Home About us Contact
|
Home About us Contact | ||
|
|
||
Dynamic Structure (dynamic + structure)
Selected AbstractsDynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2008Ying Xiong Abstract Various quantum mechanical/molecular mechanical (QM/MM) geometry optimizations starting from an x-ray crystal structure and from the snapshot structures of constrained molecular dynamics (MD) simulations have been performed to characterize two dynamically stable active site structures of phosphodiesterase-5 (PDE5) in solution. The only difference between the two PDE5 structures exists in the catalytic, second bridging ligand (BL2) which is HO, or H2O. It has been shown that, whereas BL2 (i.e. HO,) in the PDE5(BL2 = HO,) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+. It has been demonstrated that the results of the QM/MM geometry optimizations are remarkably affected by the solvent water molecules, the dynamics of the protein environment, and the electronic embedding charges of the MM region in the QM part of the QMM/MM calculation. The PDE5(BL2 = H2O) geometries optimized by using the QM/MM method in different ways show strong couplings between these important factors. It is interesting to note that the PDE5(BL2 = HO - ) and PDE5(BL2 = H2O) geometries determined by the QM/MM calculations neglecting these three factors are all consistent with the corresponding geometries determined by the QM/MM calculations that account for all of these three factors. These results suggest the overall effects of these three important factors on the optimized geometries can roughly cancel out. However, the QM/MM calculations that only account for some of these factors could lead to considerably different geometries. These results might be useful also in guiding future QM/MM geometry optimizations on other enzymes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Evaluation of correlation forecasting models for risk managementJOURNAL OF FORECASTING, Issue 7 2007Vasiliki D. Skintzi Abstract Reliable correlation forecasts are of paramount importance in modern risk management systems. A plethora of correlation forecasting models have been proposed in the open literature, yet their impact on the accuracy of value-at-risk calculations has not been explicitly investigated. In this paper, traditional and modern correlation forecasting techniques are compared using standard statistical and risk management loss functions. Three portfolios consisting of stocks, bonds and currencies are considered. We find that GARCH models can better account for the correlation's dynamic structure in the stock and bond portfolios. On the other hand, simpler specifications such as the historical mean model or simple moving average models are better suited for the currency portfolio.,,Copyright © 2007 John Wiley & Sons, Ltd. [source] Structure, function, property, and role in neurologic diseases and other diseases of the sHsp22JOURNAL OF NEUROSCIENCE RESEARCH, Issue 10 2007Zhiping Hu Abstract Small heat shock proteins are members of the heat shock proteins family. They share important identical features: 1) they form the conserved structure ,,-crystallin domain' with about 80,100 residues in the C-terminal part of the proteins; 2) they have monomeric molecular masses ranging in 12,43 kDa; 3) they associate into large oligomers consisting in many cases of subunits; 4) they increase expression under stress conditions; 5) they exhibit a highly dynamic structure; and 6) they play a chaperone-like role. Hsp22 (also known as HspB8, H11, and E2IG1) retains the structural motif of the ,,-crystallin' family of Hsps and is a member of the superfamily of sHsps. Hsp22 displays chaperone activity, autokinase activity, and trigger or block apoptosis activity. It differs from canonical family members existing as a monomer. A decrease in the HspB8 activity may contribute to the development of some neurologic diseases and others. © 2007 Wiley-Liss, Inc. [source] Protein N-glycosylation determines functionality of the Saccharomyces cerevisiae cell wall integrity sensor Mid2pMOLECULAR MICROBIOLOGY, Issue 6 2008Franziska Hutzler Summary The fungal cell wall is a highly dynamic structure that is essential to maintain cell shape and stability. Hence in yeasts and fungi cell wall integrity is tightly controlled. The Saccharomyces cerevisiae plasma membrane protein Mid2p is a putative mechanosensor that responds to cell wall stresses and morphological changes during pheromone induction. The extracellular domain of Mid2p, which is crucial to sensing, is highly O- and N-glycosylated. We showed that O-mannosylation is determining stability of Mid2p. If and how N-glycosylation is linked to Mid2p function was unknown. Here we demonstrate that Mid2p contains a single high mannose N-linked glycan at position Asn-35. The N -glycan is located close to the N-terminus and is exposed from the plasma membrane towards the cell wall through a highly O-mannosylated domain that is predicted to adopt a rod-like conformation. In contrast to O-mannosylation, lack of the N-linked glycan affects neither, stability of Mid2p nor distribution at the plasma membrane during vegetative and sexual growth. However, non-N-glycosylated Mid2p fails to perceive cell wall challenges. Our data further demonstrate that both the extent of the N-linked glycan and its distance from the plasma membrane affect Mid2p function, suggesting the N -glycan to be directly involved in Mid2p sensing. [source] Weak Identification of Forward-looking Models in Monetary Economics,OXFORD BULLETIN OF ECONOMICS & STATISTICS, Issue 2004Sophocles Mavroeidis Abstract Recently, single-equation estimation by the generalized method of moments (GMM) has become popular in the monetary economics literature, for estimating forward-looking models with rational expectations. We discuss a method for analysing the empirical identification of such models that exploits their dynamic structure and the assumption of rational expectations. This allows us to judge the reliability of the resulting GMM estimation and inference and reveals the potential sources of weak identification. With reference to the New Keynesian Phillips curve of Galí and Gertler [Journal of Monetary Economics (1999) Vol. 44, 195] and the forward-looking Taylor rules of Clarida, Galí and Gertler [Quarterly Journal of Economics (2000) Vol. 115, 147], we demonstrate that the usual ,weak instruments' problem can arise naturally, when the predictable variation in inflation is small relative to unpredictable future shocks (news). Hence, we conclude that those models are less reliably estimated over periods when inflation has been under effective policy control. [source] Influence of dynamic structure on the microstructure formation of a steel surface in the electrolyte in a steady magnetic fieldPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 12 2004Svetlana Gorobets Abstract The periodic microfabrication effect of metal element surfaces in an electrolyte solution in an external steady magnetic field was investigated. Authors have shown that corrosion velocity and periodic microstructure formation on the metal element surface can be controlled by magnetic field application. Geometric configuration of periodic microstructure depends on metal element characteristics, electrolyte solution, treatment time, magnetic field magnitude and other parameters. Investigation results have shown possibility of magnetic field influence on hydrodynamic conditions and metal surface structure under its etching in the nitric acid solution. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The Evolution of Individual Male Earnings in Great Britain: 1975,95THE ECONOMIC JOURNAL, Issue 460 2000Richard Dickens I study the dynamic structure of male wages in Great Britain using the New Earnings Survey Panel from 1975,95. Computing auto-covariances of individual wages by cohort I find evidence of a permanent component of earnings that increases over the life cycle and a highly persistent, serially correlated transitory component. In addition, the estimated variances of both these components have risen over this period, each explaining about half the rise in inequality. Using individual's occupation at age 22, I split the sample into four skill groups. I find some differences across these groups, with the rise in the permanent variance most important for the manual groups. [source] New insights into form and function of fibronectin splice variants,THE JOURNAL OF PATHOLOGY, Issue 1 2008ES White Abstract The extracellular matrix (ECM) is a highly dynamic structure that not only provides a physical framework for cells within connective tissues, but also imparts instructive signals for development, tissue homeostasis and basic cell functions through its composition and ability to exert mechanical forces. The ECM of tissues is composed of, in addition to proteoglycans and hyaluronic acid, a number of proteins, most of which are generated after alternative splicing of their pre-mRNA. However, the precise function of these protein isoforms is still obscure in most cases. Fibronectin (FN), one of the main components of the ECM, is also one of the best-known examples of a family of proteins generated by alternative splicing, having at least 20 different isoforms in humans. Over the last few years, considerable progress on elucidating the functions of the alternatively spliced FN isoforms has been achieved with the essential development of key engineered mouse strains. Here we summarize the phenotypes of the mouse strains having targeted mutations in the FN gene, which may lead to novel insights linking function of alternatively spliced isoforms of fibronectin to human pathologies. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Wall-modifying genes regulated by the Arabidopsis homolog of trithorax, ATX1: repression of the XTH33 gene as a test caseTHE PLANT JOURNAL, Issue 4 2009Ivan Ndamukong Summary The plant cell wall is a dynamic structure playing important roles in the control of plant cell growth and differentiation. These processes involve global reprogramming of the genome driven by dynamic changes in chromatin structure. The chromatin modifier ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) methylates lysine residue 4 on histone H3 (H3K4me), acting as an epigenetic mark on associated genes. The remarkable overrepresentation in the ATX1-regulated gene fraction of genes encoding plasma membrane and cell wall-remodeling activities suggested a link between two separate factors affecting growth, development and adaptation in Arabidopsis: the wall-modifying activities regulating cell extension, growth and fate, and the epigenetic mechanisms regulating chromatin structure and gene expression. A co-regulated fraction of specific wall-modifying proteins suggests that they may function together. Here, we study the ATX1-dependent expression of the gene encoding the wall-loosening factor XTH33 as a test case for development- and tissue-specific effects displayed by the chromatin modifier. In addition, we show that XTH33 is, most likely, an integral plasma membrane protein. A putative transmembrane domain is conserved in some, but not all, XTH family members, suggesting that they may be differently positioned when functioning as wall modifiers. [source] Immune subversion by chromatin manipulation: a ,new face' of host,bacterial pathogen interactionCELLULAR MICROBIOLOGY, Issue 8 2008Laurence Arbibe Summary Bacterial pathogens have evolved various strategies to avoid immune surveillance, depending of their in vivo,lifestyle'. The identification of few bacterial effectors capable to enter the nucleus and modifying chromatin structure in host raises the fascinating questions of how pathogens modulate chromatin structure and why. Chromatin is a dynamic structure that maintains the stability and accessibility of the host DNA genome to the transcription machinery. This review describes the various strategies used by pathogens to interface with host chromatin. In some cases, chromatin injury can be a strategy to take control of major cellular functions, such as the cell cycle. In other cases, manipulation of chromatin structure at specific genomic locations by modulating epigenetic information provides a way for the pathogen to impose its own transcriptional signature onto host cells. This emerging field should strongly influence our understanding of chromatin regulation at interphase nucleus and may provide invaluable openings to the control of immune gene expression in inflammatory and infectious diseases. [source] Regulation of implant surface cell adhesion: characterization and quantification of S-phase primary osteoblast adhesions on biomimetic nanoscale substratesJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 2 2007Manus J.P. Biggs Abstract Integration of an orthopedic prosthesis for bone repair must be associated with osseointegration and implant fixation, an ideal that can be approached via topographical modification of the implant/bone interface. It is thought that osteoblasts use cellular extensions to gather spatial information of the topographical surroundings prior to adhesion formation and cellular flattening. Focal adhesions (FAs) are dynamic structures associated with the actin cytoskeleton that form adhesion plaques of clustered integrin receptors that function in coupling the cell cytoskeleton to the extracellular matrix (ECM). FAs contain structural and signalling molecules crucial to cell adhesion and survival. To investigate the effects of ordered nanotopographies on osteoblast adhesion formation, primary human osteoblasts (HOBs) were cultured on experimental substrates possessing a defined array of nanoscale pits. Nickel shims of controlled nanopit dimension and configuration were fabricated by electron beam lithography and transferred to polycarbonate (PC) discs via injection molding. Nanopits measuring 120 nm diameter and 100 nm in depth with 300 nm center,center spacing were fabricated in three unique geometric conformations: square, hexagonal, and near-square (300 nm spaced pits in square pattern, but with ±50 nm disorder). Immunofluorescent labeling of vinculin allowed HOB adhesion complexes to be visualized and quantified by image software. Perhipheral adhesions as well as those within the perinuclear region were observed, and adhesion length and number were seen to vary on nanopit substrates relative to smooth PC. S-phase cells on experimental substrates were identified with bromodeoxyuridine (BrdU) immunofluorescent detection, allowing adhesion quantification to be conducted on a uniform flattened population of cells within the S-phase of the cell cycle. Findings of this study demonstrate the disruptive effects of ordered nanopits on adhesion formation and the role the conformation of nanofeatures plays in modulating these effects. Highly ordered arrays of nanopits resulted in decreased adhesion formation and a reduction in adhesion length, while introducing a degree of controlled disorder present in near-square arrays, was shown to increase focal adhesion formation and size. HOBs were also shown to be affected morphologicaly by the presence and conformation of nanopits. Ordered arrays affected cellular spreading, and induced an elongated cellular phenotype, indicative of increased motility, while near-square nanopit symmetries induced HOB spreading. It is postulated that nanopits affect osteoblast,substrate adhesion by directly or indirectly affecting adhesion complex formation, a phenomenon dependent on nanopit dimension and conformation. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 25:273,282, 2007 [source] Stromules: Mobile Protrusions and Interconnections Between PlastidsPLANT BIOLOGY, Issue 3 2001J. C. Gray Abstract: Stroma-filled tubules, recently named stromules, extend from the surface of plastids in most cell types and plant species examined. Stromules are highly dynamic structures, continuously and rapidly changing shape. They have been shown to interconnect plastids and permit the exchange of green fluorescent protein (GFP) between plastids. Stromules are enclosed by the inner and outer plastid envelope membranes and are 0.4 - 0.8 ,m in diameter and up to 65 ,m long. Movement of stromules is dependent on the actin cytoskeleton and the ATPase activity of myosin. Stromules are more abundant in cells containing a relatively small plastid volume and provide a means of enormously increasing the plastid surface area. Many important questions on the structure, function and mobility of stromules remain unanswered. [source] Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genesPLANT BIOTECHNOLOGY JOURNAL, Issue 2 2006Naser Farrokhi Summary Cell walls are dynamic structures that represent key determinants of overall plant form, plant growth and development, and the responses of plants to environmental and pathogen-induced stresses. Walls play centrally important roles in the quality and processing of plant-based foods for both human and animal consumption, and in the production of fibres during pulp and paper manufacture. In the future, wall material that constitutes the major proportion of cereal straws and other crop residues will find increasing application as a source of renewable fuel and composite manufacture. Although the chemical structures of most wall constituents have been defined in detail, the enzymes involved in their synthesis and remodelling remain largely undefined, particularly those involved in polysaccharide biosynthesis. There have been real recent advances in our understanding of cellulose biosynthesis in plants, but, with few exceptions, the identities and modes of action of polysaccharide synthases and other glycosyltransferases that mediate the biosynthesis of the major non-cellulosic wall polysaccharides are not known. Nevertheless, emerging functional genomics and molecular genetics technologies are now allowing us to re-examine the central questions related to wall biosynthesis. The availability of the rice, Populus trichocarpa and Arabidopsis genome sequences, a variety of mutant populations, high-density genetic maps for cereals and other industrially important plants, high-throughput genome and transcript analysis systems, extensive publicly available genomics resources and an increasing armoury of analysis systems for the definition of candidate gene function will together allow us to take a systems approach to the description of wall biosynthesis in plants. [source] The polychaete Platynereis dumerilii (Annelida): a laboratory animal with spiralian cleavage, lifelong segment proliferation and a mixed benthic/pelagic life cycleBIOESSAYS, Issue 3 2004Albrecht Fischer Platynereis dumerilii, a marine polychaetous annelid with indirect development, can be continuously bred in the laboratory. Here, we describe its spectacular reproduction and development and address a number of open research problems. Oogenesis is easily studied because the oocytes grow while floating in the coelom. Unlike the embryos of other model spiralians, the Platynereis embryo is transparent giving insight into the dynamic structures and processes inside the cells that accompany the prevailing anisotropic cleavages. Functional studies on cell specification and differential gene expression in embryos, larvae, and later stages are underway. Lifelong proliferation of uniform trunk segments qualifies Platynereis as a model for the study of gene expression and of the functional circuitry of this process. Platynereis can also become a stepping stone in the comparison of segmentation between annelids and arthropods because it comes closer to the putative ancestral morphology and style of development than other model annelids. BioEssays 26:314,325, 2004. © 2004 Wiley Periodicals, Inc. [source] Introduction: A Brief History Of Capillaries And Some Examples Of Their Apparently Strange BehaviourCLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 10 2000Ann L Baldwin SUMMARY 1. Over the past decade, evidence has accumulated challenging the notion that the smallest blood vessels, the capillaries, are static, uniform, semipermeable pipes with no function except as a passive barrier marking the boundary between the vascular compartments from the tissue compartment. 2. Instead, capillaries are dynamic structures that participate in the active regulation of water, waste and nutrient exchange, the formation and destruction of exchange vessels and the sites for initiation of signals to regulate the flow of blood into the exchange vascular network. 3. The following papers will provide insight into the expanded appreciation of the varied nature of capillaries and how their functions are co-ordinated to achieve ,whole organ' exchange. [source] | ||||||||||||||||