On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme

Values of and order parameters derived from NMR relaxation measurements on proteins cannot be used straightforwardly to determine protein structure because they cannot be related to a single protein structure, but are defined in terms of an average over a conformational ensemble. Molecular dynamics simulation can generate a conformational ensemble and thus can be used to restrain and order parameters towards experimentally derived target values (exp) and (exp). Application of and order-parameter restraining MD simulation to bond vectors in 63 side chains of the protein hen egg white lysozyme using 51 (exp) target values and 28 (exp) target values shows that a conformational ensemble compatible with the experimentally derived data can be obtained by using this technique. It is observed that order-parameter restraining of C−H bonds in methyl groups is less reliable than order-parameter restraining because of the possibly less valid assumptions and approximations used to derive experimental (exp) values from NMR relaxation measurements and the necessity to adopt the assumption of uniform rotational motion of methyl C−H bonds around their symmetry axis and of the independence of these motions from each other. The restrained simulations demonstrate that side chains on the protein surface are highly dynamic. Any hydrogen bonds they form and that appear in any of four different crystal structures, are fluctuating with short lifetimes in solution.     

Stabilizing AqdC,a Pseudomonas Quinolone Signal-Cleaving Dioxygenase from Mycobacteria,by FRESCO-Based Protein Engineering

The mycobacterial PQS dioxygenase AqdC, a cofactor-less protein with an α/β-hydrolase fold, inactivates the virulence-associated quorum-sensing signal molecule 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) produced by the opportunistic pathogen Pseudomonas aeruginosa and is therefore a potential anti-virulence tool. We have used computational library design to predict stabilizing amino acid replacements in AqdC. While 57 out of 91 tested single substitutions throughout the protein led to stabilization, as judged by increases in of >2 °C, they all impaired catalytic activity. Combining substitutions, the proteins AqdC-G40K-A134L-G220D-Y238W and AqdC-G40K-G220D-Y238W showed extended half-lives and the best trade-off between stability and activity, with increases in of 11.8 and 6.1 °C and relative activities of 22 and 72 %, respectively, compared to AqdC. Molecular dynamics simulations and principal component analysis suggested that stabilized proteins are less flexible than AqdC, and the loss of catalytic activity likely correlates with an inability to effectively open the entrance to the active site.     

Probing the Substrate Requirements of the In Vitro Geranylation Activity of Selenouridine Synthase (SelU)

Natural RNA modifications diversify the structures and functions of existing nucleic acid building blocks. Geranyl is one of the most hydrophobic groups recently identified in bacterial tRNAs. Selenouridine synthase (SelU, also called mnmH) is an enzyme with a dual activity which catalyzes selenation and geranylation in tRNAs containing 2-thiouridine using selenophosphate or geranyl-pyrophosphate as cofactors. In this study, we explored the in vitro geranylation process of tRNA anticodon stem loops (ASL) mediated by SelU and showed that the geranylation activity was abolished when U₃₅ was mutated to A₃₅ (ASL-tRNA^Lys_(s2U)UU to ASL-tRNA^Ile_(s2U)AU). By examining the SelU cofactor geranyl-pyrophosphate (gePP) and its analogues, we found that only the geranyl group, but not dimethylallyl- and farnesyl-pyrophosphate with either shorter or longer terpene chains, could be incorporated into ASL. The degree of tRNA geranylation in the end-point analysis for SelU follows the order of ASL^Lys_(s2UUU) ASL^Gln_(s2UUG)>ASL^Glu_(s2UUC). These findings suggest a putative mechanism for substrate discrimination by SelU and reveal key factors that might influence its enzymatic activity. Given that SelU plays an important role in bacterial translation systems, inhibiting this enzyme and targeting its geranylation and selenation pathways could be exploited as a promising strategy to develop SelU-based antibiotics.     

The Sub-picomolar Cu2+ Dissociation Constant of Human Serum Albumin

The apparent affinity of human serum albumin (HSA) for divalent copper has long been the subject of great interest, due to its presumed role as the major Cu²⁺-binding ligand in blood and cerebrospinal fluid. Using a combination of electronic absorption, circular dichroism and room-temperature electron paramagnetic resonance spectroscopies, together with potentiometric titrations, we competed the tripeptide GGH against HSA to reveal a conditional binding constant of log ^c =13.02±0.05 at pH 7.4. This rigorously determined value of the Cu²⁺ affinity has important implications for understanding the extracellular distribution of copper.     

Sampling,Embedding and Inference for CARMA Processes

A CARMA(p,q) process Y is a strictly stationary solution Y of the pth‐order formal stochastic differential equation a(D)Y_t = b(D)DL_t, where L is a two‐sided Lévy process, a(z) and b(z) are polynomials of degrees p and q respectively, with p > q, and D denotes differentiation with respect to t. Since estimation of the coefficients of a(z) and b(z) is frequently based on observations of the Δ‐sampled sequence , for some Δ > 0, it is crucial to understand the relation between Y and Y^Δ. If then Y^Δ is an ARMA sequence with coefficients depending on those of Y and the crucial problems for estimation are the determination of the coefficients of Y^Δ from those of Y (the sampling problem) and the determination of the coefficients of Y from those of Y^Δ (the embedding problem). In this article we consider both questions and use the results to determine the asymptotic distribution, as n→∞, with Δ fixed, of , where is the quasi‐maximum‐likelihood estimator of the vector of coefficients of a(z) and b(z), based on n consecutive observations of Y^Δ.     

A Helix‐Stabilized Cell‐Penetrating Peptide as an Intracellular Delivery Tool

Two types of cationic cyclic α,α‐disubstituted α‐amino acids: Api (which possesses a lysine mimic side chain) and Api^C2Gu (which possesses an arginine mimic side chain), were developed. These amino acids were incorporated into an arginine‐based peptide sequence [(l ‐Arg‐l ‐Arg‐dAA)₃: dAA=Api or Api^C2Gu], and the relationship between the secondary structures of the resulting peptides and their ability to pass through cell membranes was investigated. The peptide containing Api^C2Gu formed a stable α‐helical structure and was more effective at penetrating cells than the nonhelical Arg nonapeptide (R₉). Furthermore, the peptide was able to deliver plasmid DNA into various types of cells in a highly efficient manner.     

Effect of Sodium Halide on Micellar and Surface Properties of Cationic Silicone Surfactants

The effect of sodium halide on aggregation behavior of four cationic silicone surfactants, Si₃mamCl, Si₄mamCl, Si₄PyCl, and Si₄minCl, in solution was investigated using surface tension and conductivity measurements. The ability of sodium halide (NaCl, NaBr, and NaI) to reduce critical micelle concentration (CMC) values was in the order NaI > NaBr > NaCl. However, the γ_CMC values of the cationic silicone surfactants, Si₄mamCl, Si₄PyCl and Si₄minCl, in sodium halide solution are almost the same as those of the salt-free system. The values of and are negative, indicating that the micellization process and adsorption of the four cationic silicone surfactants at the air-solution interface are spontaneous.     

Shear rheology and scaling of semiflexible polymers: Effect of polymer-solvent interactions in the semidilute regime

Semiflexible polymers and their assemblies are important in biology as cross-linked networks of semiflexible polymers form a major structural component of tissue and living cells. This research used shear rheology to demonstrate the tuning from worm-like to rod-like conformation in semiflexible polymers by polymer-solvent interactions. The conformation was assessed by the persistence length l_p, and its influence, in the semidilute regime, was assessed by the scaling of zero-shear viscosity η_o with concentration c and molecular weight . The polymers were poly n-butyl and poly n-octyl isocyanate (PBIC and POIC, respectively). PBIC exhibited the largest l_p in chlorinated solvents, and the solutions obeyed the scaling law . However, when PBIC was dissolved in benzene the l_p was greatly reduced and the scaling law now was , consistent with a worm-like conformation. On the other hand, POIC dissolved in chlorinated and benzenic solvents exhibited a worm-like conformation and the scaling was . These results were contrasted with those of hydroxypropyl cellulose (HPC) aqueous solutions, which exhibit worm-like conformation, the solutions obeyed the scaling η_o ∝ c^2.5 . Finally, the shear viscosity of the polyisocyanates and HPC obeyed the Saito scaling, valid for anisotropic particles in solution.     

Empirical models of trigonal distortions and polarization in perovskites

Correlative models derived from empirical relations describing synthesis-structure relationships are essential to guiding and improving future research and development of functional materials, yet few models exist for the prediction of structural distortions in perovskites. In this work, a data-mining approach has been employed to collect structural data for trigonally distorted perovskites in specific model systems. Correlative models were developed which describe the relationship between the c/a ratio and the ratio of the pseudocubic lattice constant (a_pc) to the B-X bond length (r_BX). General models were then created for the c/a ratio in terms of the modified tolerance factor for trigonal perovskites with symmetry and perovskite-like compounds with R3c symmetry. These models accurately predict the lattice constants in trigonally distorted perovskites and LiNbO₃ type perovskite-like compounds. In addition, a general model was developed, which accurately predicts polarization in trigonal LiNbO₃ type perovskite-like compounds in space group R3c.     

Image quality evaluation for high dynamic range and wide color gamut applications using visual spatial processing of color differences

High dynamic range (HDR) and wide color gamut imagery has an established video ecosystem, spanning image capture to encoding and display. This drives the need for evaluating how image quality is affected by the multitudes of ecosystem parameters. The simplest quality metrics evaluate color differences on a pixel‐by‐pixel basis. In this article, we evaluate a series of these color difference metrics on four HDR and three standard dynamic range publicly available distortion databases consisting of natural images and subjective scores. We compare the performance of the well‐established CIE L*a*b* metrics (ΔE₀₀ , ΔE₉₄ ) alongside two HDR‐specific metrics (ΔE_Z [J_za_zb_z], ΔE_ITP [IC_TC_P]) and a spatial CIE L*a*b* extension (). We also present a novel spatial extension to ΔE_ITP derived by optimizing the opponent color contrast sensitivity functions. We observe that this advanced metric, , outperforms the other color difference metrics, and we quantify the improved performance with the steps of metric advancement.     

Thermal Degradation of p-Hydroxybenzoic Acid in Macadamia Nut Oil,Olive Oil,and Corn Oil

p-Hydroxybenzoic acid (PHBA) plays a significant role in sustaining the oxidative stability of macadamia nut oil (MNO). However, PHBA undergoes thermal decarboxylation and loses its bioactive antioxidant properties. In this study, we determine PHBA degradation kinetics in oils at various heating temperatures, which provides fundamental understanding of PHBA thermal degradation in oils and oil quality changes during high-temperature processing. PHBA degradation kinetics in MNO, olive oil, and corn oil were evaluated at temperatures typical for cooking and frying. PBHA headspace concentration was measured using selected ion flow tube mass spectrometry. PHBA decarboxylation followed a zero-order reaction, where degradation could be affected by factors such as the type of oil matrix having different FA compositions, antioxidants, and component interactions. PHBA degradation activation energies (E _a) showed that PHBA was more stable against thermal decarboxylation in MNO (85 kJ mol^–1) than in olive oil (40 kJ mol⁻¹) or corn oil (22 kJ mol⁻¹). The higher enthalpy () of decarboxylation in MNO (82 kJ mol⁻¹) indicates that PHBA is more inhibited from decomposition than olive oil (37 kJ mol⁻¹) or corn oil (19 kJ mol⁻¹). Moreover, the negative entropy values () of PHBA degradation from MNO (−192 J mol⁻¹ K⁻¹), olive oil (−277 J mol⁻¹ K⁻¹), and corn oil (−325 J mol⁻¹ K⁻¹) indicates that these oils impart some inhibitory properties against PHBA thermal decarboxylation.     

Phase transition,microstructure and electrical properties of K1-xNaxNbO3-based ceramic sintered in reducing atmosphere

Lead-free 0.955K_1-xNa_xNbO₃-0.045Bi_0.5Na_0.5ZrO₃+0.4% mol MnO ceramics (Abbreviated as K_1-xN_xN-0.045BNZ+0.4Mn) were prepared by a conventional solid-state sintering method in a reducing atmosphere (oxygen partial pressure : 1 × 10⁻¹¹ MPa). All K_1-xN_xN-0.045BNZ+0.4Mn samples show a pure perovskite structure with a polymorphic phase boundary (PPB) composed of rhombohedral (R) and tetragonal (T) phases. A high Na/K ratio and a low Na/K ratio can both induce an increase in the rhombohedral phase. The reverse piezoelectric coefficient and its temperature stability in K_1-xN_xN-0.045BNZ+0.4Mn ceramics can be improved by controlling the Na/K ratio. The increase in the Na/K ratio from x = 0.46 to x = 0.56 can decrease the A-site cation vacancies. The activation energy of the grain is higher than that of the grain boundary due to the accumulation of oxygen vacancies at the grain boundary. K_1-xN_xN-0.045BNZ+0.4Mn ceramics with excellent piezoelectric properties (quasi-static piezoelectric coefficient d₃₃ = 326 pC/N, and  = 472 pm/V at E_max = 25 kV/cm) were obtained at x = 0.52.     

Giant electro-strain in textured Li+-doped 0.852BNT–0.11BKT–0.038BT ternary lead-free piezoelectric ceramics

Texturing is an effective approach to improving the piezoelectricity of piezoelectric ceramics. In this work, <001> textured Li⁺-doped 0.852Bi_0.5Na_0.5TiO₃–0.11Bi_0.5K_0.5TiO₃–0.038BaTiO₃ ternary lead-free piezoelectric ceramics are prepared by the reactive templates grain growth (RTGG) method. X-ray diffraction (XRD) results demonstrate a high orientation degree of 77% along the <001> direction. Outstanding electro-strain response, which is higher than most of reported BNT-based textured ceramics, is achieved due to the contribution of oriented-grains along the <001> direction. A large electro-strain of 0.55% with a relatively low hysteresis is obtained at 6.5 kV/mm with corresponding large signal piezoelectric coefficient () of 846 pm/V in the textured ceramics, which is 49% higher than that of the random ceramics. Besides, the electro-strain could reach as high as 0.52%@5.5 kV/mm ( = 945 pm/V) at 100°C. These results indicate that the RTGG is an effective way to design high performance lead-free piezoelectric materials.     

The liquid-gas mass transfer coefficient in open channel flow is correlated to the turbulent kinetic energy at the interface

Mass transfer coefficients at the gas-liquid interface were investigated for different flow configuration systems, a stirred tank reactor and a gravity pipe. Computational fluid dynamics (CFD) simulations were performed for all tested experimental conditions. Since a poorly soluble gas (oxygen) was used, the overall mass transfer coefficient was clearly correlated to the hydrodynamic conditions in the liquid phase. However, a generic correlation between averaged interfacial liquid velocity and mass transfer coefficients was not found for both geometries. Finally, the averaged turbulent kinetic energy (TKE) at the interface is the most relevant parameter that was correlated to the mass transfer coefficient for both systems. The same relationship between oxygen mass transfer coefficient K _L,O2 and TKE () can be applied for the two geometries investigated.     

Estimation of the critical properties of compounds using volume-based thermodynamics

The importance, yet scarcity of the critical constants of thermally unstable fluids warrants the development of reliable methods for the estimation of these essential thermodynamic properties. A thorough investigation undertaken in this study on 1,589 compounds belonging to 83 chemical classes, indicated that the ratio of critical temperature to critical pressure of both low and high molecular weight compounds could be well expressed in terms of their volumetric properties. In addition, two new methodologies are presented for estimating V_c, as well as an indirect approach for prediction of T_c from surface tension data, altogether allowing the calculation of Z_c. Moreover, comparative studies are made with five group contribution methods. It is also demonstrated that by employing the Peng-Robinson EOS, and without prior knowledge of the critical properties, it is possible to calculate various thermophysical properties including P^sat., T_b, , ∆H^vap. , C_p, and even the T_c and P_c themselves.     

Dynamics adsorption of the enhanced CH4 recovery by CO2 injection

The dynamic adsorption isotherms of CO₂-EGR were measured by using an Intelligent Gravimetric Analysis system. In the initial CO₂ injecting stage, all the injected CO₂ enters into the adsorbent and the mole fraction of CH₄ in the gas phase () is maintained at 1.0. The CH₄ recovery factor () increases. The duration of this stage (t_CD) depends on the selectivity of CO₂ over CH₄ (). An adsorbent with large has long t_CD. In the second stage, the injected CO₂ competes with CH₄ for adsorption. The cumulative of the second stage is much larger than that of the initial stage. However, decreases sharply. in the whole CO₂ injection is always larger than that before CO₂ injection, suggesting that CH₄ desorption results from the displacement of CO₂ rather than from pressure depletion.     

Temperature Comparative Studies on Self-Assembly of Sodium Dodecyl Sulphate and Didodecyl Dimethyl Ammonium Bromide in Aqueous,Brine, and Trifluoroethanol Media

An approach based on experimental and theoretical methods was used to compare the self-assembly [i.e., determination of the critical micelle concentration (CMC), degree of ionization (α) and counterion binding (β)] of sodium dodecyl sulfate (SDS) and didodecyl dimethyl ammonium bromide (DDAB) in deionized water and 10 mM NaCl and 10 (vol) % trifluoroethanol solutions. Experimental methods consisted of electrical conductometry, tensiometry, fluorimetry, and determination of Krafft temperature. A critical analysis of the thermodynamics of self-assembly by the Gibbs–Helmholtz equation and the van't-Hoff rationale provided values of several parameters, such as the change of Gibbs free energy and enthalpy change of micellization ( and , respectively) and the Gibbs free energy of surfactant tail groups (∆G⁰_trans). Interfacial properties, aggregation number (N_agg), micropolarity (I₁/I₃), microviscosity (η), packing parameter (P), dielectric constant (D), anisotropy (r), and Stern–Volmer binding constant (K_SV) for SDS and DDAB in different temperatures and different systems were determined.     

Gatifloxacin–Ionic Surfactant Interactions: Volumetric,Acoustic, Voltammetric,and Spectroscopic Studies

Surfactant systems have been frequently used as pseudomodels for investigating interactions of drugs with biological membranes because of their structural similarities with the latter. This helps to understand complicated yet very important biological processes like diffusion of bioactive moieties through biomembranes. The current study deals with voltammetric and spectroscopic studies to evaluate the interaction of a potential antibacterial drug, gatifloxacin (GTF), with a cationic surfactant, dodecyltrimethylammonium bromide (DTAB), and an anionic surfactant, sodium dodecyl sulfate (SDS), under physiological conditions (phosphate buffer, pH 7.4). For more detailed insight into the GTF–ionic surfactant interactions, density and acoustic data were also recorded and used to calculate several important parameters, namely, apparent molar volume (ɸ_V ), isentropic compressibility (K_s ), and apparent molar isentropic compressibility (ɸ_K ) at T = 298.15, 303.15, 308.15, and 313.15 K. Values for partial molar volume (, partial molar expansivity , specific acoustic impedance (Z), relative association (RA), intermolecular free length (L_f), and sound velocity number (U) were also obtained. The interpretation of the concentration dependence of the above-mentioned quantities using a cosphere overlap model led to a better apprehension of solute–solute and solute–solvent intermolecular interactions present in the investigated system, whereas cyclic voltammetry and ultra violet (UV)–visible spectroscopic studies assisted in predicting the location of adsorbed GTF molecules within the DTAB and SDS micelles.     

Cycling- and heating-induced evolution of piezoelectric and ferroelectric properties of CuO-doped K0.5Na0.5NbO3 ceramic

For accepter-doped perovskite piezoelectric ceramics, macroscopic properties of the materials (eg, hardening, fatigue, and aging) are closely related to microscopic characteristics (eg, oxygen vacancies and defect dipoles). In this work, the relationship of macroscopic and microscopic characteristics in CuO-doped K_0.5Na_0.5NbO₃ (KNN) ceramic has been studied by subjecting the material to electric field cycling, quenching, heating, and consequently aging. The introduction of CuO in KNN generates and . The defect dipoles exhibit obviously the pinning effect on ferroelectric domains and thus induce a completely pinched/double P-E loop and excellent hardening piezoelectricity of high Q_m of 2235. With the destruction of short-range symmetry uniformity between defect dipoles and ferroelectric dipoles induced by electric field cycling, quenching and heating, the ceramic can be depinned and softened. As a result, the depinned ceramic possesses an opened single ferroelectric hysteresis loop and the significantly decreasing Q_m. A distinctive aging is observed in the depinned ceramic. This study provides deep insights into the evolution of electrical properties of accepter-modified alkali niobate perovskite ceramics under electric field cycling, quenching, and heating.     

Estolide Molecular Weight Distribution via Gel Permeation Chromatography

Using the universal calibration and the Mark-Houwink equation (MHE) (), three batches of oleic estolide acids and their corresponding 2-ethylhexyl esters were characterized using gel permeation chromatography (GPC). The MHE parameters in tetrahydrofuran (THF) at 40 °C were determined (for acids: α = 0.442 ± 0.003 and log₁₀K =2.505 ± 0.007, for esters: α =0.531 ± 0.006 and log₁₀K =2.794 ± 0.018). The fits of the GPC chromatograms yielded also the oligomeric composition of the estolides, which can be used to calculate the estolide number (EN) of an estolide mixture, and other molecular-weight distribution parameters, such as number-average molecular weight (M_n ), weight-average molecular weight (M_w ), and dispersity (Ð). Using the Deming line fit, we concluded that the GPC should be expected to be approximately three times more sensitive than the currently used methods for determination of EN values.