A new approach to the crystallization of proteins

A new method for the crystallization of proteins was developed. Saturated solutions of a protein for crystallization are prepared by chromatography of adsorbed proteins from an insoluble polysaccharide matrix using gradients with decreasing ionic strength, decreasing concentration of organic solvents or an appropriate shift in pH. Insulin, a-chymotrypsin and lysozyme for which the X-ray crystal structures are known, were crystallized by this method. X-ray diffraction photographs were taken to demonstrate the quality of the crystals. In addition to this analytical application, the method may be useful for the crystallization and the simultaneous purification of larger amounts of proteins.     

An approach to quality management in structural biology: biophysical selection of proteins for successful crystallization

Aggregation, incorrect folding and low stability are common obstacles for protein structure determination, and are often discovered at a very late state of protein production. In many cases, however, the reasons for failure to obtain diffracting crystals remain entirely unknown. We report on the contribution of systematic biophysical characterization to the success in structural determination of human proteins of unknown fold. Routine analysis using dynamic light scattering (DLS), differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR) was employed to evaluate fold and stability of 263 purified protein samples (98 different human proteins). We found that FTIR-monitored temperature scanning may be used to detect incorrect folding and discovered a positive correlation between unfolding enthalpy measured with DSC and the size of small, globular proteins that may be used to estimate the quality of protein preparations. Furthermore, our work establishes that the risk of aggregation during concentration of proteins may be reduced through DLS monitoring. In summary, our study demonstrates that biophysical characterization provides an ideal tool to facilitate quality management for structural biology and many other areas of biological research.     

A possible structural role for carotenoids and carotenoid precursors in etioplasts

Seedlings of wheat ( Triticum aestivum L.) were grown in darkness in different concentrations of the herbicide SAN-9789, an inhibitor of carotenoid synthesis. The ultrastructural appearance of etioplasts, containing different amounts of carotenoids, was compared to the contents of carotenoids and carotenoid precursors (phytoene and phytofluene). A correlation was found between the presence of carotenoids and the presence of partitions between prothylakoids. As the plants were grown in darkness, this correlation is interpreted as the result of a structural role of the carotenoids. The presence of the herbicide SAN-9789 resulted in an increase in size and a change from osmiophilic to non-osmiophilic plastoglobuli. This change in plastoglobuli was neither correlated to the increase in phytoene or phytofluene, nor to the decrease in carotenoids.     

The mechanism of potentiation of the glutamate-induced neurotoxicity by serum albumin. A possible role of nitric oxide

Potentiation of the delayed (Glu)-induced neurotoxicity by serum albumin (SA) was studied in experiments with cultured cerebellar granule cells. The delayed neuronal death (DND) was evaluated by counting neurons containing or excluding Trypan Blue 4 h after treatment with Glu. Cytoplasmic Ca2+ ([Ca2+]i) was measured in individual Fura-2-loaded neurons. It was shown that a 15-min application of bovine SA (4 mg/ml) together with Glu (100 microM, 10 microM glycine, Mg2+-free solution) enhanced DND in the culture 1.7 times (43.1+/-3.1%) with respect to the effect induced by Glu alone (24.6+/-0.6%). The bovine SA application did not change the dynamics of [Ca2+]i response during a short-term (1 min) and long-term (15 min) Glu-treatment. DND was prevented by simultaneous application of Glu and inhibitor of NO-synthase N omega-nitro-L-arginine methyl ester (L-NAME), 100 microM) (10.8+/-1.0%) as well as by the application of Glu with SA and L-NAME (9.8+/-1.2%). In order to evaluate the role of nitric oxide (NO) in the SA effect, the cells were incubated for 15 min with the NO-donors sodium nitroprusside (SNP, 10 and 100 microM) and sodium nitrite (NaNO2, 10 and 100 microM) together with SA and in its absence. SA also greatly enhanced the DND induced by SNP and NaNO2. Thus, the DND after simultaneous treatment with SA and SNP was 16.3+/-2.5% (10 microM) or 29.6+/-2.1% (100 microM), and 9.6+/-0.8% (10 microM) and 19.7+/-2.1% after treatment with SNP alone. Exposure to SA together with NaNO2 led to the DND increase up to 26.5+/-1.9% (10 microM) and 37.7+/-3.5% (100 microM) in comparison with 7.4+/-2.0% (10 microM) and 18.9+/-0.8% (100 microM) in experiments with NaNO2 alone. Taking into account the ability of NO and NO2 to oxidize unsaturated fatty acids and the ability of SA to bind them after their hydrolytic removal, we suggested that the SA-induced potentiation of Glu neurotoxicity resulted from exacerbation of the toxic effects of NO and other trace radicals on the neuronal membranes. This hypothesis was supported by the finding that SA also enhanced the neurotoxicity of the lipid prooxidant FeCl2. The simultaneous 15-min application of FeCl2 (10 microM) and SA caused a 51.5+/-4.0% increase in DND, which exceeded 2.4 times the effect produced by FeCl2 alone (21.3+/-2.3%).     

A pathological approach to anomalies of the posterior fossa

BACKGROUND: Both clinical and postmortem diagnoses of posterior fossa anomalies remain difficult to make and to corroborate. This is particularly true for Dandy-Walker malformation and variant. Difficulties arise for a variety of reasons, including technical and methodological ones, but also because the conditions may overlap anatomically with others, most notably mega cisterna magna, Blake's pouch cyst, and posterior fossa (arachnoid) cysts. Family counseling is difficult and complicated not only by diagnostic uncertainties but by the highly variable prognosis. METHODS: In this study, a systematic pathologic approach to study of the posterior fossa is put forth. The benefits of postmortem imaging and in situ and ex situ examination of posterior fossa contents are demonstrated. RESULTS: Normative data for cerebellar width (transverse cerebellar diameter) and height and vermian width and height are derived for the fetal period. These data will help workers recognize changes in these structures, particularly hypoplasia. CONCLUSIONS: Basic morphologic definitions of posterior fossa anomalies are advanced, in the hopes that better agreement can be reached between clinical and pathologic diagnoses and that better patient and family care will result.     

Voltage-gated sodium channels confer excitability to human odontoblasts: possible role in tooth pain transmission

Odontoblasts are responsible for the dentin formation. They are suspected to play a role in tooth pain transmission as sensor cells because of their close relationship with nerve, but this role has never been evidenced. We demonstrate here that human odontoblasts in vitro produce voltage-gated tetrodotoxin-sensitive Na(+) currents in response to depolarization under voltage clamp conditions and are able to generate action potentials. Odontoblasts express neuronal isoforms of alpha2 and beta2 subunits of sodium channels. Co-cultures of odontoblasts with trigeminal neurons indicate a clustering of alpha2 and beta2 sodium channel subunits and, at the sites of cell-cell contact, a co-localization of odontoblasts beta2 subunits with peripherin. In vivo, sodium channels are expressed in odontoblasts. Ankyrin(G) and beta2 co-localize, suggesting a link for signal transduction between axons and odontoblasts. Evidence for excitable properties of odontoblasts and clustering of key molecules at the site of odontoblast-nerve contact strongly suggest that odontoblasts may operate as sensor cells that initiate tooth pain transmission.     

Trapping crystal nucleation of cholesterol monohydrate: relevance to pathological crystallization

Crystalline nucleation of cholesterol at the air-water interface has been studied via grazing incidence x-ray diffraction using synchrotron radiation. The various stages of cholesterol molecular assembly from monolayer to three bilayers incorporating interleaving hydrogen-bonded water layers in a monoclinic cholesterol.H(2)O phase, has been monitored and their structures characterized to near atomic resolution. Crystallographic evidence is presented that this multilayer phase is similar to that of a reported metastable cholesterol phase of undetermined structure obtained from bile before transformation to the triclinic phase of cholesterol.H(2)O, the thermodynamically stable macroscopic form. According to grazing incidence x-ray diffraction measurements and crystallographic data, a transformation from the monoclinic film structure to a multilayer of the stable monohydrate phase involves, at least initially, an intralayer cholesterol rearrangement in a single-crystal-to-single-crystal transition. The preferred nucleation of the monoclinic phase of cholesterol.H(2)O followed by transformation to the stable monohydrate phase may be associated with an energetically more stable cholesterol bilayer arrangement of the former and a more favorable hydrogen-bonding arrangement of the latter. The relevance of this nucleation process of cholesterol monohydrate to pathological crystallization of cholesterol from cell biomembranes is discussed.     

A possible approach to the analysis of protease mixtures

A problem of quantitative assay of proteases in complex mixtures is solved by using a set of peptide substrates with detectable (chromogenic or fluorogenic) groups (DGs). Quantitation of separate DGs released in reaction of enzyme mixture with a set of substrates is carried out in chromatographic analysis of reaction products. Reaction of peptide derivatives of aminonaphthalene sulfamides with a mixture of thrombin and proteases from viper venom shows the amounts of produced DGs to be proportional to the amounts of both thrombin and venom proteases, confirming the validity of proposed approach. There are cases of mutual influence of some components in proteases mixtures as illustrated by inhibition of trypsin activity in presence of viper venom; one determines enzyme activities in this specific mixture rather than their amounts.     

Breakdown of accommodation in nerve: a possible role for persistent sodium current

Background  

Accommodation and breakdown of accommodation are important elements of information processing in nerve fibers, as they determine how nerve fibers react to natural slowly changing stimuli or electrical stimulation. The aim of the present study was to elucidate the biophysical mechanism of breakdown of accommodation, which at present is unknown.     

Generation of allantoin from the oxidation of urate by cytochrome c and its possible role in Reye's syndrome

Allantoin in the presence of calcium ions has been implicated as a potential toxic agent in Reye's syndrome. An investigation of possible alternative sources of allantoin in humans, which lack the enzyme uricase, has been initiated. Urate is a strong reducing agent which can reduce cytochrome c nonenzymatically, with the concomitant production of CO₂ and H⁺. The stoichiometries measured for the various reactants and products were 1 urate:2 cytochrome c:1 H⁺:1 CO₂. The initial reaction rate depended on the concentrations of both urate and cytochrome c, with reaction kinetics that were first order with respect to urate and second order with respect to cytochrome c. The participation of molecular oxygen in this reaction could not be detected. The pH and ionic strength optima for this reaction were determined to be 9.5–10.5 and 10⁻⁵m, respectively. Based on the results reported here, the following balanced equation can be written: urate⁻² + 2 cytochrome c⁺³ + 2 H₂O → allantoin + 2 cytochrome c⁺² + H⁺ + HCO₃⁻. We propose that allantoin can be generated from the oxidation of urate by cytochrome c⁺³, and that this is a potential source of allantoin in human tissues.     

Enzymatic activity of protein kinase LOSK: possible regulatory role of the structural domain

LOSK (LOng Ste20-like Kinase) protein kinases of mammals belong to a recently identified family of GCK kinases which are involved in the induction of apoptosis. LOSK have an N-terminal acidic catalytic domain and a long C-terminal basic structural domain which is cleaved off in cells by caspases during apoptosis. To study the LOSK enzymatic activity and its dependence on the structural domain, two preparations of this protein kinase were prepared: a natural full-length protein immunoprecipitated from CHO-K1 cultured cells and a recombinant N-terminal catalytic fragment synthesized in E. coli. Both preparations displayed the ability for autophosphorylation and the ability for phosphorylation of MBP and of H1 histone, and their activities were comparable. H1 histone was a better substrate for LOSK than casein and ATP was a better substrate than other nucleotides. The pH dependence of the activity of the immunoprecipitated protein was more pronounced than the pH dependence of its recombinant fragment deprived of the C-terminal domain. The catalytic and the structural domains of LOSK can interact through electrostatic forces; therefore, effects were studied of various polyions at the concentration of 0.1 mg/ml on the activity. Heparin, protamine sulfate, and poly(L-Lys) decreased tenfold the ability of the full-length kinase to phosphorylate H1 histone. Heparin did not affect the activity of the recombinant fragment, whereas protamine sulfate and poly(L-Lys) had a slight effect. Moreover, protamine increased fourfold the autophosphorylation of the immunoprecipitated protein kinase. These data suggest that the structural C-terminal domain of LOSK should be involved in the regulation of its protein kinase activity: the LOSK protein kinase with C-terminal domain cleaved off could significantly less depend on conditions in the cell than the full-size enzyme.     

Aminonitriles: possible role in chemical evolution.

The formation of HCN, ammonium cyanide, alkylnitriles, aminoacetonitrile and its C- and N-methyl homologs was demonstrated earlier in a simulated Jovian atmosphere. The polymeric material resulting in these experiments was shown to give glycine, alanine, sarcosine, aspacrtic acid and some imino dibasic acids on acid hydrolysis suggesting thereby the participation of the monomeric nitriles into the formation of the polymeric product(s). Further examination of products resulting from semi-corona and arc discharge through a mixture of methane and ammonia has provided evidence for the formation of alkylaminopropionitriles as a complex mixture and also some pyridyl and pyrimidyl type heterocyclic compounds. A GC-MS examination of the heterocylics showed resemblance with those found in some carbonaceous chondrites. The significance of these findings in relation to chemical evolution will be discussed.     

Methyleneaminoacetonitrile: possible role in chemical evolution-II.

Methyleneaminoacetonitrile (MAAN) when reacted with other amino acids, gives rise to the formation of peptides in addition to the usual hydrolytic products. It acts as a precursor of glycine and also as a dehydration condensing agent. It has been shown that MAAN is easily formed by the reaction of hydrogen cyanide, ammonia and formaldehyde as well as by the reaction of formaldehyde with aminoacetonitrile, in dilute ammoniacal solution.     

The possible role of endogenous nucleases in the structural organization of chromatin]

Two fractions of rat liver nuclei with different buoyant density have been obtained. The electrophoretic analysis of the oligonucleosome patterns of DNA out of nuclei of these two fractions revealed different levels of activity in endonucleases. In case of inhibition during the extraction of activity in Ca, Mg-dependent endonucleases, the average size of high polymeric DNA is larger for nuclei with bigger buoyant density (fraction I) than for nuclei with smaller ones (fraction II). This finding is evidence of in situ existence of two pools of liver nuclei with different endogenic nuclease activities. In nuclear chromatin fraction I DNA is torsionally stressed; in fraction II it is relaxed that correlates with larger activity of endonucleases and smaller buoyant density of this fraction. A hypothesis on a possible role of endonucleases in chromatin structure organization has been put forward. According to this hypothesis a modulation of activity in nuclear endonucleases can determine different packaging and activity of chromatin from different pools of cellular nuclei.     

Antibody as an immunological probe for studying the refolding of bovine serum albumin. An immunochemical approach to the identification of possible nucleation sites.

Specifically purified antibody to either domain I, domain III, or to subregions of domains I or III of serum albumin was added to refolding mixtures containing reduced serum albumin but no other refolding catalyst. It was found that the refolding of reduced albumin was greatly enhanced by the presence of specific antibody in the refolding mixture, that this enhancement was restricted to that domain for which the added antibody was directed, and that antibody-mediated enhancement of refolding in the NH2-terminal portion of each domain was delayed as compared to that seen in the COOH-terminal portion of each domain. Thus, an apparent COOH-terminal to NH2-terminal pathway of refolding within each domain was observed, which is consistent with the proposed evolutionary pathway of the albumin molecule and also consistent with the proposed presence of a nucleation center in the COOH-terminal double disulfide loop of each domain.