Convection-free boundary sedimentation of dilute protein solutions

Use of the density gradient sedimentation velocity technique appears to be essential for the accurate determination of the mean sedimentation coefficients of dilute protein solutions. When performed on an analytical ultracentrifuge equipped with a photoelectric-scanning-absorption optical system, the density gradient sedimentation velocity technique has been shown to be particularly useful in studying the subunit association-dissociation equilibria of multisubunit enzyme systems. The time factor has been shown to be a major advantage of the density gradient sedimentation velocity technique, as opposed to the sedimentation equilibrium technique, in studying the subunit association-dissociation equilibria of multisubunit enzymes such as rabbit muscle apo-glyceraldehyde-3-phosphate dehydrogenase, which is very unstable in dilute solution.     

Sedimentation coefficients of replicating and crosslinked DNA

The sedimentation coefficients of branched and cyclic replicating DNA structures have been calculated taking into account both chain stiffness and excluded volume effects. For branched DNA, the calculated ratio S⁰(α)/S⁰(0) of the sedimentation coefficient at degree of replication α to that at α = 0 increases from 1.000 to 1.331 as α goes from 0 to 1. For cyclic replicating DNA, S⁰(1)/S⁰(0) = 1.517. The considerable difference between these two ratios for α = 1 suggests that the two types of replicating structures may feasibly be distinguished by sedimentation velocity studies, A similar calculation has been made of the sedimentation coefficient of singly cross-linked DNA under denaturing conditions, as a function of placement of the crosslink. In 0.195M Na⁺, the ratio S⁰(α)/S⁰(0) varies from 1.000 at α = 0 to 1.124 at α = 0.5, where α is the fractional distance of the crosslink from the end of the chain.     

Density-gradient-sedimentation velocity of solvated macromolecules: Theoretical considerations about the buoyancy factor

The solvation of macromolecules lowers their sedimentation velocity in a density gradient. Some consequences of this effect are pointed out. Overlooking the solvation results in the understimation of the standard sedimentation coefficient of the macromolecules. (The error increases with partial specific volume, solvation, and the density in the gradient.) The construction of an isokinetic density gradient also requires that solvation be taken into account. This can be done when the solvation parameter, relevant in this context, is known.     

A bead and spring model for the stiffness of DNA.

The chain stiffness of linear native DNA is represented by a generalized bead and spring model recently proposed. It incorporates molecular rigidity by means of springs between beads, which are second neighbors along the contour of the chain. These springs are equivalent to elastic forces having longitudinal and transversal contributions. The model is compared with existing experimental data of sedimentation and low-angle light scattering to obtain the statistical parameters of DNA. The value of the statistical length obtained with this model is 1300 Å. The same value is obtained with the wormlike chain. Throughout this analysis, excluded volume is left out as a simplifying assumption.     

Superhelix density heterogeneity in closed circular intracellular PM2 DNA

Covalently closed intracellular DNA obtained from Pseudomonas BAL 31 20 min after infection with PM2 phage has been shown to be heterogeneous in superhelix density. Analytical band sedimentation, in the presence of low concentrations of ethidium bromide, has been carried out on fractions centripetal and centrifugal to the mode of a single band of closed circular DNA in a preparative propidium iodide–CsCl buoyant density gradient. Different average sedimentation rates, as well as different band shapes, have been observed for upper and lower fractions centrifuged at a dye concentration near the minimum in s° versus ethidium bromide concentration titrations performed on DNA from proximate intermediate fractions. Similar differences, although not as pronounced, have been obtained at a dye concentration corresponding to a point in the steep region of the titrations. Differential band sedimentation experiments performed on the same fractions have confirmed these results. Differential band sedimentation experiments on similarly fractionated mature PM2 I DNA (closed circular form) have shown slight differences in the relative sedimentation rates of upper and lower fractions at dye concentrations corresponding to the steep regions in the titrations. The same experiments, when performed on nicked circular DNA obtained from heating both the mature and intracellular fractions, showed no evidence of differences in sedimentation coefficients. Such results may indicate slight heterogeneity in the superhelix density of viral PM2 I DNA; however, the degree of this heterogeneity would be somewhat less than that of the intracellular DNA. The possibility that superhelix density heterogeneity may arise from displacement loops, which have been found at low levels in intracellular PM2 DNA, has been subjected to experimental tests. Unless such structures are originally present and removed by the isolation procedure, this possibility may be rejected.     

On the rate of ribosome translocation anisotropy and ribosome saturation in the polysome

This study examines the rate of ribosome translocation in the mammalian polysome engaged in protein synthesis by utilizing our knowledge of the hydrodynamic behavior of the rat liver polysomes, sedimenting in a linear sucrose density gradient. The average distance between adjacent ribosomes in the polysome was estimated assuming an extended linear configuration of the polysomes during sedimentation. Based on this estimate, the velocity of ribosome movement along the messenger RNA appears to be non-uniform and inversely related to the ribosome content of the polysome. Such non-uniformity prevails at stages of translation prior to ribosome “saturation” of the polysome. A correlation has been made between the results reported herein and previously published evidence on the rate of polypeptide chain synthesis. The steady-state condition for the polypeptide chain assembly is viewed as representing the state of ribosome “saturation”, characterized by a minimal ribosome velocity and a maximum density of ribosome distribution, both functions being uniform throughout the entire length of the polysome.     

Opticohydrodynamic properties of high-molecular-weight DNA. III. The effects of NaCl concentration

Excluded volume and persistence length of high-molecular-weight DNA from T2 bacteriophage have been evaluated over a range of NaCl concentrations from 0.005 to 2.0M using low-shear flow-birefringence and intrinsic-viscosity data. Uncertainty in persistence length due to ambiguity in the assignment of intrinsic birefringence has been avoided by calibrating the data at 0.2M NaCl using a recently reported persistence-length value based upon photon correlation spectroscopy [Jolly, D. & Eisenberg, H. (1976) Biopolymers 15 , 61]. Results at high salt concertrations are in satisfactory agreement with other estimates of excluded volume and chain flexibility in the literature, but at very low salt concentrations they reflect greater chain expansion than has heretofore been reported. The extinction-angle data imply a transition from a nondraining chain with excluded volume at 0.1M NaCl to an almost freely draining chain at 0.005M NaCl. Over this same salt range, the experimental persistencelength data agree very well with Flory's thermodynamic chain-expansion theory [Flory, P. J. (1953) J. Chem. Phys. 21 , 162], but are in generally poor agreement with other theoretical treatments. A detailed comparison of the results with other data in the literature suggests that the combined flow-birefringence-intrinsic-viscosity technique employed here may be more sensitive to the distribution of chain stiffness and excluded volume in polyelectroytechain expansion of DNA than are othe rhydrodynamic methods such as sedimentation or intrinsic viscosity alone.     

Characterization by sedimentation analysis of kinetoplast DNA from Trypanosoma cruzi at different stages of culture.

The kinetoplast DNA networks of Trypanosoma cruzi exist under two forms which have been studied by equilibrium density centrifugation in CsCl gradients containing ethidium bromide and by band sedimentation analysis. The relative proportion of the two forms has been measured and varies significantly between the exponential and stationary phase of growth, suggesting that one of these forms is a replicative intermediate. Both forms exhibit very high sedimentation coefficients. The sedimentation velocity ethidium titration was used to measure the superhelix density of the kinetoplast DNA after having established the validity of the method with in vitro closed DNA networks. The superhelix density of the native form of the kinetoplast DNA minicircles is very low and varies according to the physiological state of the trypanosomes. Furthermore, we observed a significant increase of the superhelix density of the kinetoplast DNA of trypanosomes grown in the presence of ethidium.     

Interaction of small peptides with lipid bilayers.

Molecular dynamics simulations of the tripeptide Ala-Phe-Ala-O-tert-butyl interacting with dimyristoylphosphatidylcholine lipid bilayers have been carried out. The lipid and aqueous environments of the peptide, the alkyl chain order, and the lipid and peptide dynamics have been investigated with use of density profiles, radial distribution functions, alkyl chain order parameter profiles, and time correlation functions. It appears that the alkyl chain region accommodates the peptides in the bilayer with minimal perturbation to this region. The peptide dynamics in the bilayer bound form has been compared with that of the free peptide in water. The peptide structure does not vary on the simulation time scale (of the order of hundreds of picoseconds) compared with the solution structure in which a random structure is observed.     

Extracellular matrix- and cytoskeleton-dependent changes in cell shape and stiffness

Cell spreading is correlated with changes in important cell functions including DNA synthesis, motility, and differentiation. Spreading is accompanied by a complex reorganization of the cytoskeleton that can be related to changes in cell stiffness. While cytoskeletal organization and the resulting cell stiffness have been studied in motile cells such as fibroblasts, less is known of these events in nonmigratory, epithelial cells. Hence, we examined the relationship between cell function, spreading, and stiffness, as measured by atomic force microscopy. Cell stiffness increased with spreading on a high density of fibronectin (1000 ng/cm(2)) but remained low in cells that stayed rounded on a low fibronectin density (1 ng/cm(2)). Disrupting actin or myosin had the same effect of inhibiting spreading, but had different effects on stiffness. Disrupting f-actin assembly lowered both stiffness and spreading, while inhibiting myosin light chain kinase inhibited spreading but increased cell stiffness. However, disrupting either actin or myosin inhibited DNA synthesis. These results demonstrate the relationship between cell stiffness and spreading in hepatocytes. They specifically show that normal actin and myosin function is required for hepatocyte spreading and DNA synthesis and demonstrate opposing effects on cell stiffness upon disruption of actin and myosin.     

Reversible jump Markov chain Monte Carlo computation and Bayesian model determination

Markov chain Monte Carlo methods for Bayesian computation haveuntil recently been restricted to problems where the joint distributionof all variables has a density with respect to some fixed standardunderlying measure. They have therefore not been available forapplication to Bayesian model determination, where the dimensionalityof the parameter vector is typically not fixed. This paper proposesa new framework for the construction of reversible Markov chainsamplers that jump between parameter subspaces of differingdimensionality, which is flexible and entirely constructive.It should therefore have wide applicability in model determinationproblems. The methodology is illustrated with applications tomultiple change-point analysis in one and two dimensions, andto a Bayesian comparison of binomial experiments.     

Comparative studies on solution characteristics of mannuronan epimerized by C-5 epimerases

Both dilute and concentrated solutions of bacterial Mannuronan (MANNA) and its epimerized products by AlgE1 at 5 and 24 h, named MANNAEp1t5h and MANNAEp1t24h, respectively, and AlgE4 (MANNAEp4) have been studied as a function of variables such as polymer concentration and ionic strength (NaCl) in order to investigate the macromolecular solution properties of these innovative polyuronic acids having the same charge density but different composition and sequence of β-d-mannuronic acid (-M-), -l-guluronic acid (-G-) or MG-blocks.

Measurements of intrinsic viscosity [η] as a function of ionic strength, I, by capillary viscometry has led to an estimate of the Smidsrød-Haug parameter B, an index useful to characterize the stiffness of polymeric chains. The results are largely consistent with much of the published data relative to chain extension and conformational freedom around the torsional angles of the glycosidic linkages occurring in alginates.

Steady shear rheometry provided information about the coil-overlapping parameter c*, which marks the transition from dilute to concentrated solution. The slopes of the double logarithmic plots of η_sp vs. c[η] both at low and high degrees of coil overlap suggest that all samples solutions behave like linear polymer entangled network systems. The value of c* is strictly influenced by the stiffness of the chains, and hence by the primary structure.

Dynamic shear rheometry shows that the frequency dependence of dynamic viscosity is only partially superimposable to the shear rate dependence of viscosity. Such behaviour may be ascribed to the presence of semiflexible polymeric coils in a non-totally destructured entangled state.

By solvent/non-solvent (H₂O/isopropanol) fractionation carried out on mannuronan, a set of samples with different average molecular weights and narrow polydispersities were obtained. Triple detection GPC allowed the evalutation of the Mark–Houwink–Sakurada parameters as well as of the characteristic ratio C_∞ for one of the fractionated MANNA samples. The chain persistence length was estimated by the wormlike chain model.     

The structure of chromatin from the pigeon brain. II. Sedimentation analysis of oligonucleosome density

Compaction of pigeon brain and rat thymus chromatin differing in the length of the linker DNA has been studied by the method of velocity sedimentation. The dependence of sedimentation coefficients of oligonucleosomes on the number of nucleosomes in the chain in solution of different ionic strength (0.005-0.085) has been analyzed. The analyses of these dependences showed that the structure of oligonucleosomes of both cell types at low ionic conditions may be described by the model of a zig-zag-shaped nucleosomal chain. The process of compaction of the oligonucleosomes at higher ionic strength (0.045-0.085) proceeds similarly for brain and thymus chromatin. The formation of a superhelical structure is determined by the interaction of no less than 6 nucleosomes; the compactness of the structure is significantly increased when the number of nucleosomes in the chain exceeds 10. The ability of the brain oligonucleosomes to form a compact structure despite the short linker allow the suggestion that in brain short chromatin the DNA chain does not form two complete turns in the nucleosome. This provides necessary flexibility of brain chromatin.     

Analysis of ribonucleoproteins of influenza virus containing genomic and complementary RNA

The density and sedimentation characteristics of ribonucleoproteins (RNP) containing genomic RNA from influenza virus and RNA complementary have been studied. Radioactive RNA from infected cells has been used for analysis. RNA classes of interest were isolated by reannealing with abundant nonradioactive genomic and complementary RNA and separation of resulting duplexes in electrophoresis. The RNP containing antigenomic virus-specific RNA are practically identical to "genomic" RNP for their sedimentation and density characteristics. The "plus" RNP is characterized by the stoichiometric mode of RNA protein interaction.     

Monte carlo computation of the supercoiling energy,the sedimentation constant,and the radius of gyration of unknotted and knotted circular DNA

Closed random Gaussian polygonal chains of N (6 < N < 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types—0, 3₁, 4₁, 5₁, and 5₂—the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw²/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N^1/4 (w/N)², and therefore depends on the writhing density and on the length of the DNA.     

A diffusion driven instability in systems that separate particles by velocity sedimentation.

Velocity sedimentation has been used extensively to separate particles according to the magnitude of their sedimentation velocity in suitable media. This technique has been used over a wide range of particle size from protein molecules, viruses, subcellular particles to whole cells. Successful separation demands that collective particle motion should not occur. In practice it is observed that such systems may, under certain circumstances, suffer from a particular type of instability which destroys the normal dependence of sedimentation velocity on particle size and density. The aim of this paper is to identify the critical parameters that determine the development of this instability. Stability criteria are deduced and predictions of the theory compared with published observations. Satisfactory agreement between theory and observation is obtained. It is concluded that the simple stability criterion, namely that stable sedimentation will occur if the total density gradient is in the direction of the sedimenting force, grossly overestimates the particle load that can be separated in practice. Some specific recommendations for optimum particle loading are included. Earlier theoretical and experimental works are briefly reviewed.     

Characterization of Inducible Bacteriophages in Bacillus licheniformis

Two morphologically distinct and physically separable defective phages have been found in Bacillus licheniformis NRS 243 after induction by mitomycin C. One of them (PBLB) is similar to the defective phage PBSX of B. subtilis, which has a density of 1.373 g/cm(3) in CsCl and a sedimentation coefficient of 160S. PBLB incorporates into its head mainly bacterial deoxyribonucleic acid (DNA) which has a sedimentation coefficient of 22S and a buoyant density in CsCl of 1.706 g/cm(3). The other phage (PBLA) has a morphology similar to the temperate phage phi105 of B. subtilis; the head diameter is about 66 nm, and it possesses a long and noncontractile tail. PBLA has a density of 1.484 g/cm(3) in CsCl and the phage-specific DNA, which is exclusively synthesized after induction by mitomycin C, has a density of 1.701 g/cm(3). PBLA DNA is double-stranded and has a sedimentation coefficient of 36S, corresponding to a molecular weight of 34 x 10(6) to 35 x 10(6) daltons. The phage DNA has one interruption per single strand, giving single-stranded segments with molecular weights of 13 x 10(6) and 4 x 10(6) daltons. Common sequences between the two phage DNA species and with their host DNA have been demonstrated by DNA-DNA hybridization studies. Both phage particles kill sensitive bacteria. However, all attempts thus far to find an indicator strain to support plaque formation have been unsuccessful.     

Evaluation of chain stiffness of partially oxidized polyguluronate

The chain stiffness of macromolecules is considered critical in their design and applications. This study utilizes polyguluronate derived from alginate, a typical polysaccharide widely utilized in many biomedical applications, as a model macromolecule to investigate how the chain stiffness can be tightly regulated by partial oxidation. Alginate has a backbone of inherently rigid alpha-L-guluronate (i.e., polyguluronate) and more flexible beta-D-mannuronate. The chain stiffness of the polyguluronate was specifically studied in this paper, as this component plays a critical role in the formation of alginate hydrogels with divalent cations and is the dominant factor in determining the chain stiffness of alginate. We have utilized size-exclusion chromatography, equipped with refractive index, viscosity, and light-scattering detectors, to determine the intrinsic viscosity and the weight-average molecular weight of each fraction of samples. The chain stiffness of partially oxidized polyguluronate was then evaluated from the exponent of the Mark-Houwink equation and the persistence length. We have found that partial oxidation can be used to tightly regulate the steric hindrance and stiffness of the polyguluronate backbone. This approach to control the chain stiffness of inherently rigid polysaccharides by partial oxidation may find many applications in biomedical utilization of these materials.     

Antigen-initiated B lymphocyte differentiation. IX. Characterization of memory AFC progenitors by buoyant density and sedimentation velocity separation.

The characteristics of memory B cell antibody-forming cell (AFC) progenitors from long-term hapten-primed CBA mice were investigated by using sedimentation velocity and buoyant density separation to isolate physically distinct B cell sub-sets. The isolated fractions were assayed by the adoptive immune response to NIP-POL antigen, under conditions where neither T cells nor other accessory cells were limiting the IgM or IgG AFC responses. The results were compared to previous studies on the IgM AFC-progenitors of unprimed adult mice. Splenic IgM and IgG memory AFC-progenitor activity was largely found among the typical B cells of slow to medium sedimentation rate, in contrast to the fastre sedimenting IgM AFC-progenitor activity of unprimed animals. Splenic IgM and IgG memory AFC-progenitor activity was found among the medium to light density cells, and so resembled by this parameter the IgM AFC-progenitor activity in unprimed animals. Thoracic duct lymphocytes from hapten-primed mice also exhibited memory IgM and IgG AFC-progenitor activity in the slow-medium sedimentation range. However, in contrast to spleen, the IgM and IgG memory AFC-progenitor activity in lymph was found among very dense B cells. Two physically distinct sub-populations of memory B cells have thus been identified, namely: i) small, medium-light density, presumably tissue-resident B lymphocytes found in spleen; and ii) small, dense, presumably recirculating B lymphocytes found in lymph. Both physical forms include IgM and IgG progenitors. Both forms are distinct from the larger, medium-light density "virgin" AFC-progenitors in the spleen of unprimed adult mice.     

The concentration-dependence of macromolecular parameters.

Theories concerning the concentration-dependence of sedimentation and diffusion coefficients for macro-molecules in dilute solution are compared and discussed, together with their experimental basis. An attempt has been made to clarify an important uncertainty still present in the literature as to whether sedimentation coefficients should be corrected for solvent or solution density. It is pointed out that the two processes yield the same extrapolation limit but different concentration-dependencies, which have, however, been related. A general expression is derived thermodynamically for the concentration-dependence of diffusion that includes the coefficient of the concentration term involved in sedimentation (on the basis of sedimentation coefficients corrected from solution density). For rigid spherical particles the expression is shown to be exactly equivalent to one given by Batchelor [(1976) J. Fluid Mech. 74, 1-29], which was derived on the basis of sedimentation coefficients corrected from solvent density. Finally, we discuss the concentration-dependence of apparent weight-average relative molecular masses ('molecular weights') (from, e.g., sedimentation equilibrium) and note an important omission in some earlier representations.