Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups.

Seven native residues on the regulatory protein calmodulin, including three key methionine residues, were replaced (one by one) by the vibrational probe amino acid cyanylated cysteine, which has a unique CN stretching vibration that reports on its local environment. Almost no perturbation was caused by this probe at any of the seven sites, as reported by CD spectra of calcium-bound and apo calmodulin and binding thermodynamics for the formation of a complex between calmodulin and a canonical target peptide from skeletal muscle myosin light chain kinase measured by isothermal titration. The surprising lack of perturbation suggests that this probe group could be applied directly in many protein-protein binding interfaces. The infrared absorption bands for the probe groups reported many dramatic changes in the probes' local environments as CaM went from apo- to calcium-saturated to target peptide-bound conditions, including large frequency shifts and a variety of line shapes from narrow (interpreted as a rigid and invariant local environment) to symmetric to broad and asymmetric (likely from multiple coexisting and dynamically exchanging structures). The fast intrinsic time scale of infrared spectroscopy means that the line shapes report directly on site-specific details of calmodulin's variable structural distribution. Though quantitative interpretation of the probe line shapes depends on a direct connection between simulated ensembles and experimental data that does not yet exist, formation of such a connection to data such as that reported here would provide a new way to evaluate conformational ensembles from data that directly contains the structural distribution. The calmodulin probe sites developed here will also be useful in evaluating the binding mode of calmodulin with many uncharacterized regulatory targets.

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.

Microorganisms produce a wide range of natural products (NPs) with clinically and agriculturally relevant biological activities. In bacteria and fungi, genes encoding successive steps in a biosynthetic pathway tend to be clustered on the chromosome as biosynthetic gene clusters (BGCs). Historically, "activity-guided" approaches to NP discovery have focused on bioactivity screening of NPs produced by culturable microbes. In contrast, recent "genome mining" approaches first identify candidate BGCs, express these biosynthetic genes using synthetic biology methods, and finally test for the production of NPs. Fungal genome mining efforts and the exploration of novel sequence and NP space are limited, however, by the lack of a comprehensive catalog of BGCs encoding experimentally-validated products. In this study, we generated a comprehensive reference set of fungal NPs whose biosynthetic gene clusters are described in the published literature. To generate this dataset, we first identified NCBI records that included both a peer-reviewed article and an associated nucleotide record. We filtered these records by text and homology criteria to identify putative NP-related articles and BGCs. Next, we manually curated the resulting articles, chemical structures, and protein sequences. The resulting catalog contains 197 unique NP compounds covering several major classes of fungal NPs, including polyketides, non-ribosomal peptides, terpenoids, and alkaloids. The distribution of articles published per compound shows a bias toward the study of certain popular compounds, such as the aflatoxins. Phylogenetic analysis of biosynthetic genes suggests that much chemical and enzymatic diversity remains to be discovered in fungi. Our catalog was incorporated into the recently launched Minimum Information about Biosynthetic Gene cluster (MIBiG) repository to create the largest known set of fungal BGCs and associated NPs, a resource that we anticipate will guide future genome mining and synthetic biology efforts toward discovering novel fungal enzymes and metabolites.

Nonadditive Interactions Unlock Small-Particle Mobility in Binary Colloidal Monolayers.

We examine the organization and dynamics of binary colloidal monolayers composed of micron-scale silica particles interspersed with smaller-diameter silica particles that serve as minority component impurities. These binary monolayers are prepared at the surface of ionic liquid droplets over a range of size ratios (σ = 0.16-0.66) and are studied with low-dose minimally perturbative scanning electron microscopy (SEM). The high resolution of SEM imaging provides direct tracking of all particle coordinates over time, enabling a complete description of the microscopic state. In these bidisperse size mixtures, particle interactions are nonadditive because interfacial pinning to the droplet surface causes the equators of differently sized particles to lie in separate planes. By varying the size ratio, we control the extent of nonadditivity in order to achieve phase behavior inaccessible to additive 2D systems. Across the range of size ratios, we tune the system from a mobile small-particle phase (σ < 0.24) to an interstitial solid (0.24 < σ < 0.33) and furthermore to a disordered glass (σ > 0.33). These distinct phase regimes are classified through measurements of hexagonal ordering of the large-particle host lattice and the lattice's capacity for small-particle transport. Altogether, we explain these structural and dynamic trends by considering the combined influence of interparticle interactions and the colloidal packing geometry. Our measurements are reproduced in molecular dynamics simulations of 2D nonadditive disks, suggesting an efficient method for describing confined systems with reduced dimensionality representations.

Resolving Enhanced Mn2+ Luminescence near the Surface of CsPbCl3 with Time-Resolved Cathodoluminescence Imaging.

Mn2+ doping of lead halide perovskites has garnered recent interest because it produces stable orange luminescence in tandem with perovskite emission. Here, we observe enhanced Mn2+ luminescence at the edges of Mn2+-doped CsPbCl3 perovskite microplates and suggest an explanation for its origin using the high spatiotemporal resolution of time-resolved cathodoluminescence (TRCL) imaging. We reveal two luminescent decay components that we attribute to two different Mn2+ populations. While each component appears to be present both near the surface and in the bulk, the origin of the intensity variation stems from a higher proportion of the longer lifetime component near the perovskite surface. We suggest that this higher emission is caused by an increased probability of electron-hole recombination on Mn2+ near the perovskite surface due to an increased trap concentration there. This observation suggests that such surface features have yet untapped potential to enhance emissive properties via control of surface-to-volume ratio.

Noninvasive Cathodoluminescence-Activated Nanoimaging of Dynamic Processes in Liquids.

In situ electron microscopy provides remarkably high spatial resolution, yet electron beam irradiation often damages soft materials and perturbs dynamic processes, requiring samples to be very robust. Here, we instead noninvasively image the dynamics of metal and polymer nanoparticles in a liquid environment with subdiffraction resolution using cathodoluminescence-activated imaging by resonant energy transfer (CLAIRE). In CLAIRE, a free-standing scintillator film serves as a nanoscale optical excitation source when excited by a low energy, focused electron beam. We capture the nanoscale dynamics of these particles translating along and desorbing from the scintillator surface and demonstrate 50 ms frame acquisition and a range of imaging of at least 20 nm from the scintillator surface. Furthermore, in contrast with in situ electron microscopy, CLAIRE provides spectral selectivity instead of relying on scattering alone. We also demonstrate through quantitative modeling that the CLAIRE signal from metal nanoparticles is impacted by multiplasmonic mode interferences. Our findings demonstrate that CLAIRE is a promising, noninvasive approach for super-resolution imaging for soft and fluid materials with high spatial and temporal resolution.