Probing Slow Backbone Dynamics in Proteins Using TROSY-Based Experiments to Detect Cross-Correlated Time-Modulation of Isotropic Chemical Shifts

The difference in the relaxation rates of zero-quantum (ZQ) and double-quantum (DQ) coherences is the result of three principal mechanisms. These include the cross-correlation between the chemical shift anisotropies of the two participating nuclei, dipolar interactions with remote protons as well as interference effects due to the time-modulation of their isotropic chemical shifts as a consequence of slow micros-ms dynamics. The last effect when present, dominates the others resulting in large differences between the relaxation rates of ZQ and DQ coherences. We present here four sets of TROSY-based (Salzmann et al., 1998) experiments that measure this effect for several pairs of backbone nuclei including (15)N, (13)C(alpha) and (13)C'. These experiments allow the detection of the presence of slow dynamic processes in the protein backbone including correlated motion over two and three bonds. Further, we define a new parameter chi which represents the extent of correlated motion on the slow (micros-ms) timescale. This methodology has been applied to (15)N,(13)C,REDPRO-(2)H-labeled (Shekhtman et al., 2002) human ubiquitin. The ubiquitin backbone is seen to exhibit extensive dynamics on the slow timescale. This is most pronounced in several residues in the N-terminal region of the alpha-helix and in the loop connecting the strands beta(4) and beta(5). These residues which include Glu24, Asn25, Glu51 and Asp 52 form a continuous surface. As an additional benefit, the measured rates confirm the dependence of the (13)C(alpha) chemical shift tensor on local secondary structure of the protein backbone.     

Purification and characterization of a potent hemolytic toxin with phospholipase A2 activity from the venom of Indian Russell's viper

A potent toxin with phospholipase A₂ (PLA₂) and hemolytic activity in vitro was purified from the Russell's viper venom of eastern India (RVV-EI). The purified protein (RVV-PFIIc) of 15.3 kDa molecular weight, and a lethal toxicity dose (LD₅₀ i.p.) of 0.1 mg/kg body weight, was the most toxic PLA₂ so far reported from the Indian subcontinent. The material also possessed anticoagulant activity as it enhanced the prothrombin induced plasma clotting time in vitro. The PLA₂ toxin (RVV-PFIIc) was shown to be different from other PLA₂s of RVV in respect to one or more of these parameters e.g. molecular weight, isoelectric pH, in vivo toxicity, specific activity of the enzyme and certain other biological activities. The first 19 amino terminal sequence (NLFQFAEMIVKMTGKEAVH) of RVV-PFIIc showed variable degree of homology (42.1–94.7%) with those of other RVV-PLA₂s described in the literature. Antisera raised against RVV-EI or RVV-PFIIc, though completely neutralized the in vivo lethal toxicity of RVV-EI or RVV-PFIIc, failed to inhibit their PLA₂ activity in vitro thereby suggesting that in vivo toxicity and in vitro activity of the enzyme may not be directly related. Apart from RVV-PFIIc, at least two other PLA₂ isozymes were found to be present in RVV-EI that were distinct from RVV-PFIIc in respect to their molecular, biological as well as serological properties. The significance of these and related data in antivenom therapy is discussed.     

Methotrexate conjugate with branched polypeptide influences Leishmania donovani infection in vitro and in experimental animals

Methotrexate (MTX) has been coupled to various structurally related, polycationic (poly[Lys(DL-Ala(m))] (AK), poly[Lys(Ser(i)-DL-Ala(m))] (SAK), poly[Lys(DL-Ala(m)-Leu(i))] (ALK)), or amphoteric (poly[Lys(Glu(i)-DL-Ala(m))] (EAK)) synthetic branched polypeptides containing poly[L-Lys] backbone by the aid of BOP reagent. The average degree of MTX incorporation was found to be dependent on the charge properties of the polymer. Under the experimental conditions used, the molar substitution ratio achieved was higher for polycations (25%) than for the amphoteric polypeptide (10%). We have studied the effect of polycationic polypeptides on Leishmania donovani infection. Results demonstrated that MTX conjugates in which the drug is covalently attached to carrier have pronounced leishmanicid activity. In this communication we showed that (a) a branched polypeptide-methotrexate conjugate with a polycationic carrier (ALK) increases the effect of MTX against Leishmania donovani infection in mice; (b) the covalent bond between the carrier and methotrexate is essential for both in vivo and in vitro activity; and (c) the number of Leishmania donovani parasites in infected macrophages are markedly reduced in conjugate treated animals. In vitro observation might also indicate that the MTX conjugate exhibits an effect through an uptake by macrophages which is different from that of the free drug.     

GAPs in Slit-Robo signaling

Neuronal migration requires the integration of a number of diverse environmental cues and subsequent translation to specific responses such as directed cytoskeletal remodeling. Accurate knowledge of the signal transduction pathways linking activation of surface receptors to actin dynamics is necessary in order to understand the regulation of such processes. Activation of the Roundabout (Robo) receptor mediates a repulsive response in certain pioneering axons and migratory neurons. Recently, Wong et al have described a signaling link between Robo activation and specific GTPase activity that appears to regulate neuronal migration. A novel family of GTPase regulators, responsive to Slit-Robo engagement, has been identified and convincingly shown to alter the migration of neuronal cells. This study not only delineates a specific signaling route from guidance receptors to directed neuronal movement, but also offers clues towards potential regulatory mechanisms that ensure specificity of the Slit-Robo response.     

Visualization of anti-histone antibodies on SV40 minichromosomes by scanning transmission electron microscopy (STEM)

The unique capabilities of the scanning transmission electron microscope (STEM) have been used for a high resolution study of antibody binding to individual SV40 minichromosomes. A method of sample preparation has been developed which allows direct visualization of the antibody molecules in a clearly recognizable form. Using this technique, we have studied the binding of anti-H2B and anti-H3 immunoglobulins to SV40 minichromosomes. The results indicate that histones H2B and H3 are located only in the nucleosomes and are absent in the linker regions.     

Studies on the mechanism of enzymatic hydrolysis of cellulosic substances.

Most cellulosic substances contain appreciable amounts of cellulose and hemicellulose, which on enzymatic hydrolysis mainly yield a mixture of glucose, cellobiose, and xylose. In this paper, studies on the mechanisms of hydrolysis of bagasse (a complex native cellulosic waste left after extraction of juice from cane sugar) by the cellulase enzyme components are described in light of their adsorption characteristics. Simultaneous adsorption of exo- and endoglucanases on hydrolyzable cellulosics is the causative factor of the hydrolysis that follows immediately after. It supports the postulate of synergistic enzyme action proposed by Eriksson. Xylanase pretreatment enhanced the hydrolysis of bagasse owing to the creation of more accessible cellulosic regions that are readily acted upon by exo- and endoglucanases. The synergistic action of the purified exoglucanase, endoglucanase, and xylanse has been found to be most effective for hydrolysis of bagasse but not for pure cellulose. Significant quantities of glucose are produced in beta-glucosidase-free cellulase action on bagasse. Individual and combined action of the purified cellulase components on hydrolysis of native and delignified bagasse are discussed in respect to the release of sugars in the hydrolysate.     

Adsorption of cellulose by Trichoderma viride

Adsorption of cellulase by Trichoderma viride QM 9414 has been studied with resting and growing cells and equations have been derived to describe the process quantitatively. It has been observed that the adsorption is a purely physical process being dependent only on cell and cellulose concentrations. It has also been demonstrated that adsorption isrequired for the induction of cellulases; some discussions are devoted to this point.     

Studies on immobilized Saccharomyces cerevisiae. I. Analysis of continuous rapid ethanol fermentation in immobilized cell reactor

Rapid fermentation of cane molasses into ethanol has been studied in batch, continuous (free-cell and cell-immobilized systems) by a strain of Saccharomyces cerevisiae at temperature 30 degrees C and pH 5.0. The maximum productivity of ethanol obtained in immobilized system was 28.6 g L(-1) h(-1). The cells were immobilized by natural mode on a carrier of natural origin and retention of 0.132 g cells/g carrier was achieved. The immobilized-cell column was operated continuously at steady state over a period of 35 days. Based on the parameter data monitored from the system, mathematical analysis has been made and rate equations proposed, and the values of specific productivity of ethanol and specific growth rate for immobilized cells computed. It has been established that immobilized cells exhibit higher specific rate of ethanol formation compared to free cells but the specific growth rate appears to be comparatively low. The yield of ethanol in the immobilized-cell system is also higher than in the free-cell system.     

Studies on immobilized Saccharomyces cerevisiae. II. Effect of temperature distribution on continuous rapid ethanol formation in molasses fermentation

Recently, considerable interest has been shown in the study and analysis of immobilized cell reactors. One of the major uses of such a reactor system is expected to be in ethanol production from carbohydrates. One distinct disadvantage of this system is carbon dioxide gas holdup associated with unsteady-state temperature distribution across the reactor. Taking into account the earlier published data and assuming steady-state-substrate balance, and unsteady-state energy balance, and an average gas holdup of 20% with the heat retained by the gas neglected, the average reaction rate in the differential element was computed. Finally, a mathematical model to predict steady-state temperature profile along the reactor was developed. It was verified with experimental data obtained from an immobilized yeast reactor column (1 m x 14.5 cm). The experimental data fit well those computed from the model within an accuracy of 5%.     

Positive selection of a pre-expansion CAG repeat of the human SCA2 gene

A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium in Utah residents with ancestry from northern and western Europe. This strikingly large linkage disequilibrium block was analyzed with statistical and experimental methods to determine whether natural selection could be implicated in shaping the current genome structure. Extended Haplotype Homozygosity and Relative Extended Haplotype Homozygosity analyses on this region mapped a core region of the strongest conserved haplotype to the exon 1 of the Spinocerebellar ataxia type 2 gene (SCA2). Direct DNA sequencing of this region of the SCA2 gene revealed a significant association between a pre-expanded allele [(CAG)₈CAA(CAG)₄CAA(CAG)₈] of CAG repeats within exon 1 and the selected haplotype of the SCA2 gene. A significantly negative Tajima's D value (−2.20, p < 0.01) on this site consistently suggested selection on the CAG repeat. This region was also investigated in the three other populations, none of which showed signs of selection. These results suggest that a recent positive selection of the pre-expansion SCA2 CAG repeat has occurred in Utah residents with European ancestry.