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Several Loops (several + loop)
Selected AbstractsCrystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymesFEBS JOURNAL, Issue 21 2006Ingunn A. Hoell We describe the cloning, overexpression, purification, characterization and crystal structure of chitinase G, a single-domain family 19 chitinase from the Gram-positive bacterium Streptomyces coelicolor A3(2). Although chitinase G was not capable of releasing 4-methylumbelliferyl from artificial chitooligosaccharide substrates, it was capable of degrading longer chitooligosaccharides at rates similar to those observed for other chitinases. The enzyme was also capable of degrading a colored colloidal chitin substrate (carboxymethyl-chitin,remazol,brilliant violet) and a small, presumably amorphous, subfraction of ,-chitin and ,-chitin, but was not capable of degrading crystalline chitin completely. The crystal structures of chitinase G and a related Streptomyces chitinase, chitinase C [Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T & Nonaka T (2006) J Mol Biol358, 472,484], showed that these bacterial family 19 chitinases lack several loops that extend the substrate-binding grooves in family 19 chitinases from plants. In accordance with these structural features, detailed analysis of the degradation of chitooligosaccharides by chitinase G showed that the enzyme has only four subsites (, 2 to +,2), as opposed to six (, 3 to +,3) for plant enzymes. The most prominent structural difference leading to reduced size of the substrate-binding groove is the deletion of a 13-residue loop between the two putatively catalytic glutamates. The importance of these two residues for catalysis was confirmed by a site-directed mutagenesis study. [source] Nodal protrusions, increased Schmidt-Lanterman incisures, and paranodal disorganization are characteristic features of sulfatide-deficient peripheral nervesGLIA, Issue 6 2007Tomiko Hoshi Abstract Galactocerebroside and sulfatide are two major glycolipids in myelin; however, their independent functions are not fully understood. The absence of these glycolipids causes disruption of paranodal junctions, which separate voltage-gated Na+ and Shaker -type K+ channels in the node and juxtaparanode, respectively. In contrast to glial cells in the central nervous system (CNS), myelinating Schwann cells in the peripheral nervous system (PNS) possess characteristic structures, including microvilli and Schmidt-Lanterman incisures, in addition to paranodal loops. All of these regions are involved in axo,glial interactions. In the present study, we examined cerebroside sulfotransferase-deficient mice to determine whether sulfatide is essential for axo,glial interactions in these PNS regions. Interestingly, marked axonal protrusions were observed in some of the nodal segments, which often contained abnormally enlarged vesicles, like degenerated mitochondria. Moreover, many transversely cut ends of microvilli surrounded the mutant nodes, suggesting that alignments of the microvilli were disordered. The mutant PNS showed mild elongation of nodal Na+ channel clusters. Even though Caspr and NF155 were completely absent in half of the paranodes, short clusters of these molecules remained in the rest of the paranodal regions. Ultrastructural analysis indicated the presence of transverse bands in some paranodal regions and detachment of the outermost several loops. Furthermore, the numbers of incisures were remarkably increased in the mutant internode. Therefore, these results indicate that sulfatide may play an important role in the PNS, especially in the regions where myelin,axon interactions occur. © 2007 Wiley-Liss, Inc. [source] Improving the performance of natural gas pipeline networks fuel consumption minimization problemsAICHE JOURNAL, Issue 4 2010F. Tabkhi Abstract As the gas industry has developed, gas pipeline networks have evolved over decades into very complex systems. A typical network today might consist of thousands of pipes, dozens of stations, and many other devices, such as valves and regulators. Inside each station, there can be several groups of compressor units of various vintages that were installed as the capacity of the system expanded. The compressor stations typically consume about 3,5% of the transported gas. It is estimated that the global optimization of operations can save considerably the fuel consumed by the stations. Hence, the problem of minimizing fuel cost is of great importance. Consequently, the objective is to operate a given compressor station or a set of compressor stations so that the total fuel consumption is reduced while maintaining the desired throughput in the line. Two case studies illustrate the proposed methodology. Case 1 was chosen for its simple and small-size design, developed for the sake of illustration. The implementation of the methodology is thoroughly presented and typical results are analyzed. Case 2 was submitted by the French Company Gaz de France. It is a more complex network containing several loops, supply nodes, and delivery points, referred as a multisupply multidelivery transmission network. The key points of implementation of an optimization framework are presented. The treatment of both case studies provides some guidelines for optimization of the operating performances of pipeline networks, according to the complexity of the involved problems. © 2009 American Institute of Chemical Engineers AIChE J, 2010 [source] Backbone dynamics of the human MIA protein studied by 15N NMR relaxation: Implications for extended interactions of SH3 domainsPROTEIN SCIENCE, Issue 3 2003Raphael Stoll MIA, melanoma inhibitory activity; NMR, nuclear magnetic resonance Abstract The melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic melanoma stages III and IV. Here, we report the backbone dynamics of human MIA studied by 15N NMR relaxation experiments. The folded core of human MIA is found to be rigid, but several loops connecting ,-sheets, such as the RT-loop for example, display increased mobility on picosecond to nanosecond time scales. One of the most important dynamic features is the pronounced flexibility of the distal loop, comprising residues Asp 68 to Ala 75, where motions on time scales up to milliseconds occur. Further, significant exchange contributions are observed for residues of the canonical binding site of SH3 domains including the RT-loop, the n-Src loop, for the loop comprising residues 13 to 19, which we refer to as the"disulfide loop", in part for the distal loop, and the carboxyl terminus of human MIA. The functional importance of this dynamic behavior is discussed with respect to the biological activity of several point mutations of human MIA. The results of this study suggest that the MIA protein and the recently identified highly homologous fibrocyte-derived protein (FDP)/MIA-like (MIAL) constitute a new family of secreted proteins that adopt an SH3 domain-like fold in solution with expanded ligand interactions. [source] Refined structure of Pyrococcus furiosus ornithine carbamoyltransferase at 1.87,AACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Jan Massant Using synchrotron radiation, X-ray data have been collected from Pyrococcus furiosus ornithine carbamoyltransferase (Pfu OTCase) to a maximal resolution of 1.87,Å, allowing the refinement of a previous structure at 2.7,Å [Villeret et al. (1998), Proc. Natl Acad. Sci. USA, 95, 2801,2806]. Thanks to the high resolution of this refined structure, two sulfate ions and 191 water molecules could be localized directly from the electron-density maps. The identification of these molecules allowed a more rigorous description of the active site and the identification of residues involved in binding carbamoyl phosphate. The improved quality of the model resulted in a better definition of several loops and the various interfaces. The dodecameric protein is composed of four catalytic trimers disposed in a tetrahedral manner. The extreme thermal stability of Pfu OTCase is mainly the result of the strengthening of the intersubunit interactions in a trimer and oligomerization of the trimers into a dodecamer. Interfaces between monomers in a catalytic trimer are characterized by an increase in ion-pair networks compared with mesophilic OTCases. However, the interfaces between catalytic trimers in the dodecameric oligomer are mainly hydrophobic and also involve aromatic,aromatic and cation,, interactions. [source] | ||||||||||