AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes.     

Chemical and Mechanical Characterization of Licorice Root and Palm Leaf Waste Incorporated into Poly(urethane-acrylate) (PUA)

A poly(urethane-acrylate) polymer (PUA) was synthesized, and a sufficiently high molecular weight starting from urethane-acrylate oligomer (UAO) was obtained. PUA was then loaded with two types of powdered ligno-cellulosic waste, namely from licorice root and palm leaf, in amounts of 1, 5 and 10%, and the obtained composites were chemically and mechanically characterized. FTIR analysis of final PUA synthesized used for the composite production confirmed the new bonds formed during the polymerization process. The degradation temperatures of the two types of waste used were in line with what observed in most common natural fibers with an onset at 270 °C for licorice waste, and at 290 °C for palm leaf one. The former was more abundant in cellulose (44% vs. 12% lignin), whilst the latter was richer in lignin (30% vs. 26% cellulose). In the composites, only a limited reduction of degradation temperature was observed for palm leaf waste addition and some dispersion issues are observed for licorice root, leading to fluctuating results. Tensile performance of the composites indicates some reduction with respect to the pure polymer in terms of tensile strength, though stabilizing between data with 5 and 10% filler. In contrast, Shore A hardness of both composites slightly increases with higher filler content, while in stiffness-driven applications licorice-based composites showed potential due to an increase up to 50% compared to neat PUA. In general terms, the fracture surfaces tend to become rougher with filler introduction, which indicates the need for optimizing interfacial adhesion.     

Ultrasound-Assisted Microencapsulation of Soybean Oil and Vitamin D Using Bare Glycogen Nanoparticles

Ultrasonically synthesized core-shell microcapsules can be made of synthetic polymers or natural biopolymers, such as proteins and polysaccharides, and have found applications in food, drug delivery and cosmetics. This study reports on the ultrasonic synthesis of microcapsules using unmodified (natural) and biodegradable glycogen nanoparticles derived from various sources, such as rabbit and bovine liver, oyster and sweet corn, for the encapsulation of soybean oil and vitamin D. Depending on their source, glycogen nanoparticles exhibited differences in size and ‘bound’ proteins. We optimized various synthetic parameters, such as ultrasonic power, time and concentration of glycogens and the oil phase to obtain stable core-shell microcapsules. Particularly, under ultrasound-induced emulsification conditions (sonication time 45 s and sonication power 160 W), native glycogens formed microcapsules with diameter between 0.3 μm and 8 μm. It was found that the size of glycogen as well as the protein component play an important role in stabilizing the Pickering emulsion and the microcapsules shell. This study highlights that native glycogen nanoparticles without any further tedious chemical modification steps can be successfully used for the encapsulation of nutrients.     

Electrochemically controlled formation/dissociation of phosphonate-cavitand/methylpyridinium complexes

The phosphorus-bridged cavitand 1 self-assembles very efficiently in CH2Cl2 with either the monopyridinium guest 2+ or the bispyridinium guest 3(2+). In the first case a 1:1 complex is obtained, whereas in the second case both 1:1 and 2:1 host-guest complexes are observed. The association between 1 and either one of the guests causes the quenching of the cavitand fluorescence; in the case of the adduct between 1 and 3(2+), the fluorescence of the latter is also quenched. Cavitand complexation is found to affect the reduction potential values of the electroactive guests. Voltammetric and spectroelectrochemical measurements show that upon one-electron reduction both guests are released from the cavity of 1. Owing to the chemical reversibility of such redox processes, the supramolecular complexes can be re-assembled upon removal of the extra electron from the guest. Systems of this kind are promising for the construction of switchable nanoscale devices and self-assembling supramolecular materials, the structure and properties of which can be reversibly controlled by electrochemical stimuli.     

Experimental and Theoretical Study of Helium Broadening and Shift of HCO+ Rotational Lines

An experimental and theoretical study of pressure broadening and pressure shift of HCO⁺ rotational lines perturbed by collisions with He is presented. Results are reported from measurements at 88 K for the lines j=4←3, 5←4 and 6←5 with frequencies ranging from 0.35 to 0.54 THz. Using a new CCSD(T)/aug‐cc‐pVQZ potential energy surface for the He–HCO⁺ interaction, the collisional line shape parameters are studied from fully quantum and semiclassical calculations. Results from the quantum treatment are in satisfactory agreement with experiments whereas the semiclassical approach can lead to appreciable differences. A study of the dependence of line width Γ and shift s as a function of the translational energy shows the presence of quantum oscillations. Calculations on a previous Hartree–Fock‐based potential energy surface lead to quite similar results for the collisional line shape parameters. Using a simplified version of the potential morphing method it is found that the line width Γ is particularly sensitive to the long‐range part of the potential energy surface. This also explains the success of the first line‐broadening calculations which date back to the 1950s.     

Cooperativity as quantification and optimization paradigm for nuclear receptor modulators

Nuclear Receptors (NRs) are highly relevant drug targets, for which small molecule modulation goes beyond a simple ligand/receptor interaction. NR–ligands modulate Protein–Protein Interactions (PPIs) with coregulator proteins. Here we bring forward a cooperativity mechanism for small molecule modulation of NR PPIs, using the Peroxisome Proliferator Activated Receptor γ (PPARγ), which describes NR–ligands as allosteric molecular glues. The cooperativity framework uses a thermodynamic model based on three-body binding events, to dissect and quantify reciprocal effects of NR–coregulator binding (K^I_D) and NR–ligand binding (K^II_D), jointly recapitulated in the cooperativity factor (α) for each specific ternary ligand·NR·coregulator complex formation. These fundamental thermodynamic parameters allow for a conceptually new way of thinking about structure–activity-relationships for NR–ligands and can steer NR modulator discovery and optimization via a completely novel approach.

A cooperativity framework describes the formation of nuclear receptor ternary complexes and deconvolutes ligand and cofactor binding into intrinsic affinities and a cooperativity factor, providing a conceptually new understanding of NR modulation.     

Ultrasonic synthesis of stable, functional lysozyme microbubbles

High-intensity ultrasound induces emulsification and cross-linking of protein molecules in aqueous medium. The stability and the functionality of the resultant protein-coated microbubbles are crucial in many of their applications. For example, the stability of drug-loaded microbubbles should be sufficiently long enough, in vivo, so that they can be ruptured only at specific sites for release of the drugs. In this study, we report the synthesis of stable and functional microbubbles, coated with chemically reduced lysozyme, using high-intensity ultrasound in aqueous solution. In the absence of chemical reduction, stable microbubbles were not produced with native lysozyme, indicating the importance of free -SH functional groups for protein cross-linking. The degree of cross-linking between lysozyme molecules was controlled by manipulating both the extent of chemical reduction of the intramolecular disulfide bonds and sonication time. The lysozyme-coated microbubbles are stable for several months and retain the enzymatic (antimicrobial) activity of lysozyme. The layer-by-layer (LbL) deposition of polyelectrolytes onto the protein-shell air-core template has been used as a versatile procedure to modify the surface properties of the microbubbles, indicating the possibility of adsorbing potential drugs and/or biolabels on the surface of these microbubbles for therapeutic and diagnostic applications.     

Determination of aflatoxins in hazelnuts by various sample preparation methods and liquid chromatography-tandem mass spectrometry

A sensitive and reliable liquid chromatography-tandem mass spectrometric with electrospray ionization method for determining aflatoxins in hazelnuts has been developed. Three different extraction techniques, such as homogenization, ultrasonic extraction, and matrix solid phase dispersion have been tested and compared in terms of recovery, matrix effect, accuracy and precision. Ultrasound extraction was the most performing sample preparation method. Absolute recoveries for analytes and I.S. ranged from 93 to 101%. Accuracy and precision were calculated using matrix matched calibration, and ranged 91-102% and 2-11%, respectively. CC alpha and CC beta for aflatoxin B1 (EU limit=2 microg/kg) were 2.15 and 2.33 microg/kg, respectively. A ruggedness test performed on three other matrices demonstrated that sonication time was critical and a matrix matched calibration must be constructed for every sort of matrix.