Soft interactions and volume exclusion by polymeric crowders can stabilize or destabilize transient structure in disordered proteins depending on polymer concentration

The effects of macromolecular crowding on the transient structure of intrinsically disordered proteins is not well‐understood. Crowding by biological molecules inside cells could modulate transient structure and alter IDP function. Volume exclusion theory and observations of structured proteins suggest that IDP transient structure would be stabilized by macromolecular crowding. Amide hydrogen exchange (HX) of IDPs in highly concentrated polymer solutions would provide valuable insights into IDP transient structure under crowded conditions. Here, we have used mass spectrometry to measure HX by a transiently helical random coil domain of the activator of thyroid and retinoid receptor (ACTR) in solutions containing 300 g L^?1 and 400 g L^?1 of Ficoll, a synthetic polysaccharide, using a recently‐developed strong cation exchange‐based cleanup method [Rusinga, et al., Anal Chem 2017;89:1275–1282]. Transiently helical regions of ACTR exchanged faster in 300 g L^?1 Ficoll than in dilute buffer. In contrast, one transient helix exchanged more slowly in 400 g L^?1 Ficoll. Nonspecific interactions destabilize ACTR helicity in 300 g L^?1 Ficoll because ACTR engages with the Ficoll polymer mesh. In contrast, 400 g L^?1 Ficoll is a semi‐dilute solution where ACTR cannot engage the Ficoll mesh. At this higher concentration, volume exclusion stabilizes ACTR helicity because ACTR is compacted in interstitial spaces between Ficoll molecules. Our results suggest that the interplay between nonspecific interactions and volume exclusion in different cellular compartments could modulate IDP function by altering the stability of IDP transient structures. Proteins 2017; 85:1468–1479. © 2017 Wiley Periodicals, Inc.     

Oxidative phosphorylation in rat liver mitochondria isolated by rate zonal centrifugation: Examination of Ficoll gradients and subpopulations of mitochondria

In order to measure the parameters of oxidative phosphorylation it is necessary to isolate physiologically intact mitochondria. The isolation of rat liver mitochondria by rate zonal centrifugation utilizing isoosmotic Ficoll gradients resulted in the uncoupling of oxidative phosphorylation in these organelles. Analysis of the Ficoll solutions used to construct the gradients indicated that the Ca²⁺ content (200–400 nmole Ca²⁺/mg protein) was sufficiently high to cause an uncoupling of oxidative phosphorylation. Treatment of the Ficoll solutions with Amberlite MB-3 resin reduced the Ca²⁺ content to levels below the limit of determination of the assay procedure. This resulted in the retention of respiratory control (1.42) in rate-zonally centrifuged mitochondria. The addition of bovine serum albumin (100 mg%) to the Ficoll gradients increased the respiratory control index to 2.10. The increase is due to an elevation in state 3 respiration rather than any change in state 4 respiration. The addition of 200 mg% bovine serum albumin to the Ficoll gradient did not further enhance the respiratory control index.Examination of subpopulations of rat liver mitochondria revealed that they are heterogeneous with regard to states 3 and 4 respiration, respiratory control indices, and ADP:O ratios. In mitochondrial subpopulations respiratory control indices ranged from 1.00 to 4.13 and ADP:O ratios ranged from 1.22 to 1.83. This investigation defined a procedure for the isolation of physiologically intact mitochondria from rat liver homogenates.     

Effect of genotype and medium on wheat (Triticum aestivum L.) anther culture

Four winter wheat (Triticum aestivum L.) and two spring wheat cultivars were evaluated in anther culture on three to four different media for their ability to initiate callus and green plants. Five media were used in the experiment: stored-potato medium with Ficoll 400, fresh-potato medium with Ficoll 400, fresh-potato medium with agar, fresh-potato liquid medium without agar or Ficoll 400, and a one tep 85D12-3 medium. Greatly different frequencies of calli and/or green plants were obtained from different cultivars and media. The callus initiation frequency varied from 2.7% for Arapahoe to 52% for Pavon, both on the stored potato medium with Ficoll 400. The frequency of green plant regeneration ranged from 0% for Arapahoe and Siouxland on the stored-potato medium with Ficoll 400 and 0% for Redland and Arapahoe in the fresh-potato medium with Ficoll 400 to 12% for Chris in the 85D12-3 medium (one-step procedure). Chris and Centurk 78, previously reported as having high levels of response, had significantly higher (P < 0.05) frequencies of green plant regeneration on the 851312-3 medium than the other cultivars. An unexpected observation is that wet MSC^– medium enhanced callus regeneration more than a drier MSC^– medium.     

Large-scale Ficoll gradient separations using a commercially available,effectively closed,system

Background aimsMultiple cell-therapy products require density separation as a part of manufacturing. The traditional method for Ficoll separation, layering cell suspensions over Ficoll in tubes, followed by centrifugation and collection of cells from the interface, is too cumbersome and poses too high a risk of contamination for clinical-scale use. Recently, a system for clinical-scale Ficoll gradient applications has been introduced (Sepax?) but this system has limited availability and is costly.MethodsFor preparations of mononuclear cells (MNC) for dendritic cell (DC) production, we developed a Ficoll separation protocol that employs the Haemonetics? Cell Saver5? surgical blood salvage and wash instrument. This system uses standard blood bags and tubing, has single-use components, and is effectively closed. We analyzed 37 recent separation processes using this instrument and protocol. We measured depletion of red blood cells (RBC) and polymorphonuclear leukocytes (PMN), and recovery of CD14⁺ monocytes and MNC.ResultsStarting cell counts were 14.6 ± 8.0 (×10⁹). Total cell recovery was 49.2 ± 15.2%, RBC depletion was 88.4 ± 2.8%, PMN depletion was 86.9 ± 6.1%, MNC recovery was 63.6 ± 5.0% and CD14⁺ monocyte recovery was 75.3 ± 9.9%.ConclusionsThe Cell Saver5? is relatively inexpensive to purchase and use. The instrument and its disposables are licensed by the United States Food and Drug Administration (FDA) for intra-operative blood salvage, and we have obtained approval for investigational use. Our method with this instrument has proven to be simple and efficient for clinical-scale Ficoll separations.     

Competitive Interactions of Ligands and Macromolecular Crowders with Maltose Binding Protein

Cellular signaling involves a cascade of recognition events occurring in a complex environment with high concentrations of proteins, polysaccharides, and other macromolecules. The influence of macromolecular crowders on protein binding affinity through hard-core repulsion is well studied, and possible contributions of protein-crowder soft attraction have been implicated recently. Here we present direct evidence for weak association of maltose binding protein (MBP) with a polysaccharide crowder Ficoll, and that this association effectively competes with the binding of the natural ligand, maltose. Titration data over wide ranges of maltose and Ficoll concentrations fit well with a three-state competitive binding model. Broadening of MBP ¹H­¹⁵N TROSY spectra by the addition of Ficoll indicates weak protein-crowder association, and subsequent recovery of sharp NMR peaks upon addition of maltose indicates that the interactions of the crowder and the ligand with MBP are competitive. We hypothesize that, in the Escherichia coli periplasm, the competitive interactions of polysaccharides and maltose with MBP could allow MBP to shuttle between the peptidoglycan attached to the outer membrane and the ATP-binding cassette transporter in the inner membrane.     

Selection of Nonmotile Tetrahymena with Ficoll Underlayers*,†

The mechanisms regulating the development of cilia in Tetrahymena are poorly understood but might be revealed through the study of ciliogenesis mutants. Failure to regenerate cilia after dibucaine deciliation results in continued absence of motility. Therefore, to isolate ciliogenesis mutants efficiently, methods for separating motile and nonmotile cells are essential. We examined the efficacy of Ficoll underlayers for these separations. Ciliates of T. thermophila strain mpr^-/mpr (6 mp sens IV) (6-methyl purine-sensitive; mating type IV) were mixed with Ficoll and added as underlayers to separatory funnels containing growth medium. At 27 C most of the cells remained motile and were found in the top layer; at 37 C, there was a time-dependent increase in the number of nonmotile cells and the number of cells in the Ficoll layer. After 150 min at 37 C, most of the cells became nonmotile and were found in the Ficoll layer. Other studies indicated that at 37 C, the cells remained alive and capable of regenerating cilia when deciliated. Thus, it is clear that the Ficoll underlayer effectively separates the majority of nonmotile cells from the majority of motile cells. Evidently, however, at 37 C wild-type T. thermophila exhibit temperature-sensitive phenotypic variability with regard to motility which should be minimized when selecting for mutations affecting motility and ciliogenesis.     

Fractionation of Hevea brasiliensis latex on ficoll density gradients

Fractionation of diluted Hevea brasiliensis latex on iso-osmotic Ficoll density gradients by sedimentation produces a sharp acid phosphatase-rich lutoid band at the density of ca1.04 g/cm³. Polyphenol oxidase (PPO) is not exclusively located in the Frey-Wyssling complexes as shown earlier by others; its distribution is variable. A complete separation of acid phosphatase and PPO activities can be obtained by flotation in a Ficoll density gradient. Ethephon stimulation of the tree reduces the acid phosphatase and PPO activities. A transient change in lutoid density soon after stimulation is observed. The occurrence of some new enzyme activities and their subcellular localization are reported.     

Effects of culture conditions on isolated microspore response of barley cultivar Igri

Pretreatment of anthers in mannitol prior to isolation of microspores by glass rod homogenization was effective for in vitro induction of embryogenesis in barley cv. Igri. A procedure for separation of viable microspores using centrifugation on 20% maltose was developed. The concentration of microspores was important and greatly increased the number of developing structures. Initial culture of microspores on FHG medium containing 62 g l^-1 maltose, 4.4 M (1 mg l^-1) BA and 200 g l^-1 Ficoll-400 resulted in high frequencies of plant regeneration. Albino plant frequency was correlated to length of time in culture. Stock plant condition appeared to be a major factor influencing induction frequency. From 868 to 1738 green plants per 100 anthers were produced. The number of calli and embryos obtained and the number of green plantlets regenerated were improved by increasing the Ficoll concentration from 100 g l^-1 to 400 g l^-1 during the culture period compared to continuous culture on FHG Ficoll 200 g l^-1.Abbreviations BA benzyladenine     

DIFFERENTIAL METABOLISM OF RNA IN NEURONAL-ENRICHED AND GLIAL-ENRICHED FRACTIONS OF RAT CEREBRUM

Cerebral tissue of rat, disrupted by passage through a custom-designed tissue press, was diluted to a 10% (w/v) cellular suspension in 10% (w/v) Ficoll and was then fractionated in the Spinco Model L ultracentrifuge into: (1) two enriched cellular layers (alpha and beta) in an isopycnic Ficoll gradient in the Spinco 40 angular rotor; or (2) into four layers (A, B, C, and D) in a discontinuous Ficoll gradient in the Spinco SW 39 swinging bucket rotor. The cellular composition of these layers was identified microscopically and enzymically as either glial-enriched (alpha and B layers) or neuronal-enriched (beta and C layers) fractions of cerebral cortex. Portions of the neuronal and glial fractions were used for determinations of total nitrogen, and for colorimetric determinations of carbonic anhydrase activity (a glial cell marker). These data established that glial contamination of the neuronal-enriched layer averaged 6·5 per cent. The data also indicated glial enrichment of Layer B, although no quantitative assessment of the amount of neuronal contamination was possible. The kinetics of metabolism of RNA in the glial-enriched and neuronal-enriched fractions were studied from 0·5 to 16 h after-intracisternal injection of either [³H]cytidine or [³H]orotic acid. In addition, the incorporation of [³H]cytidine into crude nuclear and cytoplasmic components of the layers was studied by the use of 1 h pulses. Our findings indicated greater incorporation of [³H]cytidine into nuclear fractions than into cytoplasmic fractions at 1 h and greater incorporation of both precursors into neuronal-enriched fractions than into glial-enriched fractions at all pulse times.     

Isolated microspore culture of Canadian 6× triticale cultivars

Isolated microspore culture was conducted on nine Canadian triticale cultivars (X Triticosecale Wittmack) using two induction media developed for wheat, with or without 100 g l⁻¹ Ficoll. Significant interactions were observed for the number of embryos and calluses induced, green and albino plantlets regenerated and fertility of green plants. Ficoll was beneficial in both media to increase numbers of embryos and green plants for all cultivars. Overall, medium NPB99 supplemented with ficoll provided the most suitable condition for most cultivars. AC Alta performed slightly better on CHB3 supplemented with Ficoll. Only cv. Wapiti was not amenable to androgenesis. The cultivars AC Certa, AC Copia, AC Alta, Sandro, Ultima, Frank, Pronghorn and Banjo produced respectively, 10, 9, 6, 5, 4, 3, 3 and 1 green plants per Petri dish (35,000 microspores), on their optimum treatment. Twenty-two percent of total lines produced were fertile, and considered doubled haploids. The application of isolated microspore culture to triticale, opens new possibilities in breeding triticale, for the utilization of in vitro selection and genetic engineering.     

Synaptosomes and synaptosome membrane vesicles from the brain of Mamestra configurata: Application to voltage-dependent and ATP-dependent Ca2+ ion transport studies

High yields of relatively pure, morphologically well-preserved, functionally competent synaptosomes were prepared from brains of moths of Mamestra configurata using a modified microscale Ficoll flotation technique. Typical preparations yielded 10 mg of synaptosomal protein per gram of moth brains. The moth brain synaptosomes were virtually free of endoplasmic reticulum and mitochondrial contaminants as judged from marker enzyme studies and electron microscopy.Voltage-dependent Ca²⁺ ion transport was studied using the moth brain synaptosome preparations. Synaptosomes took up radioactive ⁴⁵Ca²⁺ from the incubation medium. The rate of uptake was increased up to three-fold when the synaptosomes were incubated in a depolarizing, high [K⁺] medium. Time course studies indicated that voltage-dependent Ca²⁺ uptake was composed of an early (<2 sec) fast phase and a late (>10 sec) slow phase.ATP-dependent Ca²⁺ ion transport was studied in moth brain synaptosome membrane vesicles prepared from synaptosomes by osmotic shock and purified on a second Ficoll gradient. The inside-out synaptosome membrane vesicles contained an ATP-dependent calcium ion pump which transported ⁴⁵Ca²⁺ from the incuation medium into the interior of the vesicle in the presence of ATP. The calcium ionophore A23187 rapidly released accumulated ⁴⁵Ca²⁺ from the vesicles. The maximal rate of ATP-dependent Ca²⁺ transport occurred at a [Ca²⁺ free] of 0.1 to 0.2 nM, indicating that the transport process has a very high affinity for Ca²⁺ ions.     

Functional properties of ficoll and their influence on anther culture responses of wheat

The effects of ficoll in liquid culture media have been contradictory in previous reports. The objective of this study was to determine the functional properties of ficoll in potato 4 (P4) liquid induction medium and their influence on anther culture responses of wheat. Ficoll addition significantly (p0.01) reduced callus production from the anthers of spring wheat cv. Pavon 76. The reduction was directly related to the concentration of ficoll added within the range of 50 to 200 g l^-1 medium. Although the addition of ficoll significantly (p0.01) increased the percentage of regenerable calli and the ratio of green vs. albino plants, the final yield of green plants per 100 anthers was significantly lower. Consistent results also were obtained with four other spring wheat genotypes (Chris, Butte 86, WA 6916, and Edwall). Ficoll concentration affected the density, viscosity, and osmolality of the liquid media. The higher medium density caused by ficoll addition increased the percentage of floating calli, as well as the percentage of regenerable calli and the ratio of green vs. albino plants. However, the increased medium viscosity by ficoll addition significantly (p0.01) reduced callus production. Ficoll addition also increased medium osmolality, which affected callus production by interacting with the sugar concentration of the induction media. Using response functions, the estimated maltose concentration for maximum callus production was 105 g l^-1 for the standard P4 media, compared with 68 g l^-1 for the ficoll-containing P4 media. These results clearly demonstrate that ficoll addition to the liquid P4 induction medium containing high sucrose concentration (90 g l^-1) is deleterious to the maximum production of green plants from wheat anther culture.     

Separation of ram spermatids by sedimentation at unit gravity

Suspensions of 1 × 10⁸ ram testis cells were prepared with trypsin and separated by velocity sedimentation at unit gravity in a non-linear Ficoll gradient. An improvement was made in the technique of cell suspension preparation to increase the viability of heat-sensitive germ cells. Six bands of cells numbered from I–VI were characterized by their sedimentation velocity and modal cell volume. The distribution of various classes of germ cells in these bands, and especially spermatids at different maturation stages, was determined using histological techniques and confirmed by kinetic profiles and autoradiographic analyses of ³H-thymidine incorporation. A homogenous population of round spermatids (93–96%) was obtained in the high sedimentation velocity part of band IV. Although elongated spermatid separation does not rigorously follow the maturation stage, it gives populations which can be used for the investigation of biochemical changes during spermiogenesis. Taking into account the viability and the ultrastructure of germ cells after separation, it was shown that the use of Ficoll as a gradient material instead of bovine serum albumin causes cellular damage. We successfully applied the technique of velocity sedimentation to testis cell separation in the bull, boar, billy-goat and stallion.     

Isolation and Characterization of Vacuoles from the Ergot Fungus Claviceps purpurea

Protoplasts of Claviceps purpurea were prepared by treatment of mycelium with a lytic mixture of snail gut enzyme and cellulase from Trichoderma viride. Such protoplasts could be efficiently lysed by Triton X-100 treatment at high osmotic pressure without Ca²⁺ or Mg²⁺, allowing the release of intact vacuoles in high yields. Vacuoles obtained from cells grown in modified Vogel medium (vegetative-type cells not producing alkaloids) were isolated and purified by centrifugation from a 5% Ficoll 400 (wt/vol) phase into the interphase between two layers, one containing 0.25 M each of mannitol and sucrose, and one containing 0.5 M mannitol. Vacuoles derived from cells grown in a medium favoring ergot alkaloid synthesis (sclerotia-like cells) were isolated by gentle centrifugation of filtered protoplast lysates without addition of Ficoll 400. Biochemical analyses of the vacuole fraction isolated from either kind of cell revealed their function as compartments harboring several hydrolytic enzymes. However, the enrichment of free amino acids in vacuoles of sclerotia-like cells was less pronounced than that in vacuoles of vegetative-type cells, indicating a difference in metabolic compartmentation in the two types of cells.     

Effect of Ficoll 70 on thermal stability and structure of creatine kinase

The effect of Ficoll 70 on the thermal stability and structure of creatine kinase (CK) was studied using far-UV CD spectra and intrinsic fluorescence spectra. The thermal transition curves monitored by CD spectra were fitted to a two-state model using a modified form of the van’t Hoff equation to obtain the transition temperature (T _m) and enthalpy change (ΔH _u) of thermally induced denaturation of CK in the absence and presence of Ficoll 70. An increase in T _m with constant ΔH _u was observed with increasing Ficoll 70 concentration, suggesting that Ficoll 70 enhances the thermal stability of CK. Fluorescence spectral measurements confirmed this protective effect of Ficoll 70 on CK structure. In addition, we observed a crowding-induced compaction effect on the structure of both native state and thermally denatured state of CK in the presence of Ficoll 70, which is more obvious on the structure of the denatured ensemble compared to that of the native ensemble. Our observations qualitatively accord with the predictions of previously proposed crowding theory for the effect of intermolecular excluded volume on protein stability and structure. These findings imply that the effects of macromolecular crowding are essential to our understanding of protein folding and unfolding occurring in vivo.     

The in vivo reproductive potential of density separated cells

Murine ascites cells (L1210, L5178Y, Ehrlich ascites) were labelled with ¹³¹I-iododeoxyuridine and subjected to buoyant density centrifugation on a continuous, linear Ficoll gradient. Cell losses sustained during density centrifugation were evaluated by recording the amount of ¹³¹I recovered in the final cell fractions. The viability and proliferative capacity of the density separated cells were tested by monitoring the rate of ¹³¹I excretion following inoculation of the recovered cells into new, non-radioactive hosts.Density separation in Ficoll appeared to cause few, if any, adverse effects. Cell recovery under properly regulated experimental conditions was virtually complete (97% or higher). The reproductive potential of density-separated cells was identical to that of control cells. However, considerable cell mortality could be induced by permitting cellular aggregation in medium free of antiagglutinin or by exposure of excessive quantities of cells to a density gradient.Viability indices obtained with trypan blue proved unsuitable for predicting long-term survival. In some experiments the trypan blue data provided a 90–100% viability reading when in fact the entire cell population had been inactivated by irradiation or heat incubation. Since the trypan blue test also did not reveal the full extent of mortality among aggregated cells or cells recovered from overloaded gradients, it was concluded that the dye exclusion test, in spite of its utility for monitoring immediate cell death and membrane destruction, was of limited value for evaluating the reproductive potential of mammalian cells.     

The preparation of tightly coupled membrane vesicles from Paracoccus denitrificans

Nonequilibrium sedimentation of membrane vesicles from Paracoccus denitrificans through Ficoll gradients results in a separation into two fractions. The fraction which pellets through dense Ficoll is uncoupled. The second fraction, retarded by dense Ficoll, shows both improved concentrative transport activity and greater uncoupler stimulation of respiration as compared to the original vesicle preparation.     

Impact of Ficoll density gradient centrifugation on major and trace element concentrations in erythrocytes and blood plasma

ProjectFicoll density gradient centrifugation is widely used to separate cellular components of human blood. We evaluated the suitability to use erythrocytes and blood plasma obtained from Ficoll centrifugation for assessment of elemental concentrations.ProcedureWe determined 22 elements (from Li to U) in erythrocytes and blood plasma separated by direct or Ficoll density gradient centrifugation, using inductively coupled plasma mass spectrometry.ResultsCompared with erythrocytes and blood plasma separated by direct centrifugation, those separated by Ficoll had highly elevated iodine and Ba concentration, due to the contamination from the Ficoll-Paque medium, and about twice as high concentrations of Sr and Mo in erythrocytes. On the other hand, the concentrations of Ca in erythrocytes and plasma were markedly reduced by the Ficoll separation, to some extent also Li, Co, Cu, and U. The reduced concentrations were probably due to EDTA, a chelator present in the Ficoll medium. Arsenic concentrations seemed to be lowered by Ficoll, probably in a species-specific manner. The concentrations of Mg, P, S, K, Fe, Zn, Se, Rb, and Cs were not affected in the erythrocytes, but decreased in plasma. Concentrations of Mn, Cd, and Pb were not affected in erythrocytes, but in plasma affected by EDTA and/or pre-analytical contamination.ConclusionsFicoll separation changed the concentrations of Li, Ca, Co, Cu, As, Mo, I, Ba, and U in erythrocytes and blood plasma, Sr in erythrocytes, and Mg, P, S, K, Fe, Zn, Se, Rb and Cs in blood plasma, to an extent that will invalidate evaluation of deficiencies or excess intakes.     

Macrophage heterogeneity in tumor resistance: Cytostatic and cytotoxic activity of corynebacterium parvum-activated and proteose peptone-elicited rat macrophages against Moloney sarcoma tumor cells

Peritoneal macrophages from proteose peptone and Corynebacterium parvum (CP)-treated Lewis and Brown Norway rats were separated into subpopulations by centrifugation on discontinuous gradients of Ficoll. Four macrophage subpopulations were prepared and tested for cytostatic and cytotoxic activity against syngeneic and allogeneic Moloney sarcoma tumor cells. Macrophages were cocultured with tumor cells for 48 hr, whereupon either the inhibition of [¹²⁵I]iododeoxyuridine uptake was measured (cytostasis) or the tumor monolayers were observed for cytotoxic effects. CP-Activated macrophages from heavy-density portions of the gradient (8–10% and 10%-pellet) were highly cytostatic and cytotoxic to both the syngeneic and allogeneic tumor cells while macrophages from the light-density portions (4–6 and 6–8% Ficoll bands) were not. Proteose peptone-stimulated macrophages from the heavy-density portions of the gradient were cytostatic but not cytotoxic to the tumor cells. The effector macrophages from the CP-activated pool were large, well-differentiated cells as determined by electron microscopic examinations and had enhanced phagocytic activity when contrasted with the noncytotoxic, less dense macrophages.     

Uridine labeling of human lymphocytes: Differential uptake by T and B cells

Human peripheral blood lymphocytes were labeled with [³H]uridine and separated into immunoglobulin (Ig)-positive-enriched and Ig-negative populations by rosetting and Ficoll sedimentation. The Ig-negative (T cell-rich) fraction was found to be more heavily labeled than the B cell-enriched population, in agreement with previous results in rats. Combined autoradiography and rosetting confirmed the differential uridine labeling of T and B cells. Incorporation of cytidine and adenosine by T and B cell-enriched populations showed similar but less dramatic differential labeling.