Histidine-tag-directed chromophores for tracer analyses in the analytical ultracentrifuge

Many recombinant proteins carry an oligohistidine (His(X))-tag that allows their purification by immobilized metal affinity chromatography (IMAC). This tag can be exploited for the site-specific attachment of chromophores and fluorophores, using the same metal ion-nitrilotriacetic acid (NTA) coordination chemistry that forms the basis of popular versions of IMAC. Labeling proteins in this way can allow their detection at wavelengths outside of the absorption envelopes of un-modified proteins and nucleic acids. Here we describe use of this technology in tracer sedimentation experiments that can be performed in a standard analytical ultracentrifuge equipped with absorbance or fluorescence optics. Examples include sedimentation velocity in the presence of low molecular weight chromophoric solutes, sedimentation equilibrium in the presence of high concentrations of background protein and selective labeling to simplify the assignment of species in a complex interacting mixture.     

Challenges for the modern analytical ultracentrifuge analysis of polysaccharides

This article reviews some of the recent advances in analytical ultracentrifugation and how these advances have impacted--and can impact--on our understanding of the size, shape through conformation modelling, interactions and charge properties of polysaccharides in solution, particularly when used in combination with other solution techniques and also imaging techniques. Specifically we look at (1) polysaccharide polydispersity and simple shape analysis by sedimentation velocity, and in particular using new approaches such as SEDFIT analysis; (2) polysaccharide molecular-weight analysis by sedimentation equilibrium and MSTAR analysis and how this complements analysis of size exclusion chromatography coupled to multi-angle laser light scattering; (3) polysaccharide conformation analysis using traditional procedures such as the Wales-van Holde ratio, power law or 'scaling' relations, more specialised treatments for rigid cylindrical structures, semi-flexible chains and worm-like coils and complications through draining effects; (4) Analysis of polysaccharide interactions and in particular complex formation phenomena, focusing on interesting applications in the areas of mucoadhesion and sedimentation fingerprinting; and (5) the possibilities for macromolecular charge and charge screening measurement.     

Easily assembled digital data acquisition system for the analytical ultracentrifuge

A system for the acquisition of digital data from the analytical ultracentrifuge which uses a commercially available data acquisition board, a standard IBM compatible personal computer (PC), and an interface circuit has been developed. The system uses the signal from the standard Beckman scanner. Preliminary analysis and data reduction are performed at the PC within minutes of data acquisition using simple commercially available software, and final data fitting is performed with a mainframe computer. Procedures are described which allow approach to equilibrium to be followed and attainment of equilibrium to be demonstrated. Data density of 200 points per millimeter column height (500 points per 100 μ1 of sample) allows the use of short columns and hence short run times. Only 2 min are required to collect a complete scan, which is recorded in a format suitable for direct analysis by standard spreadsheet software. This allows multiple sequential scans to be quickly recorded at equilibrium and averaged to reduce noise prior to analysis. The combination of characteristics allows molecular weight determinations to be performed relatively quickly with only a few micrograms of protein. The system is inexpensive and easy to assemble given the centrifuge and a PC.     

A simple test for macromolecular heterogeneity in the analytical ultracentrifuge

A simple check for the presence of heterogeneity in a macromolecular system is proposed, employing comparison of Rayleigh sedimentation-equilibrium patterns for two solutions of the same fringe concentration but differing absolute concentrations. The method is illustrated by application to a bronchial glycoprotein from a cystic-fibrosis patient.     

FUGE: an analytical ultracentrifuge simulation for teaching purposes

An IBM-compatible microcomputer program for teaching purposesis described which simulates the operation of a sedimentationvelocity determination of a protein in an analytical ultracentrifugeusing schlieren optics. The program operates in speeded-up timeand simulates the major procedures which would need to be carriedout to operate such an instrument. The position of the sedimentingboundary can be observed at any time during the run, and upto six ‘photographs’ can be recorded for subsequentanalysis. Calculation of sedimentation coefficient, diffusioncoefficient and mol. wt can be made from a dot-matrix printout.Ten representative proteins are stored within the program, butprovision exists for user-supplied data. Received on June 25, 1987; accepted on September 9, 1987     

An externally adjustable motor-driven Rayleigh slit assembly for the analytical ultracentrifuge

Precise alignment of the Rayleigh optical system of the Beckman Instruments Model E analytical ultracentrifuge is prerequisite to the performance of difference sedimentation velocity, difference sedimentation equilibrium, and high-speed equilibrium ultracentrifugation. One of the components required for precise alignment is an adjustable Rayleigh slit assembly. An externally adjustable assembly has been developed which offers some advantages over previous designs. The rotational movement is motor driven, allowing external adjustment by a single operator, who can monitor visually changes in the fringe pattern while the rotor is spinning. Installation of the slit assembly is simple and requires no permanent modifications of the armor plate, since the slit assembly is attached directly to the collimating lens holder. The slit assembly can be removed and replaced easily whenever the collimating lens is cleaned. The alignment procedure, involving rotation of both slit assembly and cylinder lens, can be carried out in less than 3 hr.     

Studying polyglutamine aggregation in Caenorhabditis elegans using an analytical ultracentrifuge equipped with fluorescence detection

This work explores the heterogeneity of aggregation of polyglutamine fusion constructs in crude extracts of transgenic Caenorhabditis elegans animals. The work takes advantage of the recent technical advances in fluorescence detection for the analytical ultracentrifuge. Further, new sedimentation velocity methods, such as the multi‐speed method for data capture and wide distribution analysis for data analysis, are applied to improve the resolution of the measures of heterogeneity over a wide range of sizes. The focus here is to test the ability to measure sedimentation of polyglutamine aggregates in complex mixtures as a prelude to future studies that will explore the effects of genetic manipulation and environment on aggregation and toxicity. Using sedimentation velocity methods, we can detect a wide range of aggregates, ranging from robust analysis of the monomer species through an intermediate and quite heterogeneous population of oligomeric species, and all the way up to detecting species that likely represent intact inclusion bodies based on comparison to an analysis of fluorescent puncta in living worms by confocal microscopy. Our results support the hypothesis that misfolding of expanded polyglutamine tracts into insoluble aggregates involves transitions through a number of stable intermediate structures, a model that accounts for how an aggregation pathway can lead to intermediates that can have varying toxic or protective attributes. An understanding of the details of intermediate and large‐scale aggregation for polyglutamine sequences, as found in neurodegenerative diseases such as Huntington's Disease, will help to more precisely identify which aggregated species may be involved in toxicity and disease.     

Methods for sample labeling and meniscus determination in the fluorescence-detected analytical ultracentrifuge

The fluorescence detection system for the analytical ultracentrifuge (AU–FDS) enables the measurement of hydrodynamic properties and interactions of biomolecules at subnanomolar concentrations. In this study, we describe methods for (i) preparing and purifying fluorescently labeled biomolecules and (ii) determining the meniscus position in the AU–FDS using BODIPY 493/503 fluorescent dye suspended in light oil. We subsequently use these methods to measure the interaction of DNA with Escherichia coli Klenow fragment (KF) and show that KF binds matched DNA to form 1:1 and 2:1 (protein/DNA) complexes with dissociation constants of 4.2 and 22 nM, respectively.     

Preconstruction of density gradients in cells of the analytical ultracentrifuge

The principles and techniques of zonal centrifugation are now well established (1), but despite the advantage of requiring smaller amounts of material than conventional experiments, this procedure has not been widely applied to the analytical ultracentrifuge. In general, the method has been limited to experiments where separations are based on differences in density. Usually, this involves the generation in situ of gradients, and has been widely used in the analysis of nucleic acids (3,4); recently, the scope of this technique was enlarged by a method for fractionating the zones produced by this type of separation (5). However, Rosenbloom and Schumaker (2) showed that a preformed gradient can be constructed in the analytical cell prior to running, and this stabilised the sedimentation of a boundary or a zone of nucleic acid. Although the use of a preformed density gradient (containing initially a uniform distribution of the macromolecule(s)) could reduce the time to reach isopycnic equilibrium it is not a prerequisite for the experiment, however, a preformed gradient is essential when measuring the velocity of a zone, as in Cohen, Giraud, and Messiah (8). This communication describes a simple technique for generating density gradients in the analytical cell prior to running and with the minimum of disturbance.