SEARCH · PubMed Health

Results for “ULTRACENTRIFUGATION”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,657 records · Page 92Linked to original sources

PubMed1997

The effect of point mutations on the free energy of transmembrane alpha-helix dimerization.

Glycophorin A forms homodimers through interaction of the single, helical transmembrane domains of the monomers. The dimers are stable in sodium dodecylsulfate (SDS), permitting a number of studies that have identified a critical motif of residues that mediates dimer formation. We have used analytical ultracentrifugation to measure the energy of dimerization in a non-denaturing detergent solution and have observed the changes in energy arising from two of the mutants previously studied. Use of the detergent pentaoxyethylene octyl ether (C8E5) is a great advantage, since its micelles are neutrally buoyant and the detergent allows a reversible association to occur between monomer and dimer states of the glycophorin A transmembrane helices during the time-scale of sedimentation equilibrium. Use of this detergent in analytical ultracentrifugation may enable a wide range of studies of molecular association events in membrane proteins. We find that the glycophorin A transmembrane helix dimerizes with a dissociation constant of 240(+/-50) nM, corresponding to a free energy of dissociation of 9.0(+/-0.1) kcal mol-1. Point mutants that were found to be disruptive in SDS (L75A, I76A) reduced the dimer affinity in the C8E5 detergent environment (Kd=1.7(+/-0.2) microM and 4.2(+/-0.9) microM, respectively). Thus, the earlier findings are placed on a quantitative, relative energy scale of association by our measurements. Molecular modeling and simulations suggest that the energy differences can be accounted for as changes in van der Waals interactions between helices.

Cell Membrane↗

PubMed1999

Molecular architecture of the rod domain of the Dictyostelium gelation factor (ABP120).

The Dictyostelium discoideum gelation factor is a two-chain actin-cross-linking protein that, in addition to an N-terminal actin-binding domain, has a rod domain constructed from six tandem repeats of a 100-residue motif that has an immunoglobulin fold. To define the architecture of the rod domain of gelation factor, we have expressed in E. coli a series of constructs corresponding to different numbers of gelation factor rod repeats and have characterised them by chemical crosslinking, ultracentrifugation, column chromatography, matrix-assisted laser desorption ionisation (MALDI) mass spectrometry and NMR spectroscopy. Fragments corresponding to repeats 1-6 and 5-6 dimerise, whereas repeats 1-5 and single repeats 3 and 4 are monomeric. Repeat 6 interacts weakly and was present as monomer and dimer when analysed by analytical ultracentrifugation. Proteolytic digestion of rod5-6 resulted in the generation of two polypeptides that roughly corresponded to rod5 and part of rod6. None of these polypeptides formed dimers after chemical crosslinking. Stable dimerisation therefore appears to require repeats 5 and 6. Based on these data a model of gelation factor architecture is presented. We suggest an arrangement of the chains where only the carboxy-terminal repeats interact as was observed for filamin/ABP280, the mammalian homologue of gelation factor.

Animals↗

PubMed1999

Quaternary re-arrangement analysed by spectral enhancement: the interaction of a sporulation repressor with its antagonist.

The protein/protein interaction between SinI and SinR has been studied by analytical ultracentrifugation and gel electrophoresis in an attempt to understand how these proteins contribute to developmental control of sporulation in Bacillus subtilis. SinR was found to be tetrameric, while SinI was found to exist as monomers and dimers in a rapidly reversible equilibrium. Labelling of SinR by incorporating the tryptophan analogue 7-azatryptophan (7AW) into the protein in place of tryptophan shifts the UV absorbance spectrum, thus allowing selective monitoring of 7AWSinR at 315 nm using the UV absorption optics of the analytical ultracentrifuge. Selective monitoring of SinR in mixtures of SinR and SinI enables the binding and stoichiometry of the interaction to be investigated quantitatively and unambiguously. We demonstrate that the oligomeric forms of SinR and SinI re-arrange to form a tight 1:1 SinR:SinI complex, with no stable intermediate species. A fragment of SinR, SinR(1-69), which contains only the DNA-binding domain, was found to be monomeric, showing that the protein appears not to oligomerise in a similar manner to the Cro repressor, a protein with which it shares a marked structural similarity.

Amino Acid Sequence↗

PubMed2001

Solution studies of recombinant human stromal-cell-derived factor-1.

Stromal-cell-derived factor-1 (SDF-1alpha) is an 8-kDa chemokine that is constitutively expressed in bone-marrow-derived stromal cells and has been identified as a ligand for the CXCR4 receptor. We produced the chemokine recombinantly as methionine-SDF-1alpha in Escherichia coli without the leader peptide sequence. The protein was denatured, refolded, and further purified by reversed-phase HPLC. SDF-1alpha was shown to be >95% pure as judged by SDS-PAGE. The final yield of purified and refolded SDF-1alpha was 1-2 mg per gram of wet cell paste. The refolded protein is a ligand for the CXCR4 receptor and has been used to block HIV-mediated cell fusion and downmodulates the CXCR4 receptor. Our ability to purify hundreds of milligrams of refolded protein allowed us to conduct detailed studies of the biophysical properties of the protein. We have used a combination of biophysical techniques to study the solution properties of SDF-1alpha. The average mass of SDF-1alpha, as determined by static light scattering, gave us the first indications that the chemokine may self-associate. Further investigation with sedimentation velocity ultracentrifugation confirmed the existence of two species. The measured s(20, W) values defined two masses corresponding to monomer and dimer. Finally, sedimentation equilibrium ultracentrifugation and dynamic light scattering yielded a composite value of 150 +/- 30 microM for the dimerization constant. We conclude that SDF-1alpha exists in a monomer-dimer equilibrium.

Anti-HIV Agents↗

PubMed1988

Subcellular localisation and sedimentation behaviour of antigen 60 from Mycobacterium bovis BCG.

Preparation, composition and immunological properties of A60 of Mycobacterium bovis BCG were previously described (Cocito and Vanlinden 1986). The present study focused on the intracellular distribution of this antigen. Fractionation of mycobacterial homogenates by ultracentrifugation indicated that most of A60 was present within the cytoplasm. Some of the antigen was located within the cell wall, from which it was released by extraction with alkali. Submission of cytoplasm to high speed centrifugation caused A60 to cosediment with ribosomes; however, dissociation of ribosomes in low-Mg buffer did not alter the sedimentation pattern of A60. Labelled A60, after ultracentrifugation in sucrose density gradients without Mg2+, was distributed throughout the entire gradient: treatment of (125I)A60 with urea or detergents produced a peak of radioactivity located in the upper part of the gradient. It is concluded that A60 is represented by a heterogeneous family of molecules of increasing sizes: polymerization being enhanced by Mg2+ and reversibly prevented by urea. Some or all of the biological properties hitherto attributed to ribosomal particles may, in fact, be due to their contamination with cosedimented A60.

Antigens, Bacterial↗

PubMed1995

Interactions of myelin basic protein with palmitoyllysophosphatidylcholine: characterization of the complexes and conformations of the protein.

The stoichiometry of palmitoyllysophosphatidylcholine/myelin basic protein (PLPC/MBP) complexes, the location of the protein in the lysolipid micelles, and the conformational changes occurring in the basic protein and peptides derived from it upon interaction with lysolecithin micelles were investigated by circular dichroic spectropolarimetry, ultracentrifugation, electron paramagnetic resonance (EPR) and 31P, 13C, and 1H nuclear magnetic resonance spectroscopy (NMR), and electron magnetic resonance spectroscopy (NMR), and electron microscopy. Ultracentrifugation measurements indicated that well-defined complexes were formed by the association of one protein molecule with approximately 141 lysolipid molecules. Small-angle X-ray scattering data indicated that the PLPC/MBP complexes form particles with a radius of gyration of 3.8 nm. EPR spectral parameters of the spin labels 5-, and 16-doxylstearate incorporated into lysolecithin/basic protein aggregates, and 13C- and 1H-NMR relaxation times of PLPC indicated that the addition of the protein did not affect the environment and location of the labels and the organization of the lysolipid micelles. The data suggested that MBP lies primarily near the surface of the micelles, with segments penetrating beyond the interfacial region into the hydrophobic interior, but without any part of the protein being protected against rapid exchange of its amide groups with the aqueous environment. The basic protein acquired about 20% alpha-helix when bound to lysolipid micelles. Circular dichroic spectra of sequential peptides derived by cleavage of the protein revealed the formation of alpha-helical regions in the association with lysolecithin. Specific residues in myelin basic protein that participated in binding to the micelles were identified from magnetic resonance data on changes in the chemical shifts and intensities of assigned resonances, and line broadening of peaks by fatty acid spin-labels incorporated into the micelles.

Animals↗

PubMed1995

Current Triton X-100 treatments do not allow a complete plasminogen activator extraction from developing nervous tissue.

Determinations of plasminogen activator (PA) activity are usually performed in Triton X-100-treated tissue homogenates or crude membrane fractions. Such preparations usually involve a single Triton X-100 treatment. In the present paper we describe the pattern of variability of PA activity measured in different fractions obtained from the developing chick CNS by a repetitive procedure of Triton X-100 treatment and ultracentrifugation. To further characterize this PA activity we have also performed zymographic analyses during the embryonic development and the early postnatal life. Our results show that: a) a single Triton X-100 treatment does not completely extract the enzyme and this lead to an underestimation of the total PA activity; b) the PA activity is associated with the particulate component of the total tissue homogenate requiring its complete solubilization more drastic Triton X-100 treatments; c) better estimations of total and specific activities are obtained by using soluble fractions derived by ultracentrifugation from Triton X-100-treated membrane fractions; d) the developing chick optic lobe expresses only one kind of PA molecule along the entire development; e) the level of PA activity vary characteristically during the ontogeny and the early postnatal life indicating the existence of a developmentally regulated mechanism of PA expression.

Aging↗

PubMed1977

[Isolation and characterization of 7S-beta1-globuline from human erythrocytes (author's transl)].

A new protein was isolated from lysates of washed human erythrocytes in a two step procedure using ionexchange chromatography and gel filtration. The protein has the electrophoretic mobility of a beta1-globulin. On ultracentrifugation the purified protein when dissolved in a 0.05 M phosphate buffer (pH 6.8), containing 0.2 M NaCl sediments with 6.88 S and shows a molecular weight of 150,000-180,000 daltons. In salt solutions with higher ionic strength the molecules dissociate reversibly into subunits which have a molecular weight of 40,000-45,000 daltons. The 7S-beta1-erythrocyte protein according to its behavior at ultracentrifugation, gel filtration and SDS poly-acrylamide gel electrophreses apparently is composed of 4 identical or similar subunits which are loosely held together by noncovalent bonds. Chemically the 7S-beta1-erythrocyte protein consists of 99% amino acids and 1% carbohydrates. The concentration of this protein in erythrocytes amounts to 250 mg per 100 ml packed red blood cells. The protein is not found in the membrane. In its physical, chemical and immunochemical properties the 7S-beta1-erythrocyte protein differs from all other well defined proteins and enzymes from human red cells thus far known.

Beta-Globulins↗

PubMed1977

Evaluation of the classical methods for the diagnosis of type III hyperlipoproteinemia.

Familial type III hyperlipoproteinemia is characterized by the presence of elevated plasma levels of very low density lopoproteins (VLDL) which contain an increased amount of cholesterol and by the presence of a significant amount of lipoproteins with an intermediate density between that of VLDL and low density lipoproteins (LDL); the intermediate density lopoproteins, designated IDL or Lp III, have a slower electrophoretic migration rate than VLDL, and are found in the ultracentrifugal top fraction as a contaminant. Classically, the diagnosis of type III is based on the demonstration of beta-migrating lipoproteins in the ultracentrifugal top fraction (density less than 1.006), thus "floating beta-lipoprotein". More recently, it has been proposed that an elevated VLDL-cholesterol to triglyceride ratio is diagnostic of the disorder. In the present report, we have compared the two methods for their diagnostic value and have concluded that the chemical index definition is the more reliable method for the diagnosis of type III hyperlipoproteinemia.

Electrophoresis, Paper↗

PubMed1978

Plasma, apolipoprotein, A-I and A-II levels in hyperlipidemia.

Some of the component moieties of high density lipoproteins (HDL) were analyzed in normal subjects and in patients with hyperlipidemia. Apoproteins A-I and A-II were quantified by radioimmunoassay, HDL cholesterol and triglycerides were assessed on heparin-MnCl2 supernates of fasting plasmas. We found that HDL is enriched in triglycerides in all forms of hyperlipidemia, while the proportion of ApoA-II is unaltered and the proportion of ApoA-I is decreased. Thus, the composition of HDL is altered in hupertirglyceridemia. The molecular associations of ApoA-I and ApoA-II in plasma were also examined by assaying the apoprotein contents of plasma fractions prepared by ultracentrifugation and by gel filtration column chromatograpy. The ApoA-I contents of d smaller than 1.063 fraction increased in hyperlipidemia from smaller than 0.5% to approximately 2%, but the ApoA-I contents of the d greater than 1.21 fraction remained at less than 12% of total plasmas with triglyceride levels smaller than 1500 mg/dl. d greater than 1.21 ApoA-I rose to 23% in one plasma with a triglyceride level of greater than 1700 mg/dl. On column chromatography, ApoA-I eluted with the lipoproteins and also in a fraction whose molecular weight (MW) appeared to be approximately 50,000 daltons. The proportion of plasma ApoA-I which eluted in the 50,000 MW peak was positively correlated with plasma triglyceride levels, but at triglyceride levels of less than 1500 mg/dl, less than 20% of ApoA-I was in the 50,000 MW peak. Between levels of approximately 2000 and 12,000 mg/dl, the percentage "50,000 M.W. ApoA-1" was 20-25%. The ApoA-II contents of d smaller than 1.063 fractions were also increased in hyperlipidemia, but greater than 95% of ApoA-II was found in the HDL fractions in both normal and hyperlipidemic plasma both by column chromatography and ultracentrifugation. Thus, the molecular association of ApoA-I appears to be altered in hyperlipidemia.

Apolipoproteins↗

PubMed2005

Insight into the self-association of key enzymes from pathogenic species.

Self-association of protein monomers to higher-order oligomers plays an important role in a plethora of biological phenomena. The classical biophysical technique of analytical ultracentrifugation is a key method used to measure protein oligomerisation. Recent advances in sedimentation data analysis have enabled the effects of diffusion to be deconvoluted from sample heterogeneity, permitting the direct identification of oligomeric species in self-associating systems. Two such systems are described and reviewed in this study. First, we examine the enzyme dihydrodipicolinate synthase (DHDPS), which crystallises as a tetramer. Wild-type DHDPS plays a critical role in lysine biosynthesis in microbes and is therefore an important antibiotic target. To confirm the state of association of DHDPS in solution, we employed sedimentation velocity and sedimentation equilibrium studies in an analytical ultracentrifuge to show that DHDPS exists in a slow dimer-tetramer equilibrium with a dissociation constant of 76 nM. Second, we review works describing the hexamerisation of GDP-mannose pyrophosphorylase (GDP-MP), an enzyme that plays a critical role in mannose metabolism in Leishmania species. Although the structure of the GDP-MP hexamer has not yet been determined, we describe a three-dimensional model of the hexamer based largely on homology with the uridyltransferase enzyme, Glmu. GDP-MP is a novel drug target for the treatment of leishmaniasis, a devastating parasitic disease that infects more than 12 million people worldwide. Given that both GDP-MP and DHDPS are only active in their oligomeric states, we propose that inhibition of the self-association of critical enzymes in disease is an emerging paradigm for therapeutic intervention.

Animals↗

PubMed2005

Comparison of diafiltration and tangential flow filtration for purification of nanoparticle suspensions.

PURPOSE: The study reports evaluation of different purification processes for removing surplus surfactant and formulating stable nanoparticle dispersions. METHODS: Nanoparticle formulations prepared from poly(D,L-lactide-co-glycolide) and polyvinyl alcohol (PVA) were purified by a diafiltration centrifugal device (DCD), using 300K and 100K molecular weight cut-off (MWCO) membranes and a tangential flow filtration (TFF) system with a 300K MWCO membrane. The effects of process parameters including MWCO, transmembrane pressure (TMP), and mode of TFF on nanoparticle purification were evaluated, and two purification techniques were compared to the commonly used ultracentrifugation technique. RESULTS: Both DCD and TFF systems (concentration mode at TMP of 10 psi) with 300K MWCO membrane removed maximal percent PVA from nanoparticle dispersions (89.0 and 90.7%, respectively). T90, the time taken to remove 90% of PVA in 200-ml sample, however, was considerably different (9.6 and 2.8 h, respectively). Purified nanoparticle dispersions were stable and free of aggregation at ambient conditions over 3 days. This is in contrast to the ultracentrifugation technique, which, although it can yield a highly purified sample, suffers from drawbacks of a level of irreversible nanoparticle aggregation and loss of fine particles in the supernatant during centrifugation. CONCLUSIONS: The TFF, in concentration mode at TMP of 10 psi, is a relatively quick, efficient, and cost-effective technique for purification and concentration of a large nanoparticle batch (>or=200 ml). The DCD technique can be an alternative purification method for nanoparticle dispersions of small volumes.

Adsorption↗

PubMed1984

An automated method for determination of the sedimentation coefficient of macromolecules using a preparative centrifuge.

Following centrifugation in a preparative ultracentrifuge at relatively high speeds for 1-3 h, quartz tubes containing approximately 150 microliter of macromolecular solution are optically scanned using an apparatus and method previously described (Attri, A. K., and Minton A. P. (1983) Anal. Biochem. 133, 142-152). The resulting data are processed by microcomputer immediately upon completion of scanning to yield the sedimentation coefficient of the solute. Calculated values agree to within a few percent with those found in the literature and with the results of control experiments carried out using an analytical ultracentrifuge.

Chymotrypsinogen↗

PubMed1989

Separation and visualization of apolipoprotein B species by sodium dodecyl sulfate-agarose gel electrophoresis and immunoblotting.

A method for separation and visualization of the different apolipoprotein B species using 0.2% sodium dodecyl sulfate-1.5% agarose gel electrophoresis and immunoblotting is described. The method is capable of demonstrating the different forms of apolipoprotein B (apo B) in plasma volumes of 10-50 microliters without prior ultracentrifugation. After ultracentrifugation of samples, estimation of the ratio between apo B 48 and apo B 100 is possible by scanning of Coomassie-stained gels or immunoblots.

Apolipoproteins B↗

PubMed1990

Preparation of brain microsomes with cytochrome P450 activity using calcium aggregation method.

Microsomes have been conventionally prepared by centrifugation of the postmitochondrial supernatant at 100,000g using an ultracentrifuge. Liver microsomes have been prepared by low speed centrifugation following sedimentation of the microsomal membranes in the presence of calcium ions. However, this method has not been suitable for the preparation of microsomes from extrahepatic tissues as it often results in the loss of cytochrome P450 activity. Brain microsomes prepared by the traditional calcium aggregation method results in the loss of cytochrome P450. We now describe a modification of the calcium aggregation method for the rapid preparation of rat and mouse brain microsomes. This involves the incorporation of glycerol, dithiothreitol, and EDTA in the preparation of microsomes. Such preparations do not differ in their cytochrome P450 content and associated monooxygenase activity from the traditionally prepared microsomes using ultracentrifugation. Electron microscopic analysis also does not reveal any differences between the microsomes prepared by the two methods. As brain microsomes are relatively unstable and are obtained in low yields, rapid isolation of large quantities of microsomes, possible using the present method, should be very useful.

Animals↗

PubMed1994

Removal of Avitene microfibrillar collagen hemostat by use of suitable transfusion filters.

We assessed the ability of two commercial filters (Pall RC100 and Statlabs 20 microns) to filter out Avitene microfibrillar collagen hemostat from suspension. Quantitative determination of the collagen content as well as scanning electron and light microscopy, particle counting, and platelet aggregometry of filtrates revealed that these filters effectively remove potentially thrombogenic particles of Avitene microfibrillar collagen hemostat. The filters removed at least 97% of the total collagen, as determined by hydroxyproline analysis. The collagen that passed through the Pall filter did not pellet upon ultracentrifugation. Scanning electron and light microscopic analysis revealed no Avitene microfibrillar collagen hemostat particulates in the Pall filtrates but did reveal the presence of a significant number of approximately 1- to 8-microns particulates in the Statlabs filtrates. Concentrates of the filtrates from either of the two filters, however, did not promote platelet aggregation. Through ultracentrifugation and infrared analysis, the filtrates were found to consists of soluble, partially denatured collagen. The risk associated with the reintroduction of collagen particulates into the vasculature can be significantly reduced by use of appropriate, currently available blood-transfusion filters.

Blood Transfusion, Autologous↗

PubMed1979

Physicochemical studies of the protein-lipid interactions in melittin-containing micelles.

Complexes of melittin with detergents and phospholipids have been characterized by fluorescence, circular dichroism, ultracentrifugation, quasi-elastic light scattering and 1H nuclear magnetic resonance (NMR) experiments. By ultracentrifugation and quasi-elastic light-scattering measurements it is shown that melittin forms stoichiometrically well-defined complexes with dodecylphosphocholine micelles consisting of one melittin molecule and approximately forty detergent molecules. Evidence from fluorescence, circular dichroism and 1H nuclear magnetic resonance experiments indicates that the conformation of melittin bound to micelles of various detergents or of diheptanoyl phosphatidylcholine is largely independent of the type of lipid and furthermore appears to be quite closely related to the conformation of melittin bound to phosphatidylcholine bilayers. 1H NMR is used to investigate the conformation of micelle-bound melittin in more detail and to compare certain aspects of the melittin conformation in the micelles with the spatial structures of monomeric and self-aggregated tetrameric melittin in aqueous solution. The experience gained with this system demonstrates that high resolution NMR of complexes of membrane proteins with micelles provides a viable method for conformational studies of membrane proteins.

Bee Venoms↗

PubMed1981

Metabolic fate of VLDL apolipoproteins B and E in hepatectomized rats.

The metabolic fate of VLDL apolipoproteins B and E was examined in functionally hepatectomized rats. 1 h after hepatectomy, there was almost complete absence of ultracentrifugally isolated VLDL lipid and protein, including apolipoproteins B and E. Analysis of apolipoprotein concentrations by electroimmunoassay showed hepatectomy did not affect the total serum concentrations of apolipoproteins B and E; thus, hepatectomy caused a redistribution of these apolipoproteins from VLDL to higher density lipoproteins. In the LDL (d = 1.03--1.063 g/ml) fraction, hepatectomy, increased the concentrations of free cholesterol (40%), esterified cholesterol (57%) and protein (18--67%), due to an increase in apolipoproteins B (22--48%) and E (250--300%). After hepatectomy, the HDL fraction accumulated the greatest total amount of apolipoprotein E. Since the majority of apolipoprotein E was isolated in the d greater than 1.21 g/ml fraction after sequential ultracentrifugation, the redistribution of apolipoproteins B and E was further defined by fractionation of serum on 5 M agarose columns. Electroimmunoassay of the column fractions showed that the apolipoprotein B peak eluted before the apolipoprotein E peak. Although a considerable portion of apolipoprotein E eluted with A-I, the peak of apolipoprotein E eluted before the A-I peak in both groups. These data suggest that a portion of apolipoprotein E is associated with particles which are similar than LDL but are larger than A-I-rich HDL. Hepatectomy caused an accumulation of apolipoprotein B in LDL, and apolipoprotein E and cholesterol in particles which were smaller than LDL and may represent LDL1. It is likely that under normal physiological conditions the liver plays a role in the removal of these apolipoprotein E-rich particles which are derived, at least in part, from the metabolism of VLDL.

Animals↗