Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures

The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy, cis-trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and the cis form of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts the cis conformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolyl cis-trans isomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerization versus domain-swapped dimerization, respectively

Ligand Specificity Modulated by Prolyl Imide Bond Cis/Trans Isomerization in the Itk SH2 Domain: A Quantitative NMR Study

The Src homology 2 (SH2) domain of interleukin-2 tyrosine kinase (Itk) binds two separate ligands:  a phosphotyrosine-containing peptide and the Itk Src homology 3 (SH3) domain. Binding specificity for these ligands is regulated via cis/trans isomerization of the Asn 286−Pro 287 imide bond in the Itk SH2 domain. In this study, we develop a novel method of analyzing chemical shift perturbation and cross-peak volumes to measure the affinities of both ligands for each SH2 conformer. We find that the cis imide bond containing SH2 conformer exhibits a 3.5-fold higher affinity for the Itk SH3 domain compared with binding of the trans conformer to the same ligand, while the trans conformer binds phosphopeptide with a 4-fold greater affinity than the cis-containing SH2 conformer. In addition to furthering the understanding of this system, the method presented here will be of general application in quantitatively determining the specificities of conformationally heterogeneous systems that use a molecular switch to regulate binding between multiple distinct ligands

Flow rule, self-channelization and levees in unconfined granular flows

Unconfined granular flows along an inclined plane are investigated experimentally. During a long transient, the flow gets confined by quasistatic banks but still spreads laterally towards a well-defined asymptotic state following a nontrivial process. Far enough from the banks a scaling for the depth averaged velocity is obtained, which extends the one obtained for homogeneous steady flows. Close to jamming it exhibits a crossover towards a nonlocal rheology. We show that the levees, commonly observed along the sides of the deposit upon interruption of the flow, disappear for long flow durations. We demonstrate that the morphology of the deposit builds up during the flow, in the form of an underlying static layer, which can be deduced from surface velocity profiles, by imposing the same flow rule everywhere in the flow.Comment: 4 pages, 5 figure

Erosion waves: transverse instabilities and fingering

Two laboratory scale experiments of dry and under-water avalanches of non-cohesive granular materials are investigated. We trigger solitary waves and study the conditions under which the front is transversally stable. We show the existence of a linear instability followed by a coarsening dynamics and finally the onset of a fingering pattern. Due to the different operating conditions, both experiments strongly differ by the spatial and time scales involved. Nevertheless, the quantitative agreement between the stability diagram, the wavelengths selected and the avalanche morphology reveals a common scenario for an erosion/deposition process.Comment: 4 pages, 6 figures, submitted to PR

Conformational Changes in Pediocin AcH upon Vesicle Binding and Approximation of the Membrane-Bound Structure in Detergent Micelles

Pediocin AcH is a 44-residue antimicrobial peptide with bactericidal potency against Gram-positive bacteria such as Listeria. It belongs to a family of bacteriocins that, when membrane-associated, is predicted to contain β-sheet and α-helical regions. All bacteriocins in this family have a conserved N-terminal disulfide bond. An additional C-terminal disulfide bond in pediocin AcH is thought to confer enhanced potency and broader specificity range against sensitive bacteria. The C-terminal disulfide bond may also affect the conformation of the C-terminus. The secondary structures of pediocin AcH in aqueous solution and vesicles from susceptible cells, as well as the ability of trifluoroethanol (TFE) and detergent systems to induce secondary structures like those induced in vesicles, were studied by circular dichroism (CD) spectroscopy. Like related peptides, pediocin AcH was highly unordered in aqueous solution, 56%. However, it also contained 20% β-strand and 15% β-turn structures. Upon complete binding to vesicles, 32% α-helical structure formed, the unordered structure decreased to 32%, and the β-strand and β-turn structures remained largely unchanged. Thus, a βα domain structure formed in vesicles. The helical structure likely forces the C-terminal tail to loop back on the helix so that the C24−C44 disulfide bond can form. Detergent micelles were superior to TFE in their ability to induce secondary structural fractions in pediocin AcH comparable to those observed in vesicles. This demonstrates the importance of a hydrocarbon−water interface to pediocin AcH structure induction and suggests that it is preferable to use detergent micelles as solvents in NMR studies of pediocin AcH structure

Mass production of event simulations for the BaBar experiment using the Grid

The BaBar experiment has been taking data since 1999, investigating the violation of charge and parity (CP) symmetry in the field of High Energy Physics. Event simulation is an intensive computing task, due to the complexity of the algorithm based on the Monte Carlo method implemented using the GEANT engine. The simulation input data are stored in ROOT format, they are classified into two categories: conditions data for describing the detector status when data are recorded, and background triggers data for including the noise signal necessary to obtain a realistic simulation. In order to satisfy these requirements, in the traditional BaBar computing model events are distributed over several sites involved in the collaboration where each site manager centrally manages a private farm dedicated to simulation production. The new grid approach applied to the BaBar production framework is discussed along with the schema adopted for data deployment via Xrootd/Scalla servers, including data management using grid middleware on distributed storage facilities spread over the INFN-GRID network. A comparison between the two models is provided, describing also the custom applications developed for performing the whole production task on the grid and showing the results achieved