Gold Nanorod Plasmonic Upconversion Microlaser

Plasmonic–photonic interactions have stimulated significant interdisciplinary interest, leading to rapid innovations in solar design and biosensors. However, the development of an optically pumped plasmonic laser has failed to keep pace due to the difficulty of integrating a plasmonic gain material with a suitable pump source. In the present work, we develop a method for coating high quality factor toroidal optical cavities with gold nanorods, forming a photonic–plasmonic laser. By leveraging the two-photon upconversion capability of the nanorods, lasing at 581 nm with a 20 μW threshold is demonstrated

Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations

<div><p>Sampling enrichment toward a target state, an analogue of the improvement of sampling efficiency (SE), is critical in both the refinement of protein structures and the generation of near-native structure ensembles for the exploration of structure-function relationships. We developed a hybrid molecular dynamics (MD)-Monte Carlo (MC) approach to enrich the sampling toward the target structures. In this approach, the higher SE is achieved by perturbing the conventional MD simulations with a MC structure-acceptance judgment, which is based on the coincidence degree of small angle x-ray scattering (SAXS) intensity profiles between the simulation structures and the target structure. We found that the hybrid simulations could significantly improve SE by making the top-ranked models much closer to the target structures both in the secondary and tertiary structures. Specifically, for the 20 mono-residue peptides, when the initial structures had the root-mean-squared deviation (RMSD) from the target structure smaller than 7 Å, the hybrid MD-MC simulations afforded, on average, 0.83 Å and 1.73 Å in RMSD closer to the target than the parallel MD simulations at 310K and 370K, respectively. Meanwhile, the average SE values are also increased by 13.2% and 15.7%. The enrichment of sampling becomes more significant when the target states are gradually detectable in the MD-MC simulations in comparison with the parallel MD simulations, and provide >200% improvement in SE. We also performed a test of the hybrid MD-MC approach in the real protein system, the results showed that the SE for 3 out of 5 real proteins are improved. Overall, this work presents an efficient way of utilizing solution SAXS to improve protein structure prediction and refinement, as well as the generation of near native structures for function annotation.</p></div

Kafirin Protein Based Electrospun Fibers with Tunable Mechanical Property, Wettability, and Release Profile

Kafirin (KAF), the prolamine protein from sorghum grain, is a promising resource for fabricating renewable and biodegradable materials. However, research efforts in fulfilling its potentials are still lacking. In this work, electrospun kafirin fibers from acetic acid/dichloromethane solutions are reported for the first time. Biodegradable polycaprolactone (PCL) was blended with kafirin to obtain hybrid KAF/PCL fiber mats with desirable physical properties. Hydrogen bonding between the NH group of kafirin and the CO group of PCL was detected in each blended formulation. Our small-angle X-ray scattering results indicated that the long spacing decreased and the average spacing between crystalline lamellae of PCL increased with the increase of kafirin content. Compared to the hydrophobic surface of neat PCL fiber mat, KAF/PCL fiber mats under most of the blend ratios showed hydrophilic surface character, and the swelling property was composition-dependent. The fiber mats evolved from brittle ones to flexible ones with the increase of relative content of PCL. The most desirable mechanical performance was obtained at a kafirin/PCL mass blend ratio of 1:2. To simulate the nutraceutical release in body fluid, carnosic acid (CA) was selected as a nutraceutical model, and release behaviors in selected KAF/PCL fiber mats were found to be diffusion controlled. Whereas the amorphous region of kafirin dominated the release rate, PCL functioned as a hydrophobic skeleton to maintain the 3D scaffold of the fiber matrix. The fabricated KAF/PCL fiber mats open up new applications of underutilized cereal protein in nutraceutical delivery

Structural and SAXS profiles comparison among initial (green), target (blue) and simulation (red) structures for ubiquitin and cytochrome C using experimental target SAXS profiles.

<p>The calculated SAXS profiles are the average of all 1,250 conformations in the last 5 ns of hybrid MD-MC simulations.</p

The ratio R₂/R₁, dRMSD_T and dSE for the five representative trajectories shown in Fig 8.

<p>The ratio R₂/R₁, dRMSD_T and dSE for the five representative trajectories shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156043#pone.0156043.g008" target="_blank">Fig 8</a>.</p

The schematic flowchart of simulations in this work.

<p>The schematic flowchart of simulations in this work.</p

Sampling performance of the MD-MC method in five representative trajectories.

<p>The time evolution of RMSD_T for MD-MC (solid line) and MD (dash line), the time evolution of χ_T, as well as 3D structures and SAXS profiles of the initial (I), the target (T) and closest (C) structures for trajectories of Poly-Asn, Poly-Phe, Poly-Pro, Poly-Ala and Poly-Ser are presented.</p

Sampling efficiency as a function of R₂/R₁ and R₁.

<p>The number of trajectories, the mean of R₂, R₁ and SE are calculated based on 180 trajectories in the backward MD and MD-MC simulations at 370K. Here, R₂ is the sampling range in simulations, R₁ is RMSD between the initial structure and the target structure, SE is the sampling efficiency of a simulation trajectory and the calculated values by Reva’s model are listed in following brackets.</p

Comparison of RMSD_T, fractions of secondary structures and sampling efficiency in the backward simulations.

<p>Three parameters are calculated from 370K backward simulations against simulation time, for RMSD_T (a), fractions of accordant secondary structures to their targets (b) and the actual mean SE (c). The solid symbols are from the hybrid MD-MC simulations, and the empty symbols are those from the parallel MD simulations. The square, circle and triangle present the target with sheet, helix and coil secondary structures, respectively.</p

Characterization of AusA: A Dimodular Nonribosomal Peptide Synthetase Responsible for the Production of Aureusimine Pyrazinones

Aureusimines have been identified as potential virulence factors in <i>Staphylococcus aureus</i>. These pyrazinone secondary metabolites are produced by a nonribosomal peptide synthetase (NRPS) annotated as AusA. We report the overproduction of AusA as a 277 kDa soluble protein with A₁–T₁–C–A₂–T₂–R bimodular architecture. The substrate specificity of each adenylation (A) domain was initially probed using an ATP–pyrophosphate exchange assay with A-domain selective bisubstrate inhibitors to chemically knock out each companion A-domain. The activity of AusA was then reconstituted in vitro and shown to produce all naturally occurring aureusimines and non-natural pyrazinone products with <i>k</i>_cat values ranging from 0.4 to 1.3 min^–1. Steady-state kinetic parameters were determined for all substrates and cofactors, providing the first comprehensive steady-state characterization of a NRPS employing a product formation assay. The <i>K</i>_M values for the amino acids were up to 60-fold lower with the product formation assay than with the ATP–pyrophosphate exchange assay, most commonly used to assess A-domain substrate specificity. The C-terminal reductase (R) domain catalyzes reductive release of the dipeptidyl intermediate, leading to formation of an amino aldehyde that cyclizes to a dihydropyrazinone. We show oxidation to the final pyrazinone heterocycle is spontaneous. The activity and specificity of the R-domain was independently investigated using a NADPH consumption assay. AusA is a minimal autonomous two-module NRPS that represents an excellent model system for further kinetic and structural characterization