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Selected AbstractsInvolvement of Gln937 of Streptococcus downei GTF-I glucansucrase in transition-state stabilizationFEBS JOURNAL, Issue 13 2000Vincent Monchois Multiple alignment of deduced amino-acid sequences of glucansucrases (glucosyltransferases and dextransucrases) from oral streptococci and Leuconostoc mesenteroides has shown them to share a well-conserved catalytic domain. A portion of this domain displays homology to members of the ,-amylase family (glycoside hydrolase family 13), which all have a (,/,)8 barrel structure. In the glucansucrases, however, the ,-helix and ,-strand elements are circularly permuted with respect to the order in family 13. Previous work has shown that amino-acid residues contributing to the active site of glucansucrases are situated in structural elements that align with those of family 13. In ,-amylase and cyclodextrin glucanotransferase, a histidine residue has been identified that acts to stabilize the transition state, and a histidine is conserved at the corresponding position in all other members of family 13. In all the glucansucrases, however, the aligned position is occupied by glutamine. Mutants of glucosyltransferase I were constructed in which this glutamine, Gln937, was changed to histidine, glutamic acid, aspartic acid, asparagine or alanine. The effects on specific activity, ability to form glucan and ability to transfer glucose to a maltose acceptor were examined. Only histidine could substitute for glutamine and maintain Michaelis,Menten kinetics, albeit at a greatly reduced kcat, showing that Gln937 plays a functionally equivalent role to the histidine in family 13. This provides additional evidence in support of the proposed alignment of the (,/,)8 barrel structures. Mutation at position 937 altered the acceptor reaction with maltose, and resulted in the synthesis of novel gluco-oligosaccharides in which ,1,3-linked glucosyl units are joined sequentially to maltose. [source] Exploring the mathematics of motion through construction and collaborationJOURNAL OF COMPUTER ASSISTED LEARNING, Issue 2 2006G. Simpson Abstract In this paper, we give a detailed account of the design principles and construction of activities designed for learning about the relationships between position, velocity and acceleration, and corresponding kinematics graphs. Our approach is model-based, that is, it focuses attention on the idea that students constructed their own models , in the form of programs , to formalise and thus extend their existing knowledge. In these activities, students controlled the movement of objects in a programming environment, recording the motion data and plotting corresponding position,time and velocity,time graphs. They shared their findings on a specially designed Web-based collaboration system, and posted cross-site challenges to which others could react. We present learning episodes that provide evidence of students making discoveries about the relationships between different representations of motion. We conjecture that these discoveries arose from their activity in building models of motion and their participation in classroom and online communities. [source] Protease inhibitors derived from elafin and SLPI and engineered to have enhanced specificity towards neutrophil serine proteasesPROTEIN SCIENCE, Issue 3 2009Marie-Louise Zani Abstract The secretory leukocyte protease inhibitor (SLPI), elafin, and its biologically active precursor trappin-2 are endogeneous low-molecular weight inhibitors of the chelonianin family that control the enzymatic activity of neutrophil serine proteases (NSPs) like elastase, proteinase 3, and cathepsin G. These inhibitors may be of therapeutic value, since unregulated NSP activities are linked to inflammatory lung diseases. However SLPI inhibits elastase and cathepsin G but not proteinase 3, while elafin targets elastase and proteinase 3 but not cathepsin G. We have used two strategies to design polyvalent inhibitors of NSPs that target all three NSPs and may be used in the aerosol-based treatment of inflammatory lung diseases. First, we fused the elafin domain with the second inhibitory domain of SLPI to produce recombinant chimeras that had the inhibitory properties of both parent molecules. Second, we generated the trappin-2 variant, trappin-2 A62L, in which the P1 residue Ala is replaced by Leu, as in the corresponding position in SLPI domain 2. The chimera inhibitors and trappin-2 A62L are tight-binding inhibitors of all three NSPs with subnanomolar Kis, similar to those of the parent molecules for their respective target proteases. We have also shown that these molecules inhibit the neutrophil membrane-bound forms of all three NSPs. The trappin-2 A62L and elafin-SLPI chimeras, like wild-type elafin and trappin-2, can be covalently cross-linked to fibronectin or elastin by a tissue transglutaminase, while retaining their polypotent inhibition of NSPs. Therefore, the inhibitors described herein have the appropriate properties to be further evaluated as therapeutic anti-inflammatory agents. [source] Solution structure of the PWWP domain of the hepatoma-derived growth factor familyPROTEIN SCIENCE, Issue 3 2005Nobukazu Nameki Abstract Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins. In this study, we determined the solution structure of the PWWP domain of HDGF-related protein-3 (HRP-3) by NMR spectroscopy. The structure consists of a five-stranded ,-barrel with a PWWP-specific long loop connecting ,2 and ,3 (PR-loop), followed by a helical region including two ,-helices. Its structure was found to have a characteristic solvent-exposed hydrophobic cavity, which is composed of an abundance of aromatic residues in the ,1/,2 loop (,-, arch) and the ,3/,4 loop. A similar ligand binding cavity occurs at the corresponding position in the Tudor, chromo, and MBT domains, which have structural and probable evolutionary relationships with PWWP domains. These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity. [source] A single-amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signalingTHE PLANT JOURNAL, Issue 2 2004Dennis A. Halterman Summary Interactions between barley and the powdery mildew pathogen, Blumeria graminis f. sp. hordei, (Bgh) are determined by unique combinations of host resistance genes, designated Mildew-resistance locus (Ml), and cognate pathogen avirulence genes. These interactions occur both dependent and independent of Rar1 (required for Mla12 resistance) and Sgt1 (Suppressor of G-two allele of skp1), which are differentially required for diverse plant disease-resistance pathways. We have isolated two new functional Mla alleles, Rar1 -independent Mla7 and Rar1 -dependent Mla10, as well as the Mla paralogs, Mla6-2 and Mla13-2. Utilizing the inherent diversity amongst Mla -encoded proteins, we identified the only two amino acids exclusively conserved in RAR1-dependent MLA6, MLA10, MLA12, and MLA13 that differ at the corresponding position in RAR1-independent MLA1 and MLA7. Two- and three-dimensional modeling places these residues on a predicted surface of the sixth leucine-rich repeat (LRR) domain at positions distinct from those within the ,-sheets hypothesized to determine resistance specificity. Site-directed mutagenesis of these residues indicates that RAR1 independence requires the presence of an aspartate at position 721, as mutation of this residue to a structurally similar, but uncharged, asparagine did not alter RAR1 dependence. These results demonstrate that a single-amino acid substitution in the sixth MLA LRR can alter host signaling but not resistance specificity to B. graminis. [source] Conversion of a glutamate dehydrogenase into methionine/norleucine dehydrogenase by site-directed mutagenesisFEBS JOURNAL, Issue 22 2001Xing-Guo Wang In earlier attempts to shift the substrate specificity of glutamate dehydrogenase (GDH) in favour of monocarboxylic amino-acid substrates, the active-site residues K89 and S380 were replaced by leucine and valine, respectively, which occupy corresponding positions in leucine dehydrogenase. In the GDH framework, however, the mutation S380V caused a steric clash. To avoid this, S380 has been replaced with alanine instead. The single mutant S380A and the combined double mutant K89L/S380A were satisfactorily overexpressed in soluble form and folded correctly as hexameric enzymes. Both were purified successfully by Remazol Red dye chromatography as routinely used for wild-type GDH. The S380A mutant shows much lower activity than wild-type GDH with glutamate. Activities towards monocarboxylic substrates were only marginally altered, and the pH profile of substrate specificity was not markedly altered. In the double mutant K89L/S380A, activity towards glutamate was undetectable. Activity towards l -methionine, l -norleucine and l -norvaline, however, was measurable at pH 7.0, 8.0 and 9.0, as for wild-type GDH. Ala163 is one of the residues that lines the binding pocket for the side chain of the amino-acid substrate. To explore its importance, the three mutants A163G, K89L/A163G and K89L/S380A/A163G were constructed. All three were abundantly overexpressed and showed chromatographic behaviour identical with that of wild-type GDH. With A163G, glutamate activity was lower at pH 7.0 and 8.0, but by contrast higher at pH 9.0 than with wild-type GDH. Activities towards five aliphatic amino acids were remarkably higher than those for the wild-type enzyme at pH 8.0 and 9.0. In addition, the mutant A163G used l -aspartate and l -leucine as substrates, neither of which gave any detectable activity with wild-type GDH. Compared with wild-type GDH, the A163 mutant showed lower catalytic efficiencies and higher Km values for glutamate/2-oxoglutarate at pH 7.0, but a similar kcat/Km value and lower Km at pH 8.0, and a nearly 22-fold lower S0.5 (substrate concentration giving half-saturation under conditions where Michaelis,Menten kinetics does not apply) at pH 9.0. Coupling the A163G mutation with the K89L mutation markedly enhanced activity (100,1000-fold) over that of the single mutant K89L towards monocarboxylic amino acids, especially l -norleucine and l -methionine. The triple mutant K89L/S380A/A163G retained a level of activity towards monocarboxylic amino acids similar to that of the double mutant K89L/A163G, but could no longer use glutamate as substrate. In terms of natural amino-acid substrates, the triple mutant represents effective conversion of a glutamate dehydrogenase into a methionine dehydrogenase. Kinetic parameters for the reductive amination reaction are also reported. At pH 7 the triple mutant and K89L/A163G show 5 to 10-fold increased catalytic efficiency, compared with K89L, towards the novel substrates. In the oxidative deamination reaction, it is not possible to estimate kcat and Km separately, but for reductive amination the additional mutations have no significant effect on kcat at pH 7, and the increase in catalytic efficiency is entirely attributable to the measured decrease in Km. At pH 8 the enhancement of catalytic efficiency with the novel substrates was much more striking (e.g. for norleucine ,,2000-fold compared with wild-type or the K89L mutant), but it was not established whether this is also exclusively due to more favourable Michaelis constants. [source] What the honeybee sees: a review of the recognition system of Apis melliferaPHYSIOLOGICAL ENTOMOLOGY, Issue 1 2005Adrian Horridge Abstract., For many years, two opposing theories have dominated our ideas of what honeybees see. The earliest proposal based on training experiments was that bees detected only simple attributes or features, irrespective of the actual pattern. The features demonstrated experimentally before 1940 were the disruption of the pattern (related to spatial frequency), the area of black or colour, the length of edge, and the angle of orientation of a bar or grating. Cues discovered recently are the range, and radial and tangential edges, and symmetry, relative to the fixation point, which is usually the reward hole. This theory could not explain why recognition failed when the pattern was moved. In the second theory, proposed in 1969, the bee detected the retinotopic directions of black or coloured areas, and estimated the areas of overlap and nonoverlap on each test pattern with the corresponding positions in the training pattern. This proposal explained the progressive loss of recognition as a test pattern was moved or reduced in size, but required that the bees saw and remembered the layout of every learned pattern and calculated the mismatch with each test image. Even so, the same measure of the mismatch was given by many test patterns and could not detect a pattern uniquely. Moreover, this theory could not explain the abundant evidence of simple feature detectors. Recent work has shown that bees learn one or more of a limited number of simple cues. A newly discovered cue is the position, mainly in the vertical direction, of the common centre (centroid) of black areas combined together. Significantly, however, the trained bees look for the cues mentioned above only in the range of places where they had occurred during the training. These two observations made possible a synthesis of both theories. There is no experimental evidence that the bees detect or re-assemble the layout of patterns in space; instead, they look for a cue in the expected place. With an array of detectors of the known cues, together with their directions, this mechanism would enable bees to recognize each familiar place from the coincidences of cues in different directions around the head. [source] Role of petunia pMADS3 in determination of floral organ and meristem identity, as revealed by its loss of functionTHE PLANT JOURNAL, Issue 1 2002Meenu Kapoor Summary pMADS3, a petunia class C gene, is the candidate homologue of Arabidopsis AGAMOUS (AG), which is involved in the specification of stamens and carpels. We report the characterization of loss-of-function phenotype of pMADS3 that resulted from silencing of this gene. Silencing of pMADS3 resulted in homeotic conversion of stamens into petaloid structures, whereas the carpels were only weakly affected. Ectopic secondary inflorescences emerged from the interstamenal region in the third whorl, which is unique and has not been reported for any class C gene of other plant species. Third-order inflorescences emerged at corresponding positions in the third whorl of inner flowers of secondary inflorescences, indicating reiterative conversion of parts of the floral meristem into inflorescence meristem. On the basis of phenotypic analysis of the pMADS3 -silenced plants, we propose that pMADS3 is involved in determination of floral organ and floral meristem identity in petunia. Two hybrid studies in yeast showed that PMADS3 protein interacted specifically with FBP2, a candidate homologue of Arabidopsis SEPALLATA3 (SEP3). The evidence presented here suggest that a complex involving PMADS3 and FBP2 is responsible for specification of organ identity in the third whorl. [source] | |||||||||||||