Hydrogels obtained by acidification with glucono-δ-lactone (GDL), starting from nanoemulsions formulated with different concentrations of sodium caseinate (1–4 wt%) or 4 wt% sodium caseinate and ...sucrose (2–8 wt%), were prepared with the aim of quantifying structural parameters of both, initial nanoemulsions and hydrogels after 2.5 h of GDL addition, using the Guinier-Porod (GP) or the generalized GP models. Gelation process was followed by performing in situ temperature-controlled X-ray small angle scattering experiments (SAXS) using synchrotron radiation. In nanoemulsions, the calculated radius of gyration for oil nanodroplets (Rgoil) decreased with increasing protein concentration and for the 4 wt% protein nanoemulsion, with increasing sucrose content. Calculated values of Rgoil were validated correlating them with experimental Z-average values as measured by dynamic light scattering (DLS). For hydrogels, radii of gyration for the sphere equivalent to the hydrogel scattering object (Rgsph) were close to 3 nm while correlation distances among building blocks (Rg2) were dependent on formulation. They increased with increasing contents of sodium caseinate and sucrose. Rg2 parameter linearly correlated with hydrogel strength (G’∞): a more connected nanostructure led to a stronger hydrogel.
Display omitted
•Nanodroplets gyration ratio decreased with increasing protein and sucrose contents•Nanodroplets coverage increased with increasing protein and sucrose contents•Building blocks gyration ratio of gels were independent on composition•Building blocks correlation distances were significantly affected by composition•Rg2 distances correlated with asymptotic values of G’ (G’∞)
Understanding the biological activities of riboswitches and of RNA in general requires a thorough analysis of both the spatial arrangement of the residues and the dynamics of the structural ensemble. ...Specifically, evaluating the structural basis for riboswitch function requires analyses of many relevant states that include ligand-bound and -free, high Mg(2+), and quite possibly, the active transcription state, which is challenging to achieve by most methods. Small angle X-ray scattering (SAXS) is an enabling technique for comprehensive analyses of RNA structures in solution. Here, we describe recent SAXS tools and technologies that substantially improve the potential for accurate and comprehensive analyses of flexibility, unstructured elements, conformational selection, and induced fit in RNA function. We note equipment needed plus appropriate annealing and purification procedures. We describe key model-independent parameters (SAXS invariants) which can be used to monitor changes in a particle's thermodynamic state: the Guinier-based Rg, the volume-of-correlation (Vc), the Porod-Debye exponent (P(E)), and the power-law parameter, Q(R), that determines mass directly from the SAXS data. We also consider the value of real-space parameters and of multiphase modeling with MONSA to locate secondary structure elements within SAXS volumetric envelopes. For conformation changes, experiments with nanogold-labeled RNA analyzed using the SAXS structural comparison map and volatility ratio difference metric enable high-throughput evaluation of solution-state conformations. Collectively, the described tools and procedures enable quantitative and comprehensive measures of riboswitch structures with general implications for our views and strategies of RNA structural analysis.
Small angle scattering is frequently applied to study the anisotropy in complex soft matter systems. One emerging application is to probe the multi-scale structure in food matrices; while few models ...are available to describe the anisotropic scattering pattern in a quantitative, yet simple manner. For this purpose, anisotropy is introduced to the Guinier–Porod model to study the scattering from non-spherical objects with a preferred orientation. This generalised anisotropic Guinier–Porod model can be adapted to approximate the sector scattering from both cylinders and ellipsoids (both prolate and oblate). In practice, it is applied to describe the anisotropic scattering from fibres in a meat analogue made of calcium caseinate. A good agreement is found between fitted dimensions of the fibres and those observed from the microscopy image. The effect of orientation distribution on the shape and intensity of the scattering pattern is further discussed and three means to obtain the orientation distribution of the symmetry axis are proposed. Given the model is straightforward and the fitting remains phenomenological, it provides a novel approach to extract information from complex food systems.
Display omitted
•Anisotropy is introduced to the Guinier Porod model.•The model describes the small angle scattering from non-spherical objects with preferred orientation.•The model can study the anisotropic small angle scattering from fibres in a meat analogue.
Small angle neutron scattering (SANS) responses of particulate silica as disordered and ordered porous and non-porous powders were obtained. Each classification provided distinct scattering patterns ...which were fitted and analysed using Guinier-Porod and mass-surface fractal (msf) models. The resulting particle dimensions showed good agreement with the same from nitrogen gas adsorption analyses. Additionally, the excellent fit of the msf model to the non-porous silica scattering response resulted in an agreement between the mass and surface fractal dimension values for it and similar analyses and results published previously for fumed silica. The msf fitting gave additional insight into particle and cluster scattering dimensions with particle dimensions being consistent with those from the G-P analyses.
Display omitted
•Small angle neutron scattering analyses of powdered silica.•Ordered, disordered, and nonporous silica scattering effects identified.•Particle and scattering entity dimensions defined and equated.•Fractal analysis provides insight into surface roughness.•Combined standard uncertainty defined for each derived variable.
U Državnim arhivima u Zadru i Dubrovniku čuvaju se obiteljske memorabilije i rukopisna građa na temelju kojih se rekonstruira životopis Marije Natali Zamagna (1807-1891). Njegov tijek otkriva životni ...prostor žene u 19. stoljeću ispunjen majčinskim i obiteljskim poslanjem u duhu običaja i pravila vremena. Propitivanjem različitih aspekata uloge žene i njezina statusa unutar obiteljskih i društvenih odnosa, iščitava se povijest žene i njezina mentaliteta, strategije braka i majčinstva.
The freely rotating chain is one of the classic discrete models of a polymer in dilute solution. It consists of a broken line of
N
straight segments of fixed length such that the angle between ...adjacent segments is constant and the
N
-
1
torsional angles are independent, identically distributed, uniform random variables. We provide a rigorous proof of a folklore result in the chemical physics literature stating that under an appropriate scaling, as
N
→
∞
, the freely rotating chain converges to a random curve defined by the property that its derivative with respect to arclength is a Brownian motion on the unit sphere. This is the Kratky-Porod model of semi-flexible polymers. We also investigate limits of the model when a stiffness parameter, called the persistence length, tends to zero or infinity. The main idea is to introduce orthogonal frames adapted to the polymer and to express conformational changes in the polymer in terms of stochastic equations for the rotation of these frames.
To accurately model double-stranded DNA in a manner that is computationally efficient, coarse-grained models of DNA are introduced, where model parameters are selected by fitting the spectrum of ...observable DNA knots: We develop a general method to fit free parameters of coarse-grained chain models by comparing experimentally obtained knotting probabilities of short DNA chains to knotting probabilities that are computed in Monte Carlo simulations, resulting in coarse-grained DNA models which are tailored to reflect DNA topology in the best possible way. The method is exemplified by fitting ideal chain models as well as a bead-spring model with excluded volume interactions, to model double-stranded DNA for physiological as well as for high salt concentrations. The resulting coarse-grained DNA models predict the correct persistence length and effective diameter of double-stranded DNA, and can in principle be used for dynamical investigations using Molecular Dynamics. Our modelling ansatz thus provides a blueprint for building coarse-grained models of polymers, which are solely based on knotting spectra.
We analyzed the structure of horseradish peroxidase (HRP) under denaturing conditions of 9 M urea or 6 M guanidine hydrochloride (GdnHCl). Far-UV circular dichroism (CD) spectra indicated the ...existence of native-like secondary structure of holo-HRP in 9 M urea. In addition, slight changes in near-UV and Soret region CD spectra of holo-HRP in 9 M urea suggest that the tertiary structure of holo-HRP and the binding of heme remain partially intact in this condition. A transition in the thermal unfolding transition curve of holo-HRP in 9 M urea indicated the existence of a considerable amount of secondary structure. However, no secondary structure, tertiary structure, or interaction between heme and HRP were observed in holo-HRP in 6 M GdnHCl. Small-angle X-ray scattering indicated that although distal and proximal domains of holo-HRP in 9 M urea might be partially unfolded, the central region that contains the heme might maintain its tertiary structure. Our results suggest that retention of the heme is essential for maintenance of the structure of HRP under highly denaturing conditions.
PDF
