Home About us Contact
|
Home About us Contact | ||
|
|
||
Flexible Nature (flexible + nature)
Selected AbstractsNumerical simulation of viscous flow interaction with an elastic membraneINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 11 2008Lisa A. Matthews Abstract A numerical fluid,structure interaction model is developed for the analysis of viscous flow over elastic membrane structures. The Navier,Stokes equations are discretized on a moving body-fitted unstructured triangular grid using the finite volume method, taking into account grid non-orthogonality, and implementing the SIMPLE algorithm for pressure solution, power law implicit differencing and Rhie,Chow explicit mass flux interpolations. The membrane is discretized as a set of links that coincide with a subset of the fluid mesh edges. A new model is introduced to distribute local and global elastic effects to aid stability of the structure model and damping effects are also included. A pseudo-structural approach using a balance of mesh edge spring tensions and cell internal pressures controls the motion of fluid mesh nodes based on the displacements of the membrane. Following initial validation, the model is applied to the case of a two-dimensional membrane pinned at both ends at an angle of attack of 4° to the oncoming flow, at a Reynolds number based on the chord length of 4 × 103. A series of tests on membranes of different elastic stiffness investigates their unsteady movements over time. The membranes of higher elastic stiffness adopt a stable equilibrium shape, while the membrane of lowest elastic stiffness demonstrates unstable interactions between its inflated shape and the resulting unsteady wake. These unstable effects are shown to be significantly magnified by the flexible nature of the membrane compared with a rigid surface of the same average shape. Copyright © 2007 John Wiley & Sons, Ltd. [source] Clear strategy screens for macromolecular crystallizationJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2001Andrzej Marek Brzozowski The development of high-throughput crystallography combined with the wealth of already accumulated information about protein crystallization properties requires constant revision of current crystallization screening procedures. Two complementary 6 × 4 matrix `clear strategy screens' (CSS) have been developed and tested on a number of previously non-crystallized proteins. The screens yielded diffraction-quality crystals of a wide range of proteins (enzymes, transcription factors, structural proteins, etc.) in cases where the applications of commercially available screens were unsuccessful. Both their inherently simple design and their flexible nature provide an experimenter with a logical platform for further modification and optimization. Furthermore, the screens facilitate cryoprotection and potential incorporation of anomalous scatterers for multiple/single-wavelength anomalous dispersion (MAD/SAD) experiments. [source] Food Microbiology,Design and Testing of a Virtual Laboratory ExerciseJOURNAL OF FOOD SCIENCE EDUCATION, Issue 4 2010Steve Flint They were presented with a food-contamination case, and then walked through a number of diagnostic steps to identify the microorganism. At each step, the students were asked to select 1 of 4 tests. All tests had an associated cost. Feedback was given on selection and once the right test was selected, students were shown the results and could progress. At the end of the exercise, students had determined a number of characteristics of the microorganism. They were then required to identify the organism using a variety of reference material and present a report on the significance of the microorganism identified. A student survey showed they enjoyed the exercise and felt it fulfilled the aims and objectives of the lesson. There was a positive response to its flexible nature and the inclusion of test costs. This virtual laboratory was less expensive and 10 times faster than a traditional laboratory exercise yet achieved the same learning outcomes for students who were already familiar with laboratory techniques. The virtual lab was developed with a generic template that could be used for future lessons. [source] Synthesis and characterization of metal binding pseudotripeptidesJOURNAL OF PEPTIDE SCIENCE, Issue 8 2003Sebastian Kuenzel Abstract Metal complexes with peptide or pseudopeptide type ligands can serve as good model compounds for a deeper understanding of enzymatic catalysis, but ligands with a high selectivity for different transition metal cations are hard to find due to the rather flexible nature of peptides. Since such ligands would be the sine qua non condition for the synthesis of heterodinuclear peptide metal complexes with catalytic activity, the search for small, affine and selective metal chelating sequences is of interest. Using four different amino acids (His, Lys, Asp, Glu) a set of 16 pseudotripeptides of the common structure Bz-AS1 -Sar-AS2 -NH2 has been synthesized, purified and characterized by mass spectrometry and 1H-NMR. Their ability to form metal complexes has been investigated leading to short motifs capable of selectively binding only one or two transition metal cations with high affinity. As expected, the complexation of transition metal cations by pseudotripeptides is strongly dependent not only on the amino acid composition, but also on the sequence with regard to the stability of the resulting complexes, as well as the selectivity of the ligands towards Cu2+, Co2+, Ni2+, Zn2+ and Mn2+. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoproteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2009Jeffrey E. Lee The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008), Nature (London), 454, 177,182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glycoprotein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B -value-sharpened electron-density maps and the proper sequence register was confirmed by building alternate sequences using N-linked glycan sites as anchors and secondary-structural predictions. [source] Terahertz time-domain spectroscopy of poly- L -lysineBIOPOLYMERS, Issue 8 2010Ohki Kambara Abstract Poly- L -lysine is known to have three different secondary structures depending on solvent conditions because of its flexible nature. In previous work (Kambara et al., Phys Chem Chem Phys 2008, 10, 5042-5044), we observed two different types of structural changes in poly- L -lysine. In the present study, we investigated the low-frequency spectrum of poly- L -lysine with a ,-sheet structure in the solid state by terahertz time-domain spectroscopy. On the basis of this spectroscopic analysis, we found that the low-frequency dynamics differed from those of other polypeptides. Furthermore, we performed powder X-ray diffraction measurement on poly- L -lysine, which was found to be highly amorphous compared with other polypeptides. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 735,739, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] The immediate-early oncoproteins Fra-1, c-Fos, and c-Jun have distinguishable surface behavior and interactions with phospholipidsBIOPOLYMERS, Issue 9 2009Marķa Cecilia Gaggiotti Abstract This work explores the surface properties of the transcription factor Fra-1 and compares them with those of two other immediate early proteins, c-Fos and c-Jun, to establish generalities and differences in the surface behavior and interaction with phospholipids of this type of proteins. We present several experimental clues of the flexible nature of Fra-1, c-Fos, and c-Jun that support sequence-based predictions of their intrinsical disorder. The values of surface parameters for Fra-1 are similar in general to those of c-Fos and c-Jun. However, we find differences in the interactions of the three proteins with phospholipids. The closely related Fra-1 and c-Fos share affinity for anionic lipids but the former has more affinity for a condensed phase and senses a change in DPPC phase, while the latter has more affinity for an expanded phase. These features are in contrast with our previous finding that c-Jun is not selective for phospholipid polar head group or charge. We show here that at least some immediate early transcription factors can interact with membrane phospholipids in a distinguishable manner, and this shall provide a basis for their potential capacity to regulate membrane-mediated cellular processes. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 710,718, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] G-protein-coupled receptor phosphorylation: where, when and by whomBRITISH JOURNAL OF PHARMACOLOGY, Issue S1 2008A B Tobin Almost all G-protein coupled receptors (GPCRs) are regulated by phosphorylation and this process is a key event in determining the signalling properties of this receptor super-family. Receptors are multiply phosphorylated at sites that can occur throughout the intracellular regions of the receptor. This diversity of phospho-acceptor sites together with a lack of consensus phosphorylation sequences has led to the suggestion that the precise site of phosphorylation is not important in the phosphorylation-dependent regulation of GPCR function but rather it is the increase in bulk negative charge of the intracellular face of the receptor which is the significant factor. This review investigates the possibility that the multi-site nature of GPCR phosphorylation reflects the importance of specific phosphorylation events which mediate distinct signalling outcomes. In this way receptor phosphorylation may provide for a flexible regulatory mechanism that can be tailored in a tissue specific manner to regulate physiological processes. By understanding the flexible nature of GPCR phosphorylation if may be possible to develop agonists or allosteric modulators that promote a subset of phosphorylation events on the target GPCR and thereby restrict the action of the drug to a particular receptor mediated signalling response. British Journal of Pharmacology (2008) 153, S167,S176; doi:10.1038/sj.bjp.0707662; published online 14 January 2008 [source] | ||||||||||