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Dynamic Motion (dynamic + motion)
Selected AbstractsA Dynamically Entangled Coordination Polymer: Synthesis, Structure, Luminescence, Single-Crystal-to-Single-Crystal Reversible Guest Inclusion and Structural TransformationEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 24 2010Arshad Aijaz Abstract A ZnII coordination polymer {[Zn2(cpa)2(bpy)]·3H2O}n (1) (cpa2, = 4-(methoxycarbonyl)benzoate and bpy = 4,4,-bipyridine) has been synthesized under solvothermal condition and structurally characterized. This coordination polymer has nanotubular threefold entangled (2D,3D) structure with embedded water molecules; the water molecules can be partially exchanged in reversible single-crystal-to-single-crystal (SC-SC) fashion by different solvent molecules like methanol, ethanol and acetone giving rise to {[Zn2(cpa)2(bpy)]·(0.5MeOH)·(2.5H2O)}n (2), {[Zn2(cpa)2(bpy)]·(0.5EtOH)·(0.5H2O)}n (3) and {[Zn2(cpa)2(bpy)]·(0.5Me2CO)·(H2O)}n (4). Inclusion of EtOH or MeOH leaves the size of the voids in the framework unaltered. Inclusion of acetone, however, is accompanied by shrinking of the voids in the framework. Heating of 1 at 100 °C under vacuum for 4 h affords the de-solvated compound, {Zn2(cpa)2(bpy)}n (1,). Single-crystal X-ray structure of 1, shows sliding of the individual nanotubular components expanding the overall framework. Thus, the coordination polymer exhibits dynamic motion of the molecular components in SC-SC fashion. All compounds were further characterized via IR spectroscopy, PXRD, elemental and TGA analysis. When 1 is placed in benzene at 100 °C for 2 days, compound {[Zn2(cpa)2(bpy)]·(2.5H2O)}n (5) is formed in a SC-SC fashion where coordination number of ZnII ion increases from four to five. Compound 1 also exhibits reversible guest-dependent photoluminescence properties. [source] Complex patterns of mitochondrial dynamics in human pancreatic cells revealed by fluorescent confocal imagingJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 1-2 2010Andrey V. Kuznetsov Abstract Mitochondrial morphology and intracellular organization are tightly controlled by the processes of mitochondrial fission,fusion. Moreover, mitochondrial movement and redistribution provide a local ATP supply at cellular sites of particular demands. Here we analysed mitochondrial dynamics in isolated primary human pancreatic cells. Using real time confocal microscopy and mitochondria-specific fluorescent probes tetramethylrhodamine methyl ester and MitoTracker Green we documented complex and novel patterns of spatial and temporal organization of mitochondria, mitochondrial morphology and motility. The most commonly observed types of mitochondrial dynamics were (i) fast fission and fusion; (ii) small oscillating movements of the mitochondrial network; (iii) larger movements, including filament extension, retraction, fast (0.1,0.3 ,m/sec.) and frequent oscillating (back and forth) branching in the mitochondrial network; (iv) as well as combinations of these actions and (v) long-distance intracellular translocation of single spherical mitochondria or separated mitochondrial filaments with velocity up to 0.5 ,m/sec. Moreover, we show here for the first time, a formation of unusual mitochondrial shapes like rings, loops, and astonishingly even knots created from one or more mitochondrial filaments. These data demonstrate the presence of extensive heterogeneity in mitochondrial morphology and dynamics in living cells under primary culture conditions. In summary, this study reports new patterns of morphological changes and dynamic motion of mitochondria in human pancreatic cells, suggesting an important role of integrations of mitochondria with other intracellular structures and systems. [source] Investigation of structure and dynamics in the sodium metallocenes CpNa and CpNa·THF via solid-state NMR, X-ray diffraction and computational modellingMAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2007Cory M. Widdifield Abstract Solid-state 23Na NMR spectra of two organometallic complexes, cyclopentadienylsodium (CpNa) and the tetrahydrofuran (THF) solvate of CpNa (CpNa·THF), are presented. Analytical simulations of experimental spectra and calculated 23Na electric-field gradient (EFG) tensors confirm that both complexes are present in microcrystalline samples of CpNa recrystallized from THF. For the solvate, 23Na NMR experiments at 9.4 T and 11.7 T elucidate sodium chemical shielding (CS) tensor parameters, and establish that the EFG and CS tensor frames are non-coincident. Single-crystal X-ray diffraction (XRD) experiments are used to determine the crystal structure of CpNa·THF: Cmca (a = 9.3242(15) Å, b = 20.611(3) Å, c = 9.8236(14) Å, , = , = , = 90° , V = 1887.9(5)Å3, Z = 8). For CpNa, 23Na NMR data acquired at multiple field strengths establish sodium CS tensor parameters more precisely than in previous reports. Variable-temperature (VT) powder XRD (pXRD) experiments determine the temperature dependence of the CpNa unit cell parameters. The combination of 23Na quadrupolar NMR parameters, pXRD data and calculations of 23Na EFG tensors is used to examine various models of dynamic motion in the solid state. It is proposed that the sodium atom in CpNa undergoes an anisotropic, temperature-dependent, low frequency motion within the ab crystallographic plane, in contrast with previous models. Copyright © 2007 John Wiley & Sons, Ltd. [source] Solution Structure of a DNA Duplex Containing a Biphenyl PairCHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2008Zeena Johar Abstract Hydrogen-bonding and stacking interactions between nucleobases are considered to be the major noncovalent interactions that stabilize the DNA and RNA double helices. In recent work we found that one or multiple biphenyl pairs, devoid of any potential for hydrogen bond formation, can be introduced into a DNA double helix without loss of duplex stability. We hypothesized that interstrand stacking interactions of the biphenyl residues maintain duplex stability. Here we present an NMR structure of the decamer duplex d(GTGACXGCAG), d(CTGCYGTCAC) that contains one such X/Y biaryl pair. X represents a 3,,,5,,-dinitrobiphenyl- and Y a 3,,,4,,-dimethoxybiphenyl C -nucleoside unit. The experimentally determined solution structure shows a B-DNA duplex with a slight kink at the site of modification. The biphenyl groups are intercalated side by side as a pair between the natural base pairs and are stacked head to tail in van der Waals contact with each other. The first phenyl rings of the biphenyl units each show tight intrastrand stacking to their natural base neighbors on the 3,-side, thus strongly favoring one of two possible interstrand intercalation structures. In order to accommodate the biphenyl units in the duplex the helical pitch is widened while the helical twist at the site of modification is reduced. Interestingly, the biphenyl rings are not static in the duplex but are in dynamic motion even at 294,K. [source] Bench,shelf system dynamic characteristics and their effects on equipment and contentsEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 13 2006Tara C. Hutchinson Abstract Economic losses during past earthquakes are strongly associated with damage and failure to nonstructural equipment and contents. Among the vast types of nonstructural elements, one important category, is scientific equipment in biological or chemical laboratories. These equipment are often mounted on heavy ceramic bench-tops of bench,shelf systems, which in turn may amplify the dynamic motions imposed. To investigate the seismic response of these types of systems, a series of shake table and field experiments were conducted considering different representative bench and shelf-mounted equipment and contents. Results from shake table experiments indicate that these equipment are generally sliding-dominated. In addition, the bench,shelf system is observed to be very stiff and when lightly loaded, has a fundamental frequency between 10 and 16 Hz. An approximate 50% reduction in the first and second fundamental frequencies is observed considering practical loading conditions. Insight into a broader range of system response is provided by conducting eigenvalue and time history analyses. Non-linear regression through the numerical data indicate acceleration amplification ratios , range from 2.6 to 1.4 and from 4.3 to 1.6, for fixed,fixed and pinned,pinned conditions, respectively. Both the experimental and numerical results support the importance of determining the potential dynamic amplification of motion in the context of accurately determining the maximum sliding displacement of support equipment and contents. Copyright © 2006 John Wiley & Sons, Ltd. [source] Proximal ligand motions in H93G myoglobinFEBS JOURNAL, Issue 19 2002Stefan Franzen Resonance Raman spectroscopy has been used to observe changes in the iron,ligand stretching frequency in photoproduct spectra of the proximal cavity mutant of myoglobin H93G. The measurements compare the deoxy ferrous state of the heme iron in H93G(L), where L is an exogenous imidazole ligand bound in the proximal cavity, to the photolyzed intermediate of H93G(L)*CO at 8 ns. There are significant differences in the frequencies of the iron,ligand axial out-of-plane mode ,(Fe,L) in the photoproduct spectra depending on the nature of L for a series of methyl-substituted imidazoles. Further comparison was made with the proximal cavity mutant of myoglobin in the absence of exogenous ligand (H93G) and the photoproduct of the carbonmonoxy adduct of H93G (H93G-*CO). For this case, it has been shown that H2O is the axial (fifth) ligand to the heme iron in the deoxy form of H93G. The photoproduct of H93G-*CO is consistent with a transiently bound ligand proposed to be a histidine. The data presented here further substantiate the conclusion that a conformationally driven ligand switch exists in photolyzed H93G-*CO. The results suggest that ligand conformational changes in response to dynamic motions of the globin on the nanosecond and longer time scales are a general feature of the H93G proximal cavity mutant. [source] Multiple diverse ligands binding at a single protein site: A matter of pre-existing populationsPROTEIN SCIENCE, Issue 2 2002Buyong Ma Abstract Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising when one considers that binding is a dynamic process with populations in equilibrium and that the shape of the binding site is strongly influenced by the molecular partner. It derives implicitly from the concept of populations. All proteins, specific and nonspecific, exist in ensembles of substates. If the library of ligands in solution is large enough, favorably matching ligands with altered shapes and sizes can be expected to bind, with a redistribution of the protein populations. Point mutations at spatially distant sites may exert large conformational rearrangements and hinge effects, consistent with mutations away from the binding site leading to population shifts and (cross-)drug resistance. A similar effect is observed in protein superfamilies, in which different sequences with similar topologies display similar large-scale dynamic motions. The hinges are frequently at analogous sites, yet with different substrate specificity. Similar topologies yield similar conformational isomers, although with different distributions of population times, owing to the change in the conditions, that is, the change in the sequences. In turn, different distributions relate to binding of different sizes and shapes. Hence, the binding site shape and size are defined by the ligand. They are not independent entities of fixed proportions and cannot be analyzed independently of the binding partner. Such a proposition derives from viewing proteins as dynamic distributions, presenting to the incoming ligands a range of binding site shapes. It illustrates how presumably specific binding molecules can bind multiple ligands. In terms of drug design, the ability of a single receptor to recognize many dissimilar ligands shows the need to consider more diverse molecules. It provides a rationale for higher affinity inhibitors that are not derived from substrates at their transition states and indicates flexible docking schemes. [source] | ||||||||||