Diffusion-ordered NMR spectroscopy: a versatile tool for the molecular weight determination of uncharged polysaccharides

Diffusion-ordered NMR spectroscopy (DOSY) experiments have been carried out on dilute aqueous solutions of uncharged saccharide systems and, in particular, on six well characterized pullulan fractions of different molecular weights. The values of diffusion coefficients and hydrodynamic radii determined for the pullulan fractions are in good agreement with the results obtained with other methodologies such as light scattering. Fitting the diffusion coefficients data as a function of the molecular weight allows for the determination of a calibration curve that can be applied to a wide range of mono-, oligo-, and polysaccharides. Therefore, DOSY is proposed as a versatile tool for achieving a simple estimation of the molecular weight of uncharged polysaccharides. Mixtures of homopolymers of different molecular weight can be nicely separated. An advantage of the method is that the same sample used for the NMR characterization can be used for the molecular weight determination without any further manipulation. Other water soluble polymers, such as poly(ethylene oxide) and poly(vinylpyrrolidone), can be roughly characterized using the same calibration curve.     

Useful applications of DOSY experiments for the study of mushroom polysaccharides

DOSY analysis has been performed on different mushroom extracts and fractions with the aim to describe a general method for the study of high molecular weight polysaccharides. These NMR experiments can be exploited to monitor the fractionation pathways performed on crude extracts in order to isolate polysaccharides. DOSY can also rapidly verify the purity of the isolated compounds, as well as evaluate their molecular size. In spite of the complexity of DOSY spectra of mixtures, this NMR technique seems to be a valid analytical tool that could be adopted as a routine method for the study of polysaccharides from different sources.     

Laser light scattering measurements on vitreous and rooster comb hyaluronic acids

Molecular weights and translational diffusion coefficients have been measured for rooster comb and vitreous hyaluronic acid (HA) at pH 7.2 and 11. The results indicate that the molecular weight, second virial coefficient and translational diffusion coefficient for vitreous HA can be reversibly decreased by increasing the solution pH from 7.2 to 11, whereas the physical properties of rooster comb HA are independent of pH studied. In addition, it is reported that the second virial coefficient for vitreous HA is negative, suggesting intermolecular interactions exist in solution at both neutral and alkaline pH as opposed to rooster comb HA which exhibits a positive second vitrial coefficient associated with decreasing molecular weights may be related to the accessibility and number of hydrogen bond forming groups. Differences in the dependence of molecular weight on pH between vitreous and rooster comb HA may be due to differences in the number of intramolecular interactions per molecule. These studies indicate that molecules of low molecular weight HA are able to form higher molecular weight complexes and differences in the organization of the polysaccharide chains may contribute to the differences in molecular weight of HAs isolated from various tissues.     

Comparison of the complexed and free forms of rat liver arginyl-tRNA synthetase and origin of the free form

Arginyl-tRNA synthetase is found in multiple molecular weight forms in extracts from a variety of mammalian tissues. The rat liver enzyme can be isolated either as a component of the synthetase complex (Mr greater than 10(6) or as a free protein (Mr = 60,000). However, based on activity measurements after sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the molecular weight of the free form differs from its counterpart in the complex (Mr = 72,000). Both forms of arginyl-tRNA synthetase cross-react with an antibody directed against the complex, and both have similar catalytic properties. Thus, the two proteins have similar apparent Km values for arginine and ATP, the same pH optimum, are inhibited equally by elevated ionic strength and PPi, and they aminoacylate the same population of tRNA molecules. On the other hand, the free and complexed forms differ with respect to their apparent Km values for tRNA (free, 4 microM; complexed, 28 microM), their temperature sensitivity (complexed greater sensitivity), and their hydrophobicity (complexed more hydrophobic). Limited proteolysis of the synthetase complex with papain releases a low molecular weight form of arginyl-tRNA synthetase whose size, temperature sensitivity, and hydrophobicity are similar to that of the endogenous free form. Nevertheless, the usual 2:1 ratio of complexed-to-free form of rat liver arginyl-tRNA synthetase is not altered by a variety of homogenization or incubation conditions in the presence or absence of multiple protease inhibitors. In contrast to extracts of rat liver, rabbit liver extracts do not contain a free form of arginyl-tRNA synthetase. These results suggest that the complexed and free forms of arginyl-tRNA synthetase are probably the same gene product and that the free form in rat liver extracts is derived from the complexed form by a limited endogenous proteolysis that removes the portion of the protein required for anchoring it in the complex. The question of whether the free form is an artifact of isolation or whether it pre-exists in the cell is discussed.     

A method for the estimation of proteins in colored or turbid solutions

The many photometric methods of protein estimation give unsatisfactory results with highly colored solutions. Some plant pigment-protein complexes are not precipitable with trichloracetic acid; therefore the dye binding methods are not applicable. A rapid procedure has been devised where the protein is complexed with excess copper, the noncomplexed copper removed by an ion-exchange resin, and the copper complexed to polypeptide then estimated by atomic absorption spectrophotometry. The copper complex is proportional to the amount of protein and different proteins give the same result in the range of 0.05 to 1 mg.     

Comparison of the enzymatic behavior of high molecular weight and free lysyl-tRNA synthetase from rat liver: kinetic analysis of lysylation of tRNA

Lysyl-tRNA synthetase occurs in the high molecular weight form in rat liver. The high molecular weight lysyl-tRNA synthetase has been previously demonstrated to exist as multienzyme complexes of aminoacyl-tRNA synthetases. The multienzyme complexes can be dissociated by hydrophobic interaction chromatography and yield fully active, free lysyl-tRNA synthetase. The free form is found to be twice as active as the complexed form in lysylation. Bisubstrate and product inhibition kinetics of lysylation are systematically carried out for highly purified free lysyl-tRNA synthetase and the 18 S synthetase complex. Surprisingly, the two enzyme forms exhibit distinctly different kinetic patterns in bisubstrate and product inhibition kinetics under identical conditions. The 18 S synthetase complex shows kinetic patterns consistent with an ordered bi uni uni bi ping pong mechanism, while the results of free lysyl-tRNA synthetase do not. We conclude that structural organization of lysyl-tRNA synthetase beyond quaternary structure of proteins may alter the enzyme behavior.     

Characterization of sugar diffusion coefficients in alginate membranes

The diffusivity of several monosaccharides and disaccharides in calcium alginate gels was determined using a specially designed diaphragm cell. The diffusion coefficients of the tested sugars are 4 to 18% smaller in alginate gel than in water and, with the exception of fructose, this difference increases with increasing sugar molecular weight. Also the position of the carbonyl group seems to be determined in the value of the diffusion coefficient - ketoses have lower diffusion coefficients than aldoses.     

Regulation of the activity of matriptase on epithelial cell surfaces by a blood-derived factor.

Matriptase is an epithelial-derived, integral membrane, trypsin-like serine protease. We have shown previously that matriptase exists both in complexed and noncomplexed forms. We now show that the complexed matriptase is an activated, two-chain form, which is inhibited in an acid-sensitive, reversible manner through binding to its cognate, Kunitz-type inhibitor, HAI-1 (hepatocyte growth factor activator inhibitor-1). Conversely, the majority of the noncomplexed matriptase is a single-chain zymogen, which lacks binding affinity to HAI-1, suggesting that matriptase, similar to most other serine proteases, is activated by proteolytic cleavage at a canonical activation motif. We have now generated mAbs specific for the conformational changes associated with the proteolytic activation of matriptase. Using these mAbs, which specifically recognize the two-chain form of matriptase, we demonstrate that matriptase is transiently activated on 184A1N4 human mammary epithelial cell surfaces following their exposure to serum. The ability of serum to activate matriptase is highly conserved across reptilian, avian, and mammalian species. This serum-dependent activation of matriptase on epithelial cell surfaces is followed by ectodomain shedding of both matriptase and its Kunitz-type inhibitor.     

Hydrodynamic parameters of native C-reactive protein molecule in a solution

The hydrodynamic properties of the C-reactive protein in solution (pH 6.8) were studied using quasi-elastic light scattering and size-exclusion liquid chromatography. It was shown that the solution containing the C-reactive protein represents a polydisperse system. The values of the translation diffusion coefficient and the apparent molecular weight of the C-reactive protein in solution at pH 6.8 were determined. The values of the translation diffusion coefficient, molecular weight and the hydration radius obtained suggest that the native pentameric C-reactive protein is the major form of the protein in solution at pH 6.8.     

Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity

In addition to hydrogen bonds, van der Waals forces contribute to the affinity of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the complexes of the L-arabinose-binding protein (ABP) with monosaccharides have been studied by means of site-directed mutagenesis, equilibrium and rapid kinetic binding techniques, and X-ray crystallography. ABP, a periplasmic transport receptor of Escherichia coli, binds L-arabinose, D-galactose, and D-fucose with preferential affinity in the order of Ara greater than Gal much greater than Fuc. Well-refined, high-resolution structures of ABP complexed with the three sugars revealed that the structural differences in the ABP-sugar complexes are localized around C5 of the sugars, where the equatorial H of Ara has been substituted for CH3 (Fuc) or CH2OH (Gal). The side chain of Met108 undergoes a sterically dictated, ligand-specific, conformational change to optimize nonpolar interactions between its methyl group and the sugar. We found that the Met108Leu ABP binds Gal tighter than wild-type ABP binds Ara and exhibits a preference for ligand in the order of Gal much greater than Fuc greater than Ara. The differences in affinity can be attributed to differences in the dissociation rates of the ABP-sugar complexes. We have refined at better than 1.7-A resolution the crystal structures of the Met108Leu ABP complexed with each of the sugars and offer a molecular explanation for the altered binding properties.     

Diffusion ordered spectroscopy as a complement to size exclusion chromatography in oligosaccharide analysis

A series of N-acetyl-chitooligosaccharides (GlcNAc)(1-6) have been studied by a nuclear magnetic resonance (NMR) method, diffusion ordered spectroscopy (DOSY). DOSY has also been applied to two additional synthetic related oligosaccharides [GlcNH(2)-(GlcNAc)(4) and GlcNH(2)-(GlcNAc)(2)-GlcNAcSO(3)Na]. A plot of the log of the determined diffusion coefficients (logD) of (GlcNAc)(n) versus the log of molecular weight was linear (6 points, R(2) = 0.995). The molecular weights of the two synthetic chitin derivatives could be estimated to within 10% error. The processed NMR data of all the chitooligosaccharides was also plotted in a polyacrylamide gel-like format to aid visual interpretation. Moreover, the logD value of the NMR signal resonances of a chitin-binding protein (hevein) changed as a function of a given titrated ligand, (GlcNAc)(6). Evidence for a 2:1 hevein:(GlcNAc)(6) complex is detected by DOSY at high hevein:(GlcNAc)(6) ratios. This data is consistent with published analytical ultracentrifugation and isothermal titration calorimetry data. A 1:1 complex is preferred at higher ligand concentrations. DOSY can complement size exclusion chromatography in carbohydrate research with the advantage that oligosaccharides are more readily detected by NMR.     

Immunostimulatory polysaccharides from Chlorella pyrenoidosa. A new galactofuranan. measurement of molecular weight and molecular weight dispersion by DOSY NMR

Fractionation of the hot water extract of Chlorella pyrenoidosa was performed using a combination of ethanol precipitation, size exclusion chromatography, and anion exchange chromatography. One fraction contained a new polysaccharide, and this compound was shown to be a 1-->2-linked beta-d-galactofuranan from its 1D and 2D (1)H and (13)C NMR spectra, with a molecular weight of 15 kDa from DOSY NMR measurements. A number of other fractions were shown to have the same repeating unit as the previously identified arabinogalactan. However, arabinogalactans from different fractions were shown by DOSY NMR to have different molecular weights, which ranged from 27 to 1020 kDa. Agreement with molecular weights measured for some of these fractions by SEC-MALS was very good, further confirming the relationship established by Viel et al. between molecular weights of neutral polysaccharides and self-diffusion coefficients. The smaller molecular weight polysaccharides, the galactofuranan and the 27 and 50 kDa arabinogalactans, were shown to be close to monodisperse by analysis of the distributions of the self-diffusion coefficients for the polymers. The larger arabinogalactans had considerable variation in their molecular weights (188 +/- 109 kDa and 1020 +/- 370 kDa). Only the two larger arabinogalactans showed immunostimulatory activity.     

Effect of Growth Conditions on the Formation of the Relaxation Complex of Supercoiled ColE1 Deoxyribonucleic Acid and Protein in Escherichia coli

Colicinogenic factor E1 (ColE1) is present in Escherichia coli strain JC411 (ColE1) cells to the extent of about 24 copies per cell. This number does not appear to vary in situations which give rise to twofold differences in the amount of chromosomal deoxyribonucleic acid (DNA) present per cell. If cells are grown in the absence of glucose, approximately 80% of the ColE1 molecules can be isolated as strand-specific DNA-protein relaxation complexes. When glucose is present in the medium, only about 30% of the plasmid molecules can be isolated as relaxation complexes. Medium shift experiments in which glucose was removed from the medium indicate that within 15 min after the shift the majority (>60%) of the plasmid can be isolated as relaxation complex. This rapid shift to the complexed state is accompanied by a two- to threefold increase in the rate of plasmid replication. The burst of replication and the shift to the complexed state are both inhibited by the presence of chloramphenicol. Inhibition of protein synthesis in log cultures by the addition of chloramphenicol or amino acid starvation allows ColE1 DNA to continue replicating long after chromosomal replication has ceased. Under these conditions, noncomplexed plasmid DNA accumulates while the amount of DNA that can be isolated in the complexed state remains constant at the level that existed prior to treatment. In the presence of chloramphenicol, there appears to be a random dissociation and association of ColE1 DNA and “relaxation protein” during or between rounds of replication.     

Mechanisms of controlled release from silk fibroin films

The controlled release of fluorescein-iso-thio-cyanate (FITC)-labeled dextrans from methanol-treated and untreated silk fibroin films was modeled to characterize the release kinetics and mechanisms. Silk films were prepared with FITC-dextrans of various molecular weights (4, 10, 20, 40 kDa). Methanol treatment was used to promote crystallinity. The release data were assessed with two different models, an empirical exponential equation commonly fit to release data and a mechanism-based semiempirical model derived from Fickian diffusion through a porous film. The FITC-dextran release kinetics were evaluated as a function of molecular weight and compared between the untreated- and methanol-treated films. For the empirical model, the estimated values of the model parameters decreased with the molecular weight of the analyte and showed no significant difference between untreated- and methanol-treated films. For the diffusion-based model, the estimated diffusion coefficient was smaller for the methanol-treated films than for the untreated films. Also, the diffusion coefficient was observed to decrease linearly with increasing molecular weight of the analyte. The percent of FITC-dextran loading entrapped and not released was less for the methanol-treated films than for untreated films and linearly increased with molecular weight. A linear regression was fit to the relationship between molecular weight and the percent of entrapped FITC-dextran particles. Using these defined linear relationships, we present an updated version of the diffusion model for simulating release of FITC-dextran of varied molecular weights from methanol-treated and untreated silk films.     

In vitro reconstitution of heat shock protein-peptide complexes for generating peptide-specific vaccines against cancers and infectious diseases

Known commonly as molecular chaperones for proteins, heat shock proteins (HSPs) have also been found to chaperone small molecular weight cellular peptides. HSP-peptide complexes can prime T cell immunity specific against the peptides bound to HSPs, but not against HSPs per se. This immunomodulatory functions of HSPs are based on two intrinsic properties. One, HSPs are excellent adjuvants due to their ability to activate dendritic cells (DCs). Two, HSPs can bind directly to their receptors on DCs to then channel HSP-associated peptides to associate with MHC molecules. When a specific antigenic peptide is defined, this peptide can also be complexed with either tissue derived or recombinant HSPs in vitro to generate HSP-peptide complexes as peptide-specific vaccines. This article focuses on the methods commonly used to reconstitute HSP-peptide complexes, and discusses assays to verify the efficiency of complexing for immunotherapy against cancers and infectious diseases.     

Data handling for interactive metabolomics: tools for studying the dynamics of metabolome-macromolecule interactions

All published metabolomics studies investigate changes in either absolute or relative quantities of metabolites. However, blood plasma, one of the most commonly studied biofluids for metabolomics applications, is a complex, heterogeneous mixture of lipoproteins, proteins, small organic molecules and ions which together undergo a variety of possible molecular interactions including metal complexation, chemical exchange processes, micellular compartmentation of metabolites, enzyme-mediated biotransformations and small-molecule-macromolecule binding. In particular, many low molecular weight (MW) compounds (including drugs) can exist both ‘free’ in solution and bound to proteins or within organised aggregates of macromolecules. To study the effects of e.g. disease on these interactions we suggest that new approaches are needed. We have developed a technique termed ‘interactive metabolomics’ or i-metabolomics. i-metabolomics can be defined as: “The study of interactions between low MW biochemicals and macromolecules in heterogeneous biosamples such as blood plasma, without pre-selection of the components of interest”. Standard 1D NMR experiments commonly used in metabolomics allow metabolite concentration differences between samples to be investigated because the intensity of each peak depends on the concentration of the compound in question. On the other hand, the instrument can be set-up to measure molecular interactions by monitoring the diffusion coefficients of molecules. According to the Stokes–Einstein equation, the diffusion coefficient of a molecule is inversely proportional to its effective size, as represented by the hydrodynamic radius. Therefore, when low MW compounds are non-covalently bound to proteins, the observed diffusion coefficient for the compound will be intermediate between those of its free and bound forms. By measuring diffusion by NMR, the degree of protein binding can be estimated for either low MW endogenous biochemicals or xenobiotics. This type of experiment is referred to as either Diffusion-Ordered Spectroscopy (DOSY) or Diffusion-Edited Spectroscopy, depending on the type of post-acquisition data processing applied to the spectra. Results presented in this paper demonstrate approaches for the non-selective modelling of metabolite-macromolecule interactions (i-metabolomics), whilst additionally highlighting some of the all too frequently ignored issues associated with interpretation of data derived from profiling of blood plasma.

     

Diffusion characteristics of substrates in Ca-alginate gel beads

The diffusion characteristics of several substrates of varying molecular sizes into and from Ca-alginate gel beads in well-stirred solutions were investigated. The values of the diffusion coefficient (D) of substrates such as glucose, L-tryptophan, and alpha-lactoalbumin [with molecular weight (MW) less than 2 x 10(4)] into and from the gel beads agreed with those in the water system. Their substrates could diffuse freely into and from the gel beads without disturbance by the pores in the gel beads. The diffusion of their substrates into and from the gel beads was also not disturbed by increasing the Ca-alginate concentration in the beads and the CaCl(2) concentration used in the gel preparation. In the case of higher molecular weight substances such as albumin (MW = 6.9 x 10(4)), gamma-globulin (MW = 1.54 x 10(5)) and fibrinogen (MW = 3.41 x 10(5)), the diffusion behaviors of the substrates into and from the gel beads were very different. No diffusion of their substrates into the gel beads from solutions was observed, and only albumin was partly absorbed on the surface of the gel beads. The values of D of their substrates from the gel beads into their solutions were smaller than their values in the water system, but all their substrates could diffuse from the gel beads. The diffusion of high molecular weight substrates was limited more strongly by the increase of Ca-alginate concentration in the gel beads than by the increase of the CaCl(2) concentration used in the gel preparation. Using these results, the capacity of Ca-alginate gel as a matrix of immobilization was discussed.     

Data handling for interactive metabolomics: tools for studying the dynamics of metabolome-macromolecule interactions

All published metabolomics studies investigate changes in either absolute or relative quantities of metabolites. However, blood plasma, one of the most commonly studied biofluids for metabolomics applications, is a complex, heterogeneous mixture of lipoproteins, proteins, small organic molecules and ions which together undergo a variety of possible molecular interactions including metal complexation, chemical exchange processes, micellular compartmentation of metabolites, enzyme-mediated biotransformations and small-molecule-macromolecule binding. In particular, many low molecular weight (MW) compounds (including drugs) can exist both ‘free’ in solution and bound to proteins or within organised aggregates of macromolecules. To study the effects of e.g. disease on these interactions we suggest that new approaches are needed. We have developed a technique termed ‘interactive metabolomics’ or i-metabolomics. i-metabolomics can be defined as: “The study of interactions between low MW biochemicals and macromolecules in heterogeneous biosamples such as blood plasma, without pre-selection of the components of interest”. Standard 1D NMR experiments commonly used in metabolomics allow metabolite concentration differences between samples to be investigated because the intensity of each peak depends on the concentration of the compound in question. On the other hand, the instrument can be set-up to measure molecular interactions by monitoring the diffusion coefficients of molecules. According to the Stokes–Einstein equation, the diffusion coefficient of a molecule is inversely proportional to its effective size, as represented by the hydrodynamic radius. Therefore, when low MW compounds are non-covalently bound to proteins, the observed diffusion coefficient for the compound will be intermediate between those of its free and bound forms. By measuring diffusion by NMR, the degree of protein binding can be estimated for either low MW endogenous biochemicals or xenobiotics. This type of experiment is referred to as either Diffusion-Ordered Spectroscopy (DOSY) or Diffusion-Edited Spectroscopy, depending on the type of post-acquisition data processing applied to the spectra. Results presented in this paper demonstrate approaches for the non-selective modelling of metabolite-macromolecule interactions (i-metabolomics), whilst additionally highlighting some of the all too frequently ignored issues associated with interpretation of data derived from profiling of blood plasma.     

Molecular weights of mitochondrial and cytoplasmic aminoacyl-tRNA synthetases of beef liver and their complexes

In eukaryotes, multienzyme complexes containing five to nine aminoacyl-tRNA synthetase activities have frequently been reported. In this study, we report the existence, in bovine liver cytoplasm, of a multienzyme complex containing at least 16 activities which can be disrupted by homogenization to give rise to smaller complexes and noncomplexed synthetases. Determination of the size and component activity of these complexes and of the molecular weights of all 20 free synthetases suggests that the smaller complexes and free activities normally identified arise from the larger complex by well-defined stages during homogenization. We also show that similar, though not identical, complexes are found in bovine liver mitochondria and give the molecular weights of 16 mitochondrial synthetases.