mosquito-borne diseases of high epidemic relevance. The viral NS2B-NS3 proteases play crucial roles in the pathogen replication cycle and are validated drug targets. They can adopt at least two conformations depending on the position of the NS2B cofactor.

A competition smFRET assay to study ligand-induced conformational changes of the dengue virus protease.

Ligand binding to proteins often is accompanied by conformational transitions. Here, we describe a competition assay based on single molecule Förster resonance energy transfer (smFRET) to investigate the ligand-induced conformational changes of the dengue virus (DENV) NS2B-NS3 protease, which can adopt at least two different conformations. First, a competitive ligand was used to stabilize the closed conformation of the protease.

Nuclear Spin Relaxation in Viscous Liquids: Relaxation Stretching of Single-Particle Probes.

Spin-lattice relaxation rates (ω,), probed via high-field and field-cycling nuclear magnetic resonance (NMR), are used to test the validity of frequency-temperature superposition (FTS) for the reorientation dynamics in viscous liquids. For several liquids, FTS is found to apply so that master curves can be generated. The susceptibility spectra are highly similar to those obtained from depolarized light scattering (DLS) and reveal an excess wing.

Conformational Dynamics of the Dengue Virus Protease Revealed by Fluorescence Correlation and Single-Molecule FRET Studies.

The dengue virus protease (DENV-PR) represents an attractive target for counteracting DENV infections. It is generally assumed that DENV-PR can exist in an open and a closed conformation and that active site directed ligands stabilize the closed state. While crystal structures of both the open and the closed conformation were successfully resolved, information about the prevalence of these conformations in solution remains elusive.

State transition identification in multivariate time series (STIMTS) applied to rotational jump trajectories from single molecules.

Time resolved data from single molecule experiments often suffer from contamination with noise due to a low signal level. Identifying a proper model to describe the data thus requires an approach with sufficient model parameters without misinterpreting the noise as relevant data. Here, we report on a generalized data evaluation process to extract states with piecewise constant signal level from simultaneously recorded multivariate data, typical for multichannel single molecule experiments.

Single Semiconductor Nanocrystals under Compressive Stress: Reversible Tuning of the Emission Energy.

The photoluminescence of individual CdSe/CdS/ZnS core/shell nanocrystals has been investigated under external forces. After mutual alignment of a correlative atomic force and confocal microscope, individual particles were colocalized and exposed to a series of force cycles by using the tip of the AFM cantilever as a nanoscale piston. Thus, force-dependent changes of photophysical properties could be tracked on a single particle level.

Impact of local compressive stress on the optical transitions of single organic dye molecules.

The ability to mechanically control the optical properties of individual molecules is a grand challenge in nanoscience and could enable the manipulation of chemical reactivity at the single-molecule level. In the past, light has been used to alter the emission wavelength of individual molecules or modulate the energy transfer quantum yield between them. Furthermore, tensile stress has been applied to study the force dependence of protein folding/unfolding and of the chemistry and photochemistry of single molecules, although in these mechanical experiments the strength of the weakest bond limits the amount of applicable force.

Probing the electronic state of a single coronene molecule by the emission from proximate fluorophores.

We measured electronic transitions of the 2D graphene-type molecule hexa-peri-hexabenzocoronene (HBC) at the single-molecule level. The large intersystem crossing rate and long triplet state lifetime in the range of seconds are prohibitive for direct single-molecule observation. By covalently coupling fluorescent acceptor molecules (perylenecarboximide, PMI) to HBC, efficient singlet energy transfer gives rise to strong PMI fluorescence.

Assembly and separation of semiconductor quantum dot dimers and trimers.

Repeated precipitation of colloidal semiconductor quantum dots (QD) from a good solvent by adding a poor solvent leads to an increasing number of QD oligomers after redispersion in the good solvent. By using density gradient ultracentrifugation we have been able to separate QD monomer, dimer, and trimer fractions from higher oligomers in such solutions. In the corresponding fractions QD dimers and trimers have been enriched up to 90% and 64%, respectively.

Single molecule probing of dynamics in supercooled polymers.

Fluorescence experiments with single BODIPY molecules embedded in a poly(methyl acrylate) matrix have been performed at various temperatures in the supercooled regime. By using pulsed excitation, fluorescence lifetime and linear dichroism time trajectories were accessible at the same time. Both observables have been analyzed without data binning.

Quantification of the singlet-singlet annihilation times of individual bichromophoric molecules by photon coincidence measurements.

Singlet-singlet annihilation (SSA) times in individual bichromophoric molecules have been quantified by time-resolved photon coincidence measurements. An analytical expression has been derived to obtain the SSA times from the coincidence histograms. The results have been confirmed by Monte Carlo simulations.

Statistical analysis of time resolved single molecule fluorescence data without time binning.

We depict two algorithms to calculate correlation functions from two different time resolved single molecule fluorescence experiments without the need of time binning. Our first procedure allows to calculate the reduced linear dichroism from polarization resolved fluorescence data. Since we process single photon counts instead of time binned data, considerably faster fluctuations of the dichroism can be analyzed than with conventional methods.

Control of the electronic energy transfer pathway between two single fluorophores by dual pulse excitation.

We report on the control of the energy transfer pathway in individual donor-acceptor dyads by proper timing of light pulses matching the donor and acceptor transition frequencies, respectively. Excitation of both chromophores at virtually the same time induces efficient singlet-singlet annihilation, whereby excitation energy effectively flows from the acceptor to the donor. The dual pulse excitation scheme implemented here allows for all-optical switching of the fluorescence intensity at the single-molecule level.

Analysis of the exponential character of single molecule rotational correlation functions for large and small fluorescence collection angles.

Coarse-grained molecular dynamics simulations and single molecule fluorescence microscopy experiments have been performed in order to investigate the influence of the numerical aperture (NA) of the microscope objective on the exponential character of the rotational correlation functions of probes embedded in complex matrices. The results obtained by using either a dry lens (NA=0.95) or an oil objective (NA=1.

Intramolecular electronic excitation energy transfer in donor/acceptor dyads studied by time and frequency resolved single molecule spectroscopy.

Electronic excitation energy transfer has been studied by single molecule spectroscopy in donor/acceptor dyads composed of a perylenediimide donor and a terrylenediimide acceptor linked by oligo(phenylene) bridges of two different lengths. For the shorter bridge (three phenylene units) energy is transferred almost quantitatively from the donor to the acceptor, while for the longer bridge (seven phenylene units) energy transfer is less efficient as indicated by the occurrence of donor and acceptor emission. To determine energy transfer rates and efficiencies at the single molecule level, several methods have been employed.

Theoretical investigation of electronic excitation energy transfer in bichromophoric assemblies.

Electronic excitation energy transfer (EET) rates in rylene diimide dyads are calculated using second-order approximate coupled-cluster theory and time-dependent density functional theory. We investigate the dependence of the EET rates on the interchromophoric distance and the relative orientation and show that Forster theory works quantitatively only for donor-acceptor separations larger than roughly 5 nm. For smaller distances the EET rates are over- or underestimated by Forster theory depending on the respective orientation of the transition dipole moments of the chromophores.

Correlation of primary relaxations and high-frequency modes in supercooled liquids. II. Evidence from spin-lattice relaxation weighted stimulated-echo spectroscopy.

Using spin-lattice relaxation weighted stimulated-echo spectroscopy, we report evidence for a correlation of the primary and secondary relaxation times. The experiments are performed using deuteron nuclear magnetic resonance somewhat above the calorimetric glass-transition of ortho-terphenyl, D-sorbitol, and cresolphthalein-dimethylether. The data analysis is based on the procedure outlined in the accompanying theoretical paper [B.

Flexibility of phenylene oligomers revealed by single molecule spectroscopy.

The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently.

Correlation of primary and secondary relaxations in a supercooled liquid.

The widespread assumption that primary and secondary relaxations in glass-forming materials are independent processes is scrutinized using spin-lattice relaxation weighted stimulated-echo spectroscopy. This nuclear magnetic resonance (NMR) technique is simultaneously sensitive to the dynamics on well-separated time scales. For the deeply supercooled liquid sorbitol, which exhibits a strong secondary relaxation, the primary relaxation (that is observable using NMR) can be modified by suppressing the contributions of those subensembles which are characterized by relatively slow secondary relaxations.

Time-resolved measurements of intramolecular energy transfer in single donor/acceptor dyads.

We have investigated electronic excitation energy transfer in a specifically designed bichromophoric donor/acceptor dyad in which the donor (perylenediimide) and acceptor (terrylenediimide) are linked by a rigid heptaphenyl-spacer. Because of the choice of the bridge, which defines the distance and orientation of the two chromophores, donor as well as acceptor emission is observed. The significantly smaller photostability of the donor allows for time-resolved measurements of the acceptor emission at the single-molecule level with and without energy transfer from the donor.

Formation of self-supporting reversible cellular networks in suspensions of colloids and liquid crystals.

In mixtures of thermotropic liquid crystals with spherical poly (methyl methacrylate) particles, self-supporting networklike structures are formed during slow cooling past the isotropic-to-nematic phase transformation. To characterize the process of network formation in terms of morphology, phase transformation kinetics, and mechanical properties, we have combined data from polarization and laser scanning confocal microscopy with calorimetric, NMR, and rheological results. Our data suggest that the mechanism of network formation is dominated by a broadened temperature and time interval of phase transformation rather than by particle size or concentration.

A comparison of relaxation processes in structurally related van der Waals glass formers: the role of internal degrees of freedom.

Depolarized dynamic light scattering (DLS), dielectric relaxation (DS), and deuterium NMR studies of fragile van der Waals glass forming liquids phenylphthalein-dimethylether (PDE) and cresolphthalein-dimethylether (KDE) are presented. In PDE a new dielectric loss process was found, which can be attributed to the 180 degrees flip of the phenyl rings. The previous finding that the distribution of the structural relaxation times measured for PDE and KDE by DS is substantially narrower than that measured by DLS is explained by partial decoupling of the dynamics of the dipole moment from the structural relaxation of the sample.

Rotational correlation functions of single molecules.

Single molecule rotational correlation functions are analyzed for several reorientation geometries. Even for the simplest model of isotropic rotational diffusion our findings predict nonexponential correlation functions to be observed by polarization sensitive single molecule fluorescence microscopy. This may have a deep impact on interpreting the results of molecular reorientation measurements in heterogeneous environments.

From strong to fragile glass formers: secondary relaxation in polyalcohols.

We have studied details of the molecular origin of slow secondary relaxation near T(g) in a series of neat polyalcohols by means of dielectric spectroscopy and (2)H NMR. From glycerol to threitol, xylitol, and sorbitol the appearance of the secondary relaxation changes gradually from a wing-type scenario to a pronounced beta peak. It is found that in sorbitol the dynamics of the whole molecule contributes equally to the beta process, while in glycerol the hydrogen bond forming OH groups remain rather rigid compared to the hydrogens bonded to the carbon skeleton.