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Peptide Domain (peptide + domain)
Selected AbstractsFlexibility and communication within the structure of the Mycobacterium smegmatis methionyl-tRNA synthetaseFEBS JOURNAL, Issue 19 2010Henrik Ingvarsson Two structures of monomeric methionyl-tRNA synthetase, from Mycobacterium smegmatis, in complex with the ligands methionine/adenosine and methionine, were analyzed by X-ray crystallography at 2.3 Å and at 2.8 Å, respectively. The structures demonstrated the flexibility of the multidomain enzyme. A new conformation of the structure was identified in which the connective peptide domain bound more closely to the catalytic domain than described previously. The KMSKS(301-305) loop in our structures was in an open and inactive conformation that differed from previous structures by a rotation of the loop of about 90° around hinges located at Asn297 and Val310. The binding of adenosine to the methionyl-tRNA synthetase methionine complex caused a shift in the KMSKS domain that brought it closer to the catalytic domain. The potential use of the adenosine-binding site for inhibitor binding was evaluated and a potential binding site for a specific allosteric inhibitor was identified. [source] Estimation of global structural and transport properties of peptides through the modeling of their CZE mobility dataJOURNAL OF SEPARATION SCIENCE, JSS, Issue 16 2010Maria V. Piaggio Abstract Peptide electrophoretic mobility data are interpreted through a physicochemical CZE model, providing estimates of the equivalent hydrodynamic radius, hydration, effective and total charge numbers, actual ionizing pK, pH-near molecule and electrical permittivity of peptide domain, among other basic properties. In this study, they are used to estimate some peptide global structural properties proposed, providing thus a distinction among different peptides. Therefore, the solvent drag on the peptide is obtained through a characteristic friction power coefficient of the number of amino acid residues, defined from the global chain conformation in solution. As modeling of the effective electrophoretic mobility of peptides is carried out in terms of particle hydrodynamic size and shape coupled to hydration and effective charge, a packing dimension related to chain conformation within the peptide domain may be defined. In addition, the effective and total charge number fractions of peptides provide some clues on the interpretation of chain conformations within the framework of scaling laws. Furthermore, the model estimates transport properties, such as sedimentation, friction and diffusion coefficients. As the relative numbers of ionizing, polar and non-polar amino acid residues vary in peptides, their global structural properties defined here change appreciably. Needs for further research are also discussed. [source] Protease-activated receptors: novel central role in modulation of gastric functionsNEUROGASTROENTEROLOGY & MOTILITY, Issue 4 2010K. N. Browning Abstract, Protease-activated receptors (PARs) are members of a subfamily of G-protein-coupled receptors that regulate diverse cell functions in response to proteolytic cleavage of an anchored peptide domain that acts as a ,tethered' receptor-activating ligand. PAR-1 and PAR-2 in particular are present throughout the gastrointestinal (GI) tract and play prominent roles in the regulation of GI epithelial function, motility, inflammation and nociception. In a recent article in Neurogastroenterology and Motility, Wang et al. demonstrate, for the first time, that PAR-1 and PAR-2 are present on preganglionic parasympathetic neurons within the rat brainstem. As in other cellular systems, proteases such as thrombin and trypsin activate PAR-1 and PAR-2 on neurons of the dorsal motor nucleus of the vagus (DMV), leading to an increase in intracellular calcium levels via signal transduction mechanisms involving activation of phospholipase C and inositol triphosphate (IP3). The authors also report that the level of PAR-1 and PAR-2 transcripts in DMV tissue is increased following experimental colitis, suggesting that inflammatory conditions may modulate neuronal behavior or induce plasticity within central vagal neurocircuits. It seems reasonable to hypothesize, therefore, that the activity and behavior of vagal efferent motoneurons may be modulated directly by local and/or systemic proteases released during inflammation. This, in turn, may contribute to the increased incidence of functional GI disorders, including gastric dysmotility, delayed emptying and gastritis observed in patients with inflammatory bowel diseases. [source] Identification and characterization of a new conserved motif within the presequence of proteins targeted into complex diatom plastidsTHE PLANT JOURNAL, Issue 2 2005Oliver Kilian Summary Several groups of algae evolved by secondary endocytobiosis, which is defined as the uptake of a eukaryotic alga into a eukaryotic host cell and the subsequent transformation of the endosymbiont into an organelle. Due to this explicit evolutionary history such algae possess plastids that are surrounded by either three or four membranes. Protein targeting into plastids of these organisms depends on N-terminal bipartite presequences consisting of a signal and a transit peptide domain. This suggests that different protein targeting systems may have been combined during establishment of secondary endocytobiosis to enable the transport of proteins into the plastids. Here we demonstrate the presence of an apparently new type of transport into diatom plastids. We analyzed protein targeting into the plastids of diatoms and identified a conserved amino acid sequence motif within plastid preprotein targeting sequences. We expressed several diatom plastid presequence:GFP fusion proteins with or without modifications within that motif in the diatom Phaeodactylum tricornutum and found that a single conserved phenylalanine is crucial for protein transport into the diatom plastids in vivo, thus indicating the presence of a so far unknown new type of targeting signal. We also provide experimental data about the minimal requirements of a diatom plastid targeting presequence and demonstrate that the signal peptides of plastid preproteins and of endoplasmic reticulum-targeted preproteins in diatoms are functionally equivalent. Furthermore we show that treatment of the cells with Brefeldin A arrests protein transport into the diatom plastids suggesting that a vesicular transport step within the plastid membranes may occur. [source] | ||||||||||