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.