Sedimentation Coefficient Distributions Research Articles

Biochemical Characterization of the Transcriptional Regulator BzdR from Azoarcus sp. CIB

The BzdR transcriptional regulator that controls the P(N) promoter responsible for the anaerobic catabolism of benzoate in Azoarcus sp. CIB constitutes the prototype of a new subfamily of transcriptional regulators. Here, we provide some insights about the functional-structural relationships of the BzdR protein. Analytical ultracentrifugation studies revealed that BzdR is homodimeric in solution. An electron microscopy three-dimensional reconstruction of the BzdR dimer has been obtained, and the predicted structures of the respective N- and C-terminal domains of each BzdR monomer could be fitted into such a reconstruction. Gel retardation and ultracentrifugation experiments have shown that the binding of BzdR to its cognate promoter is cooperative. Different biochemical approaches revealed that the effector molecule benzoyl-CoA induces conformational changes in BzdR without affecting its oligomeric state. The BzdR-dependent inhibition of the P(N) promoter and its activation in the presence of benzoyl-CoA have been established by in vitro transcription assays. The monomeric BzdR4 and BzdR5 mutant regulators revealed that dimerization of BzdR is essential for DNA binding. Remarkably, a BzdRΔL protein lacking the linker region connecting the N- and C-terminal domains of BzdR is also dimeric and behaves as a super-repressor of the P(N) promoter. These data suggest that the linker region of BzdR is not essential for protein dimerization, but rather it is required to transfer the conformational changes induced by the benzoyl-CoA to the DNA binding domain leading to the release of the repressor. A model of action of the BzdR regulator has been proposed.

Determination of the Surfactant Density on SWCNTs by Analytical Ultracentrifugation

We report on the extensive characterization of single-walled carbon nanotubes (SWCNTs) dispersed in a variety of surfactants, such as sodium dodecyl benzene sulfonate (SDBS), sodium cholate (SC), and three synthesized perylene-based surfactants, by using differential sedimentation in H(2)O and D(2)O. Multidimensional evaluation of the absorption profiles over radius, wavelength, and time allows the determination of the anhydrous specific volumes of the SWCNT-surfactant complexes as well as the concentration of the surfactant reservoir in free micelles with very slow sedimentation coefficients (<1 Svedberg). Among the perylene bisimide surfactants, the smallest derivative is densely adsorbed on the nanotube backbone with an anhydrous specific volume significantly above that of SC or SDBS. Bulky Newkome dendritic groups on one or both ends of the perylene moiety gradually reduce the adsorption density, in accord with the absolute adsorption between 0.66 and 1.7 mmol surfactant per gram SWCNTs. Furthermore, hydrodynamic analysis reveals that SDBS favors the "tails-on" configuration. The distribution of sedimentation coefficients of SWCNTs prepared by high-pressure carbon monoxide decomposition (HiPco) is broader and shifted to faster sedimentation than those prepared by using cobalt-molybdenum catalysis (CoMoCAT), which reflects the polydispersity in diameter and length.

Maturation Mechanism of Severe Acute Respiratory Syndrome (SARS) Coronavirus 3C-like Proteinase

The 3C-like proteinase (3CLpro) of the severe acute respiratory syndrome (SARS) coronavirus plays a vital role in virus maturation and is proposed to be a key target for drug design against SARS. Various in vitro studies revealed that only the dimer of the matured 3CLpro is active. However, as the internally encoded 3CLpro gets matured from the replicase polyprotein by autolytic cleavage at both the N-terminal and the C-terminal flanking sites, it is unclear whether the polyprotein also needs to dimerize first for its autocleavage reaction. We constructed a large protein containing the cyan fluorescent protein (C), the N-terminal flanking substrate peptide of SARS 3CLpro (XX), SARS 3CLpro (3CLP), and the yellow fluorescent protein (Y) to study the autoprocessing of 3CLpro using fluorescence resonance energy transfer. In contrast to the matured 3CLpro, the polyprotein, as well as the one-step digested product, 3CLP-Y-His, were shown to be monomeric in gel filtration and analytic ultracentrifuge analysis. However, dimers can still be induced and detected when incubating these large proteins with a substrate analog compound in both chemical cross-linking experiments and analytic ultracentrifuge analysis. We also measured enzyme activity under different enzyme concentrations and found a clear tendency of substrate-induced dimer formation. Based on these discoveries, we conclude that substrate-induced dimerization is essential for the activity of SARS-3CLpro in the polyprotein, and a modified model for the 3CLpro maturation process was proposed. As many viral proteases undergo a similar maturation process, this model might be generally applicable.

Novel Recombinant Engineered gp41 N-terminal Heptad Repeat Trimers and Their Potential as Anti-HIV-1 Therapeutics or Microbicides

Peptides derived from N-terminal heptad repeat (NHR) of the HIV-1 gp41 are generally poor inhibitors of HIV-1 entry, because they tend to aggregate and do not form a trimeric coiled-coil. In this study, we have fused portions of gp41 NHR, e.g. N36 or N28, to the T4 fibritin trimerization domain, Foldon (Fd), thus constructing novel NHR trimers, designated N36Fd or N28Fd, which could be expressed in Escherichia coli cells. The purified N36Fd and N28Fd exhibited SDS-resistant trimeric coiled-coil conformation with improved alpha-helicity compared with the corresponding N-peptides. They could interact with a C-peptide (e.g. C34) to form stable six-helix bundle and possessed potent anti-HIV-1 activity against a broad spectrum of HIV-1 strains. N28Fd was effective against T20-resistant HIV-1 variants and more resistant to proteinase K compared with T20 (enfuvirtide), a C-peptide-based HIV fusion inhibitor. Therefore, N28Fd trimer has great potentials for further development as an affordable therapeutic or microbicide for treatment and prevention of HIV-1 infection.

Critical Salt Bridges Guide Capsid Assembly, Stability, and Maturation Behavior in Bacteriophage HK97

HK97 is a double-stranded DNA bacteriophage that undergoes dramatic conformational changes during viral capsid maturation and for which x-ray structures, at near atomic resolution, of multiple intermediate and mature capsid states are available. Both amide H/(2)H exchange and crystallographic comparisons between the pre-expanded Prohead II particles and the expanded Head II of bacteriophage HK97 revealed quaternary interactions that remain fixed throughout maturation and appear to maintain intercapsomer integrity at all quasi- and icosahedral 3-fold axes. These 3-fold staples are formed from Arg and Glu residues and a metal binding site. Mutations of either Arg-347 or Arg-194 or a double mutation of E344Q and E363A resulted in purification of the phage in capsomer form (hexamers and pentamers). Mutants that did assemble had both decreased thermal stability and decreased in vitro expansion rates. Amide H/(2)H exchange mass spectrometry showed that in the wild type capsid some subunits had a bent "spine" helix (highly exchanging), whereas others were straight (less exchanging). Similar analysis of the never assembled mutant capsomers showed uniform amide exchange in all of these that was higher than that of the straight spine helices (characterized in more mature intermediates), suggesting that the spine helix is somewhat bent prior to capsid assembly. The result further supports a previously proposed mechanism for capsid expansion in which the delta domains of each subunit induce a high energy intermediate conformation, which now appears to include a bent helix during capsomer assembly.

Studies on macromolecular interactions in ternary mixtures of konjac glucomannan, xanthan gum and sodium alginate

Covalent and non-covalent macromolecular interactions were studied in the proprietary commercial product, PGX ® (PolyGlycopleX ®) which is manufactured from konjac glucomannan, xanthan gum and sodium alginate using a proprietary manufacturing process (EnviroSimplex ®). Analytical techniques established the absence of changes in primary covalent structure of any of the component polysaccharides which may have occurred when the product was manufactured. However, non-covalent interactions between the polysaccharides were apparent in aqueous solutions of proprietary ternary mixtures by comparing their flow behaviour with those of unmixed controls. The interactions indicated by the flow behaviour confirmed those observed in the sedimentation behaviour, published earlier (Abdelhameed, A. S., Ang, S., Morris, G. A., Smith, I., Lawson, C., Gahler, R., et al. (2010). Carbohydrate Polymers, 81, 145–148). Non-covalent macromolecular interactions between konjac glucomannan and xanthan gum are already known in binary mixtures but the flow behaviour of solutions of laboratory-prepared ternary powder mixtures with variable sodium alginate content was consistent with a ternary macromolecular interaction involving sodium alginate at below 5% but this was significantly enhanced by heat treating the solutions when the sodium alginate content exceeded 5%. Sedimentation coefficient distribution analysis from analytical ultracentrifugation supports these observations showing a clear shift to higher sedimentation coefficients in the heat-treated solutions of ternary mixtures at sodium alginate concentrations >8%, and over a greater range compared with unheated material. Calcium ion addition failed to precipitate calcium alginate from solutions of PGX ® (containing all three polysaccharides) but precipitates were obtained from solutions of binary mixtures prepared with either konjac glucomannan or xanthan gum plus sodium alginate. The results are consistent with an interaction between a konjac glucomannan–xanthan gum complex and sodium alginate to form a new, ternary complex.

Molecular Weight Distribution Evaluation of Polysaccharides and Glycoconjugates Using Analytical Ultracentrifugation

We review here the advances that have been made in methodology using the analytical ultracentrifuge for characterising polydisperse polymer systems with a quasi-continuous distribution of molecular weight. These advances include improved ways of defining the weight and z-average molecular weights of a distribution from sedimentation equilibrium experiments and hence the ratio Mz/Mw, off-line calibration of size exclusion chromatography by sedimentation equilibrium and conversion of a sedimentation coefficient distribution into a molecular weight distribution. Although these methods are applicable to other polymeric systems, we focus on polysaccharides, mucins and other glycoconjugates, systems which particularly benefit from the availability of recently available long optical path length cells for the minimisation of complications through thermodynamic non-ideality.

SEDVIEW, Real‐time Sedimentation Analysis

The ability to obtain a sedimentation coefficient distribution as the run proceeds, and to get an early idea of the quality of a particular sample, has not been made available in real-time during the run in any of the existing software packages. It is desirable on many occasions to be able to see the number of components present in a sample at an early stage of the run. The ability to ascertain the extent of heterogeneity of sample would help enormously to reduce the amount of time that is necessary to obtain that information. Most software packages currently available require that the run be completed before analysis is carried out or at least some of the early scans analyzed off-line to determine if the run should continue. A software package called SEDVIEW has been developed by us to allow early analysis in real-time.

Diffusion of the Reaction Boundary of Rapidly Interacting Macromolecules in Sedimentation Velocity

Sedimentation velocity analytical ultracentrifugation combines relatively high hydrodynamic resolution of macromolecular species with the ability to study macromolecular interactions, which has great potential for studying dynamically assembled multiprotein complexes. Complicated sedimentation boundary shapes appear in multicomponent mixtures when the timescale of the chemical reaction is short relative to the timescale of sedimentation. Although the Lamm partial differential equation rigorously predicts the evolution of concentration profiles for given reaction schemes and parameter sets, this approach is often not directly applicable to data analysis due to experimental and sample imperfections, and/or due to unknown reaction pathways. Recently, we have introduced the effective particle theory, which explains quantitatively and in a simple physical picture the sedimentation boundary patterns arising in the sedimentation of rapidly interacting systems. However, it does not address the diffusional spread of the reaction boundary from the cosedimentation of interacting macromolecules, which also has been of long-standing interest in the theory of sedimentation velocity analytical ultracentrifugation. Here, effective particle theory is exploited to approximate the concentration gradients during the sedimentation process, and to predict the overall, gradient-average diffusion coefficient of the reaction boundary. The analysis of the heterogeneity of the sedimentation and diffusion coefficients across the reaction boundary shows that both are relatively uniform. These results support the application of diffusion-deconvoluting sedimentation coefficient distributions c(s) to the analysis of rapidly interacting systems, and provide a framework for the quantitative interpretation of the diffusional broadening and the apparent molar mass values of the effective sedimenting particle in dynamically associating systems.

Biochemical and Biophysical Characterization of the Mg2+-induced 90-kDa Heat Shock Protein Oligomers

The 90-kDa heat shock protein (Hsp90) is involved in the regulation and activation of numerous client proteins essential for diverse functions such as cell growth and differentiation. Although the function of cytosolic Hsp90 is dependent on a battery of cochaperone proteins regulating both its ATPase activity and its interaction with client proteins, little is known about the real Hsp90 molecular mechanism. Besides its highly flexible dimeric state, Hsp90 is able to self-oligomerize in the presence of divalent cations or under heat shock. In addition to dimers, oligomers exhibit a chaperone activity. In this work, we focused on Mg(2+)-induced oligomers that we named Type I, Type II, and Type III in increasing molecular mass order. After stabilization of these quaternary structures, we optimized a purification protocol. Combining analytical ultracentrifugation, size exclusion chromatography coupled to multiangle laser light scattering, and high mass matrix-assisted laser desorption/ionization time of flight mass spectrometry, we determined biochemical and biophysical characteristics of each Hsp90 oligomer. We demonstrate that Type I oligomer is a tetramer, and Type II is an hexamer, whereas Type III is a dodecamer. These even-numbered structures demonstrate that the building brick for oligomerization is the dimer up to the Type II, whereas Type III probably results from the association of two Type II. Moreover, the Type II oligomer structure, studied by negative stain transmission electron microscopy tomography, exhibits a "nest-like" shape that forms a "cozy chaperoning chamber" where the client protein folding/protection could occur.

Size and density dependent sedimentation analysis of advanced nanoparticle systems

Various functional colloidal systems like polymer grafted inorganic particles, complex multi-component mixtures, organic–inorganic hybrid particles, inorganic–inorganic core–shell particles and swellable particles were characterized by sedimentation coefficient analysis in analytical ultracentrifuge owing to the accurate correlation of the sedimentation coefficient with variations in size and density of the materials. The sedimentation coefficient is absolute in nature and does not require any property information beforehand. By following the changes in the sedimentation coefficient and its distribution, it could be established if the polymer grafting on the surface of the inorganic particles took place or if the organic–inorganic or inorganic–inorganic hybrid was formed or if the particles were strongly crosslinked or swellable. The complex particle mixtures were also quantified for the number of components contained in them and their exact amounts by following the sedimentation coefficient distributions.

A polycystin-2 (TRPP2) dimerization domain essential for the function of heteromeric polycystin complexes

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in two genes, PKD1 and PKD2, which encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively. Earlier work has shown that PC1 and PC2 assemble into a polycystin complex implicated in kidney morphogenesis. PC2 also assembles into homomers of uncertain functional significance. However, little is known about the molecular mechanisms that direct polycystin complex assembly and specify its functions. We have identified a coiled coil in the C-terminus of PC2 that functions as a homodimerization domain essential for PC1 binding but not for its self-oligomerization. Dimerization-defective PC2 mutants were unable to reconstitute PC1/PC2 complexes either at the plasma membrane (PM) or at PM-endoplasmic reticulum (ER) junctions but could still function as ER Ca2+-release channels. Expression of dimerization-defective PC2 mutants in zebrafish resulted in a cystic phenotype but had lesser effects on organ laterality. We conclude that C-terminal dimerization of PC2 specifies the formation of polycystin complexes but not formation of ER-localized PC2 channels. Mutations that affect PC2 C-terminal homo- and heteromerization are the likely molecular basis of cyst formation in ADPKD.

An analytical ultracentrifuge study on ternary mixtures of konjac glucomannan supplemented with sodium alginate and xanthan gum

Mixed solutions of konjac glucomannan supplemented with xanthan and alginate were studied using the technique of sedimentation velocity in the analytical ultracentrifuge. Interactions – as manifested by changes in the sedimentation coefficient distributions compared to unmixed controls – were observed for ternary mixtures in the presence of alginate. The complexes observed also appeared sensitive to the presence of the ionic concentration of the supporting solvent, but were clearly significant at low ionic strength.

C-reactive Protein Exists in an NaCl Concentration-dependent Pentamer-Decamer Equilibrium in Physiological Buffer

C-reactive protein (CRP) is an acute phase protein of the pentraxin family that binds ligands in a Ca(2+)-dependent manner, and activates complement. Knowledge of its oligomeric state in solution and at surfaces is essential for functional studies. Analytical ultracentrifugation showed that CRP in 2 mM Ca(2+) exhibits a rapid pentamer-decamer equilibrium. The proportion of decamer decreased with an increase in NaCl concentration. The sedimentation coefficients s(20,w)(0) of pentameric and decameric CRP were 6.4 S and in excess of 7.6 S, respectively. In the absence of Ca(2+), CRP partially dissociates into its protomers and the NaCl concentration dependence of the pentamer-decamer equilibrium is much reduced. By x-ray scattering, the radius of gyration R(G) values ranged from 3.7 nm for the pentamer to above 4.0 nm for the decamer. An averaged K(D) value of 21 microM in solution (140 mM NaCl, 2 mM Ca(2+)) was determined by x-ray scattering and modeling based on crystal structures for the pentamer and decamer. Surface plasmon resonance showed that CRP self-associates on a surface with immobilized CRP with a similar K(D) value of 23 microM (140 mM NaCl, 2 mM Ca(2+)), whereas CRP aggregates in low salt. It is concluded that CRP is reproducibly observed in a pentamer-decamer equilibrium in physiologically relevant concentrations both in solution and on surfaces. Both 2 mM Ca(2+) and 140 mM NaCl are essential for the integrity of CRP in functional studies and understanding the role of CRP in the acute phase response.

Heterodimerization of the Sialidase NEU1 with the Chaperone Protective Protein/Cathepsin A Prevents Its Premature Oligomerization

Lysosomal neuraminidase-1 (NEU1) forms a multienzyme complex with beta-galactosidase and protective protein/cathepsin A (PPCA). Because of its association with PPCA, which acts as a molecular chaperone, NEU1 is transported to the lysosomal compartment, catalytically activated, and stabilized. However, the mode(s) of association between these two proteins both en route to the lysosome and in the multienzyme complex has remained elusive. Here, we have analyzed the hydrodynamic properties of PPCA, NEU1, and a complex of the two proteins and identified multiple binding sites on both proteins. One of these sites on NEU1 that is involved in binding to PPCA can also bind to other NEU1 molecules, albeit with lower affinity. Therefore, in the absence of PPCA, as in the lysosomal storage disease galactosialidosis, NEU1 self-associates into chain-like oligomers. Binding of PPCA can reverse self-association of NEU1 by causing the disassembly of NEU1-oligomers and the formation of a PPCA-NEU1 heterodimeric complex. The identification of binding sites between the two proteins allowed us to create innovative structural models of the NEU1 oligomer and the PPCA-NEU1 heterodimeric complex. The proposed mechanism of interaction between NEU1 and its accessory protein PPCA provides a rationale for the secondary deficiency of NEU1 in galactosialidosis.

Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization

AMPA and kainate receptors mediate fast synaptic transmission. AMPA receptor ligand-binding domains form dimers, which are key functional units controlling ion-channel activation and desensitization. Dimer stability is inversely related to the rate and extent of desensitization. Kainate and AMPA receptors share common structural elements, but functional measurements suggest that subunit assembly and gating differs between these subtypes. To investigate this, we constructed a library of GluR6 kainate receptor mutants and directly measured changes in kainate receptor dimer stability by analytical ultracentrifugation, which, combined with electrophysiological experiments, revealed an inverse correlation between dimer stability and the rate of desensitization. We solved crystal structures for a series of five GluR6 mutants, to understand the molecular mechanisms for dimer stabilization. We demonstrate that the desensitized state of kainate receptors acts as a deep energy well offsetting the stabilizing effects of dimer interface mutants, and that the deactivation of kainate receptor responses is dominated by entry into desensitized states. Our results show how neurotransmitter receptors with similar structures and gating mechanisms can exhibit strikingly different functional properties.

Peptide binding affects the conformation and ATPase activity of the Bacterial AAA+ domain 2 of ClpA

ClpA consists of 3 domains, an N‐terminal and two ATP‐binding domains, D1 and D2. ClpA recognizes specific motifs on the termini of proteins and mediates unfolding and translocation to the protease, ClpP. We have performed sedimentation velocity measurements on ClpA in the absence and presence of 30‐fold excess of SsrA peptide, a C‐terminal tag that targets proteins to ClpXP and ClpAP, and we have analyzed the kinetics of ATP hydrolysis of ClpA mutants in the presence or absence of SsrA. Ultracentrifugation of ClpA in the presence of a non‐hydrolysable ATP analog, ATP ?×S, gave a distribution of sedimentation coefficients that becomes narrower in the presence of SsrA. Similar effect persists with a mutant lacking the N terminal domain, while the effect is not present in mutant lacking the D2, indicating that the effect of SsrA can be ascribed to the presence of D2. Stimulation of ATP hydrolysis mediated by SsrA binding was observed only with wild type ClpA or mutants with a functional D2 domain. Changes in activity upon SsrA binding to mixed hexamers of wild type ClpA and ClpA with inactive D2 revealed that, differently from the absence of SsrA, a single subunit with a mutated D2 exerted a negative allosteric effect, completely blocking the activity of the other subunits. Our results indicate that SsrA binding reduces conformation flexibility in the ClpA hexamer and affects interactions and catalytic properties of the D2 domains.

Enhanced resolution of sedimentation coefficient distribution profiles by extrapolation to infinite time

Sedimentation velocity experiments can be used to identify two or more independent non-interacting macromolecules, which differ in their size by only a few percent. The procedure requires the extrapolation of differential apparent sedimentation coefficient distributions obtained at different running time to t --> infinity and works because it eliminates or greatly reduces diffusion effects. Here, we present an improved time extrapolation function of sedimentation distribution profiles originally presented by Stafford (In: Harding, Rowe, Horton (eds.) Analytical ultracentrifugation in biochemistry and polymer science, 1992). We describe a computing procedure with the program LAMM: to analyze concentration profiles obtained by absorbance or interference optics that utilizes suitable smoothing methods for noisy data sets and present examples which include time invariant noises.

Investigation of β-carotene–gelatin composite particles with a multiwavelength UV/vis detector for the analytical ultracentrifuge

A multiwavelength UV/vis detector for the analytical ultracentrifuge (MWL-AUC) has been developed recently. In this work, β-carotene–gelatin composite particles are investigated with MWL-AUC. Band centrifugation with a Vinograd cell is used to ensure maximum sample separation. Spectral changes of the system are observed in dependence of the sedimentation coefficient and are attributed to a previously unknown inhomogeneity of the β-carotene chemical composition with both H- and J-aggregates coexisting in a mixture. In addition, our data suggest that pure H- and J-aggregates exist in a particle while their relative concentrations in a mixture determine the color characteristics of the sample. The unique abilities and properties of MWL-AUC include sedimentation coefficient distributions for all possible wavelengths, full UV/vis spectra of each different species in the mixture and 3D movies of the sedimentation process. These properties significantly extend the scope of the analytical ultracentrifuge technique and show that complex biopolymer multicomponent mixtures can be resolved into their individual species.Electronic supplementary materialThe online version of this article (doi:10.1007/s00249-009-0412-6) contains supplementary material, which is available to authorized users.

Assembly of Oligomeric Death Domain Complexes during Toll Receptor Signaling

The Drosophila Toll receptor is activated by the endogenous protein ligand Spätzle in response to microbial stimuli in immunity and spatial cues during embryonic development. Downstream signaling is mediated by the adaptor proteins Tube, the kinase Pelle, and the Drosophila homologue of myeloid differentiation primary response protein (dMyD88). Here we have characterized heterodimeric (dMyD88-Tube) and heterotrimeric (dMyD88-Tube-Pelle) death domain complexes. We show that both the heterodimeric and heterotrimeric complexes form kidney-shaped structures and that Tube is bivalent and has separate high affinity binding sites for dMyD88 and Pelle. Additionally we found no interaction between the isolated death domains of Pelle and dMyD88. These results indicate that the mode of assembly of the heterotrimeric dMyD88-Tube-Pelle complex downstream of the activated Toll receptor is unique. The measured dissociation constants for the interaction between the death domains of dMyD88 and Tube and of Pelle and a preformed dMyD88-Tube complex are used to propose a model of the early postreceptor events in Drosophila Toll receptor signaling.