SEDNTERP: a calculation and database utility to aid interpretation of analytical ultracentrifugation and light scattering data

Proper interpretation of analytical ultracentrifugation (AUC) data for purified proteins requires ancillary information and calculations to account for factors such as buoyancy, buffer viscosity, hydration, and temperature. The utility program SEDNTERP has been widely used by the AUC community for this purpose since its introduction in the mid-1990s. Recent extensions to this program (1) allow it to incorporate data from diffusion as well as AUC experiments; and (2) allow it to calculate the refractive index of buffer solutions (based on the solute composition of the buffer), as well as the specific refractive increment (dn/dc) of proteins based on their composition. These two extensions should be quite useful to the light scattering community as well as helpful for AUC users. The latest version also adds new terms to the partial specific volume calculations which should improve the accuracy, particularly for smaller proteins and peptides, and can calculate the viscosity of buffers containing heavy isotopes of water. It also uses newer, more accurate equations for the density of water and for the hydrodynamic properties of rods and disks. This article will summarize and review all the equations used in the current program version and the scientific background behind them. It will tabulate the values used to calculate the partial specific volume and dn/dc, as well as the polynomial coefficients used in calculating the buffer density and viscosity (most of which have not been previously published), as well as the new ones used in calculating the buffer refractive index.

Quantifying the concentration dependence of sedimentation coefficients for globular macromolecules: a continuing age-old problem

This retrospective investigation has established that the early theoretical attempts to directly incorporate the consequences of radial dilution into expressions for variation of the sedimentation coefficient as a function of the loading concentration in sedimentation velocity experiments require concentration distributions exhibiting far greater precision than that achieved by the optical systems of past and current analytical ultracentrifuges. In terms of current methods of sedimentation coefficient measurement, until such improvement is made, the simplest procedure for quantifying linear s-c dependence (or linear concentration dependence of 1/s) for dilute systems therefore entails consideration of the sedimentation coefficient obtained by standard c(s), g*(s) or G(s) analysis) as an average parameter (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \overline{s} $$\end{document}s¯) that pertains to the corresponding mean plateau concentration (following radial dilution) (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \overline{c} $$\end{document}c¯) over the range of sedimentation velocity distributions used for the determination of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \overline{s} $$\end{document}s¯. The relation of this with current descriptions of the concentration dependence of the sedimentation and translational diffusion coefficients is considered, together with a suggestion for the necessary improvement in the optical system.

Sedimentation Velocity Methods for the Characterization of Protein Heterogeneity and Protein Affinity Interactions

Sedimentation velocity analytical ultracentrifugation is a powerful and versatile tool for the characterization of proteins and macromolecular complexes in solution. The direct modeling of the sedimentation process using modern computational strategies allows among others to assess the homogeneity/heterogeneity state of protein samples and to characterize protein associations. In this chapter, we will provide theoretical backgrounds and protocols to analyze the size distribution of protein samples and to determine the affinity of protein-protein hetero-associations.

Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs

Analytical ultracentrifugation (AUC) has emerged as a robust and reliable technique for biomolecular characterization with extraordinary sensitivity. AUC is widely used to study purity, conformational changes, biomolecular interactions, and stoichiometry. Furthermore, AUC is used to determine the molecular weight of biomolecules such as proteins, carbohydrates, and DNA and RNA. Due to the multifaceted role(s) of non-coding RNAs from viruses, prokaryotes, and eukaryotes, research aimed at understanding the structure-function relationships of non-coding RNAs is rapidly increasing. However, due to their large size, flexibility, complicated secondary structures, and conformations, structural studies of non-coding RNAs are challenging. In this review, we are summarizing the application of AUC to evaluate the homogeneity, interactions, and conformational changes of non-coding RNAs from adenovirus as well as from Murray Valley, Powassan, and West Nile viruses. We also discuss the application of AUC to characterize eukaryotic long non-coding RNAs, Xist, and HOTAIR. These examples highlight the significant role AUC can play in facilitating the structural determination of non-coding RNAs and their complexes.

A comparison of data quality using quartz vs. sapphire cell windows in analytical ultracentrifugation

Analytical ultracentrifugation (AUC) cells use either quartz or sapphire windows as end caps for the cell housing. Current generation sapphire windows are not recommended for absorbance data collection below 235 nm, because the window material shows a precipitous drop in transmittance at low wavelengths due to impurities in the sapphire. Quartz windows can be used below 235 nm as they do not exhibit adverse transmittance at low wavelengths. In this study, we demonstrate the optical properties of new generation sapphire windows and compare them to those of quartz windows across a wide range of wavelengths and present the results of sedimentation velocity experiments on BSA using both types of windows using data collected at both the 280 nm absorbance maxima as well as the 230-240 nm (closer to the peptide bond maximum). Our results show that the quartz and new generation sapphire windows deliver identical results in absorbance mode. We also demonstrate that quartz windows suffer significant mechanical deformation while spinning at very high speeds, while sapphire windows do not. This renders Rayleigh interference mode data collected at high speeds using quartz windows much noisier than with sapphire windows-which we have quantified by measuring how the signal to noise ratio of Fourier transformed Rayleigh interference scans degrades at high speed. Thus, we conclude that new-generation sapphire windows can be used for all AUC experiments through almost the entire mid UV range-obviating the need for quartz windows, unless wavelengths below 220 nm must be accessed.

Asp isomerization increases aggregation of α-crystallin and decreases its chaperone activity in human lens of various ages

α-Crystallin, comprising 40-50 subunits of αA- and αB-subunits, is a long-lived major soluble chaperone protein in lens. During aging, α-crystallin forms aggregates of high molecular weight (HMW) protein and eventually becomes water-insoluble (WI). Isomerization of Asp in α-crystallin has been proposed as a trigger of protein aggregation, ultimately leading to cataract formation. Here, we have investigated the relationship between protein aggregation and Asp isomerization of αA-crystallin by a series of analyses of the soluble α-crystallin, HMW and WI fractions from human lens samples of different ages (10-76 years). Analytical ultracentrifugation showed that the HMW fraction had a peak sedimentation coefficient of 40 S and a wide distribution of values (10-450 S) for lens of all ages, whereas the α-crystallin had a much smaller peak sedimentation coefficient (10-20 S) and was less heterogeneous, regardless of lens age. Measurement of the ratio of isomers (Lα-, Lβ-, Dα-, Dβ-) at Asp58, Asp91/92 and Asp151 in αA-crystallin by liquid chromatography-mass spectrometry showed that the proportion of isomers at all three sites increased in order of aggregation level (α-crystallin < HMW < WI fractions). Among the abnormal isomers of Asp58 and Asp151, Dβ-isomers were predominant with a very few exceptions. Notably, the chaperone activity of HMW protein was minimal for lens of all ages, whereas that of α-crystallin decreased with increasing lens age. Thus, abnormal aggregation caused by Asp isomerization might contribute to the loss of chaperone activity of α-crystallin in aged human lens.

Stabilisation of oil-in-water emulsions with non-chemical modified gelatinised starch

In this research, stabilisation of oil-in-water emulsions with non-chemically modified gelatinised starch is presented. Thus far only octenyl succinic anhydride (OSA) modified gelatinised starch has been known to adsorb at emulsion droplet interfaces, acting as emulsifiers. Screening a range of commercially available food starches revealed that a non-waxy rice starch, a waxy rice starch and the waxy maize starch PRIMA600 showed oil-in-water emulsifying ability following gelatinisation. The microstructure of emulsions formulated with 20% oil and 1% starch was stable for at least 3 months. Thermal, crystallinity and molecular property analyses as well as amylose and protein content revealed no obvious link to this property. Nevertheless, this research has provided the food industry with exciting results for the formulation of clean label emulsions. Moreover, it presents a concept for oral release food emulsions with destabilisation via salivary amylase digestion of the stabilising starch emulsifier.

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Non-chemically modified gelatinised starches screened for emulsifier functionality.

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High shear overhead processing of oil-in-water emulsions.

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A waxy & non-waxy rice & waxy maize starch adsorbed at oil droplets, others did not.

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Not related to thermal, crystallinity & molecular properties, amylose, protein.

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Functionality as clean label emulsifier clearly demonstrated.

Allowance for boundary sharpening in the determination of diffusion coefficients by sedimentation velocity: a historical perspective

This review summarizes endeavors undertaken in the middle of last century to employ the Lamm equation for quantitative analysis of boundary spreading in sedimentation velocity experiments on globular proteins, thereby illustrating the ingenuity required to achieve that goal in an era when an approximate analytical solution of that nonlinear differential equation of second order provided the only means for its application. Application of procedures based on that approximate solution to simulated sedimentation velocity distributions has revealed a slight disparity (about 3%) between returned and input values of the diffusion coefficient-a discrepancy comparable with that of estimates obtained by current simulative analyses based on numerical solution of the Lamm equation. Although the massive technological developments in the gathering and treatment of sedimentation velocity data over the past three to four decades have changed dramatically the manner in which boundary spreading is analyzed, they have not led to any significant improvement in the accuracy of the diffusion coefficient thereby deduced.

Allowance for radial dilution in evaluating the concentration dependence of sedimentation coefficients for globular proteins

The accuracy with which the concentration dependence of the sedimentation coefficient, s = s ⁰(1 - kc), can be quantified for globular proteins by commonly used procedures has been examined by subjecting simulated sedimentation velocity distributions for ovalbumin to c(s)‒s analysis. Because this procedure, as well as its g(s)‒s counterpart, is based on assumed constancy of s over the time course of sedimentation coefficient measurement in a given experiment, the best definition of the concentration coefficient k is obtained by associating the measured s with the mean of plateau concentrations for the initial and final distributions used for its determination. The return of a slightly underestimated k (by about 3%) is traced to minor mislocation of the air‒liquid meniscus position as the result of assuming time independence of s in a given experiment. Although more accurate quantification should result from later SEDFIT and SEDANAL programs incorporating the simultaneous evaluation of s ⁰ and k, the procedures based on assumed constancy of s suffice for determining the limiting sedimentation coefficient s ⁰-the objective of most s‒c dependence studies.

Characterization of Intrinsically Disordered Proteins by Analytical Ultracentrifugation

Intrinsically disordered proteins have traditionally been largely neglected by structural biologists because a lack of rigid structure precludes their study by X-ray crystallography. Structural information must therefore be inferred from physicochemical studies of their solution behavior. Analytical ultracentrifugation yields important information about the gross conformation of an intrinsically disordered protein. Sedimentation velocity studies provide estimates of the weight-average sedimentation and diffusion coefficients of a given macromolecular state of the protein.

Elucidating Complicated Assembling Systems in Biology Using Size-and-Shape Analysis of Sedimentation Velocity Data

Sedimentation velocity analytical ultracentrifugation (SV-AUC) has seen a resurgence in popularity as a technique for characterizing macromolecules and complexes in solution. SV-AUC is a particularly powerful tool for studying protein conformation, complex stoichiometry, and interacting systems in general. Deconvoluting velocity data to determine a sedimentation coefficient distribution c(s) allows for the study of either individual proteins or multicomponent mixtures. The standard c(s) approach estimates molar masses of the sedimenting species based on determination of the frictional ratio (f/f0) from boundary shapes. The frictional ratio in this case is a weight-averaged parameter, which can lead to distortion of mass estimates and loss of information when attempting to analyze mixtures of macromolecules with different shapes. A two-dimensional extension of the c(s) analysis approach provides size-and-shape distributions that describe the data in terms of a sedimentation coefficient and frictional ratio grid. This allows for better resolution of species with very distinct shapes that may co-sediment and provides better molar mass determinations for multicomponent mixtures. An example case is illustrated using globular and nonglobular proteins of different masses with nearly identical sedimentation coefficients that could only be resolved using the size-and-shape distribution. Other applications of this analytical approach to complex biological systems are presented, focusing on proteins involved in the innate immune response to cytosolic microbial DNA.